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"planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
author nml
date Thu, 21 Nov 2019 12:53:20 -0500
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0
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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1 #!/usr/bin/env perl
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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2 # Copyright (C) 2008 Genome Research Limited. All Rights Reserved.
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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3 #
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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4 # This program is free software; you can redistribute it and/or
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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5 # modify it under the terms of the GNU General Public License
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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6 # as published by the Free Software Foundation; either version 2
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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7 # of the License, or (at your option) any later version.
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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8 #This program is distributed in the hope that it will be useful,
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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11 # GNU General Public License for more details.
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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12 #
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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13 # You should have received a copy of the GNU General Public License
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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14 # along with this program; if not, write to the Free Software
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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15 # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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16
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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17
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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18 use strict;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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19 use warnings;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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20 use POSIX qw(ceil floor);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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21 use Getopt::Std;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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23 #-------------------------------------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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24
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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25 if (@ARGV < 1) { usage();}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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27 my ($help, $reference, $query_file, $choice, $sen, $seed, $mlfas, $fasta_bin, $avoid_Ns,
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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28 $tbx, $min_id, $min_cov, $diff_cov, $min_len,$add_bin_2ps, $pick_primer,
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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29 $flank, $chk_uniq,$redoMummer, $is_circular,$escapeToPrimers, $debug, $gaps_2file, $prefix)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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30 =checkUserInput( @ARGV );
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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31
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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32 my $ref_inline;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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33 if ($escapeToPrimers ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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34 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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35 pickPrimers ($reference, $query_file, $flank, $chk_uniq);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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36 exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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37 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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38 #BEGIN
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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39 #-------------------------------------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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40 print_header();
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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41
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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42 $ref_inline = Ref_Inline($reference);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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43 #Get length of the reference sequence
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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44 my $ref_len = length($ref_inline);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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45 print "PREPARING DATA FOR $choice \n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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46
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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47 ###################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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48 # Running MUMmer #
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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49 ###################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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50 my ($path_dir, $run_mum, $path_toPass);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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51 if ($debug)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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52 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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53 print "the seed is $seed \n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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54 print "RedoMummer= ",$redoMummer."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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55 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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56 my @do_mum_return;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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57 if ($redoMummer)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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58 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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59 @do_mum_return = doMummer($reference, $query_file, $choice,$sen,$seed,$min_id, $min_cov, $diff_cov,$min_len, $debug, $is_circular) or die "Couldn't run MUMmer\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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60 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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61
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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62 ####################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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63 # Processing tiling output #
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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64 ####################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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65 if ($debug) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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66 print "Do tiling...\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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67 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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68
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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69 #--------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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70 my $mummer_tiling = $do_mum_return[0];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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71 $path_dir = $do_mum_return[2];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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72 $path_toPass = $do_mum_return[1];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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73 ##################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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74 #Do Tiling
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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75 #-------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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76 doTiling ($mummer_tiling, $path_toPass, $path_dir,$reference, $query_file, $choice, $prefix,$mlfas, $fasta_bin, $avoid_Ns, $ref_len, $gaps_2file, $ref_inline, $add_bin_2ps, $pick_primer, $flank, $chk_uniq, $tbx);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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77
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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78
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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79
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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80
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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81
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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82 ##########################################################################################################################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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83 #################################Contig ordering ##########################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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84 ###########################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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85
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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86 sub help
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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87 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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88
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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89 die <<EOF
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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90
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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91 ***********************************************************************************
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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92 * ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences *
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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93 * *
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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94 * *
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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95 * Copyright (C) 2009 The Wellcome Trust Sanger Institute, Cambridge, UK. *
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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96 * All Rights Reserved. *
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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97 * *
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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98 ***********************************************************************************
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
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diff changeset
99
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
100 USAGE
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
101 abacas.pl -r <reference file: single fasta> -q <query sequence file: fasta> -p <nucmer/promer> [OPTIONS]
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
102
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
103 -r reference sequence in a single fasta file
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
104 -q contigs in multi-fasta format
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
105 -p MUMmer program to use: 'nucmer' or 'promer'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
106 OR
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
107 abacas.pl -r <reference file: single fasta> -q <pseudomolecule/ordered sequence file: fasta> -e
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
108 OPTIONS
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
109 -h print usage
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
110 -d use default nucmer/promer parameters
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
111 -s int minimum length of exact matching word (nucmer default = 12, promer default = 4)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
112 -m print ordered contigs to file in multifasta format
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
113 -b print contigs in bin to file
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
114 -N print a pseudomolecule without "N"s
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
115 -i int mimimum percent identity [default 40]
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
116 -v int mimimum contig coverage [default 40]
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
117 -V int minimum contig coverage difference [default 1]
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
118 -l int minimum contig length [default 1]
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
119 -t run tblastx on contigs that are not mapped
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
120 -g string (file name) print gaps on reference to file name
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
121 -a append contigs in bin to the pseudomolecule
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
122 -o prefix output files will have this prefix
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
123 -P pick primer sets to close gaps
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
124 -f int number of flanking bases on either side of a gap for primer design (default 350)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
125 -R Redo mummer [default 1, use -R 0 to avoid running mummer]
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
126 -e Escape contig ordering i.e. go to primer design
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
127 -c Reference sequence is circular
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
128
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
129 EOF
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
130 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
131 ########
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
132 sub usage
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
133 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
134
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
135 die <<EOF
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
136
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
137 USAGE
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
138 abacas.pl -r <reference file: single fasta> -q <query sequence file: fasta> -p <nucmer/promer> [OPTIONS]
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
139 -r reference sequence in a single fasta file
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
140 -q contigs in multi-fasta format
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
141 -p MUMmer program to use: 'nucmer' or 'promer'
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
142 for contig ordering and primer design
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
143
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
144 OR
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
145 abacas.pl -r <reference file: single fasta> -q <pseudomolecule/ordered sequence file: fasta> -e 1
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
146 to escape contig ordering and go directly to primer design
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
147
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
148 OR
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
149 abacas.pl -h for help
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
150
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
151 EOF
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
152 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
153 ########
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
154 ##################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
155 sub print_header
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
156 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
157 print "
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
158 ***********************************************************************************
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
159 * ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences *
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
160 * *
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
161 * *
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
162 * Copyright (C) 2009 The Wellcome Trust Sanger Institute, Cambridge, UK. *
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
163 * All Rights Reserved. *
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
164 * *
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
165 ***********************************************************************************
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
166 \n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
167 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
168 #########################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
169 sub checkUserInput{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
170 my %options;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
171 getopts('hr:q:p:ds:mbNi:v:V:l:tg:ao:Pf:R:u:ecD', \%options);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
172
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
173 my ($help, $reference, $query_file, $choice, $sen, $seed, $mlfas, $fasta_bin, $avoid_Ns,
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
174 $tbx, $min_id, $min_cov, $diff_cov, $min_len,$add_bin_2ps, $pick_primer,
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
175 $flank, $chk_uniq,$redoMummer, $is_circular,$escapeToPrimers, $debug, $gaps_2file, $prefix);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
176
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
177 if($options{h}) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
178 $help = $options{h};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
179 help();
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
180 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
181 else{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
182 $help =0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
183 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
184 if ($options{r} && $options{q} ){
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
185 ($reference, $query_file) = ($options{r},$options{q});
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
186
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
187 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
188 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
189 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
190 usage() unless $options{e};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
191 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
192
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
193 if ($options{p})
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
194 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
195 $choice = $options{p};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
196 unless ($choice eq "nucmer" || $choice eq "promer"){
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
197 print "Unknown MuMmer function\n Please use nucmer or promer\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
198 exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
199 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
200 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
201 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
202 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
203 usage() unless $options{e};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
204 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
205 if ($options{e}) #$escapeToPrimers)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
206 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
207 print_header();
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
208 print "Primer design selected,... escaping contig ordering\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
209 $escapeToPrimers = 1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
210 $chk_uniq = "nucmer";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
211 $choice = "";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
212 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
213 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
214 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
215 $escapeToPrimers = 0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
216 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
217 if ($options{d}) {$sen =1;} else {$sen =0;} #print $sen , " ---sen\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
218 #print $options{t}, "\n"; exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
219 if($options{t}) {$tbx = 1;} else {$tbx = 0;} #print $tbx, " ---tbx\n"; #
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
220 unless ($options{s}){
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
221 if ($choice eq "nucmer"){
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
222 $seed = 12;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
223 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
224 else{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
225 $seed =4;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
226 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
227 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
228 if ($options{m}){$mlfas =1;} else { $mlfas =0; } #print $mlfas , " ---mlfasta\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
229 if ($options{b}) { $fasta_bin =1;} else {$fasta_bin =0;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
230 if ($options {N}) {$avoid_Ns =1;} else {$avoid_Ns=0;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
231
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
232 unless($options{i}) {$min_id =40;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
233 unless ($options{v}) {$min_cov =40;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
234 unless ($options{V}) {$diff_cov =1;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
235 unless ($options {l}) {$min_len = 1;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
236 if ($options{a}) {$add_bin_2ps = 1; }else {$add_bin_2ps =0;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
237 if ($options{P}) {$pick_primer=1;} else {$pick_primer =0;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
238 if ($options{f}) {$flank = $options{f};} else {$flank = 1000;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
239 if ($options{u}) {$chk_uniq = $options{u}; } else {$chk_uniq = "nucmer";}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
240
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
241 if($options{R}) {$redoMummer = $options{R}; }else {$redoMummer = 1;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
242 unless ($options{c}) {$is_circular = 0;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
243 if ($options{g}) {$gaps_2file = $options{g};} else {$gaps_2file ="";}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
244 if($options{o}) {$prefix = $options{o};} else {$prefix = "";}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
245 unless ($options{D}) {$debug =0};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
246 if ($tbx ==1 && $fasta_bin !=1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
247 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
248 print "ERROR: Please use -t -b if you want to run tblastx on contigs in bin\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
249 exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
250 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
251 #print $tbx, "\n"; exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
252 return ($help, $reference, $query_file, $choice, $sen, $seed, $mlfas, $fasta_bin, $avoid_Ns,
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
253 $tbx, $min_id, $min_cov, $diff_cov, $min_len,$add_bin_2ps, $pick_primer,
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
254 $flank, $chk_uniq,$redoMummer, $is_circular,$escapeToPrimers, $debug, $gaps_2file, $prefix);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
255
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
256 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
257 #############
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
258 ## get the reference sequence in one line
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
259 #--------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
260 sub Ref_Inline
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
261 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
262 my $ref = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
263 open (refFH, $ref) or die "Could not open file\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
264 my $seq ="";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
265 my @r = <refFH>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
266 my $num_chr =0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
267 foreach(@r){
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
268 if ($_ =~ /\>/){
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
269 $num_chr +=1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
270 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
271 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
272 if ($num_chr > 1){
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
273 print "\nERROR: Please use a single fasta reference file. You can simply merge chromosomes in to a union fasta file.\n\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
274 exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
275 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
276 shift @r;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
277 foreach(@r){
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
278 chomp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
279 $seq = $seq.$_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
280 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
281 return $seq;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
282 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
283 ################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
284 # Run mummer
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
285 #--------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
286 sub doMummer
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
287 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
288 my ($reference, $query_file, $choice, $sen,$seed,$min_id, $min_cov, $diff_cov,$min_len, $debug, $is_circular ) = @_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
289
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
290 my $df = 'delta-filter';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
291 my $st = 'show-tiling';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
292 my $ask = 'which';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
293 my ($path_toPass, $run_mum); # params to return...
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
294 my ($command, $Path, $dir) = checkProg($choice);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
295 my ($run_df, $df_path, $df_dir) = checkProg($df);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
296 my ($run_st, $st_path, $st_dir) = checkProg($st);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
297 my (@running, @deltaRes, @coordsRes);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
298 if ($choice eq "nucmer")
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
299 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
300 if ($sen ==0)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
301 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
302 @running = `$command --maxmatch -l $seed -p $choice $reference $query_file &> /dev/null`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
303 @deltaRes = `$run_df -q $choice.delta >$choice.filtered.delta`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
304 if ($is_circular == 1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
305 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
306 @coordsRes = `$run_st -c -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
307 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
308 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
309 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
310 @coordsRes = `$run_st -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
311
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
312 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
313 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
314 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
315 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
316 @running = `$command -p $choice $reference $query_file &> /dev/null`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
317 @deltaRes = `$run_df -q $choice.delta >$choice.filtered.delta`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
318 if ($is_circular ==1) {@coordsRes = `$run_st -c -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
319 else { @coordsRes = `$run_st -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
320 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
321
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
322 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
323 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
324 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
325 if ($sen ==0)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
326 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
327 @running = `$command --maxmatch -l $seed -x 1 -p $choice $reference $query_file &> /dev/null`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
328 @deltaRes = `$run_df -q $choice.delta >$choice.filtered.delta`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
329 if ($is_circular == 1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
330 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
331 @coordsRes= `$run_st -c -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
332 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
333 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
334 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
335 @coordsRes= `$run_st -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
336 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
337 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
338 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
339 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
340 @running = `$command -l $seed -p $choice $reference $query_file &> /dev/null`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
341 @deltaRes = `$run_df -q $choice.delta >$choice.filtered.delta`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
342 if ($is_circular == 1) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
343 @coordsRes= `$run_st -c -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
344 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
345 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
346 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
347 @coordsRes= `$run_st -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
348 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
349 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
350 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
351 my $Coordsfull= "$choice.tiling";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
352 return ($Coordsfull,$Path, $dir);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
353 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
354
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
355 ## #############################################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
356 sub checkProg{ #checks if a given excutable is in the path...
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
357 my $prog = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
358 my $ask = 'which';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
359 my @check_prog = `$ask $prog`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
360 my $path_toPass;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
361 my $path_dir;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
362 my $command;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
363 if (defined $check_prog[0] && $check_prog[0] =~ /$prog$/)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
364 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
365 $path_toPass = $prog;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
366 $command = $prog;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
367 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
368 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
369 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
370 print "\nENTER the directory for your ", $prog, " executables [default ./]: ";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
371 my $path=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
372 chomp $path;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
373 $path_dir = $path;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
374 if ($path_dir =~/\/$/)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
375 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
376 $path_dir = $path_dir;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
377 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
378 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
379 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
380 $path_dir = $path_dir."/";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
381 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
382 my @final_check = `$ask $command`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
383 if (exists $final_check[0] && $final_check[0] =~ /$prog$/)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
384 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
385 $command = $path_dir.$prog;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
386 $path_toPass = $command;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
387 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
388 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
389 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
390 print "ERROR: Could not run ", $prog, ", please check if it is installed in your path\n or provide the directory \n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
391 exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
392 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
393 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
394
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
395 return ($command, $path_toPass, $path_dir);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
396 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
397
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
398 ##############################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
399 # converts a fasta file to an ordered single line
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
400 #--------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
401 sub Fasta2ordered
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
402 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
403 if( @_ != 1 )
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
404 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
405 print "Usage: Fasta2ordered <fasta_file>\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
406 exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
407 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
408 my $fast = shift; #print $fast; exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
409 my @fasta = split (/\n/, $fast);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
410 if ($fasta[0] =~ /\>/ ) #remove chromosome name if exists in the onput sequence.
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
411 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
412 my $ch_name = $fasta[0];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
413 shift @fasta;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
414 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
415 #print $fasta[0]; exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
416 foreach(@fasta){chomp;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
417 my $num_lines = scalar(@fasta);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
418 my $dna = '';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
419 for(my $i=0; $i< $num_lines; $i+=1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
420 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
421 $dna = $dna.$fasta[$i];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
422 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
423 my $ordered_dna = $dna;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
424 return $ordered_dna;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
425 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
426 ##############################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
427 # Hash input contigs
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
428 #------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
429
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
430 sub hash_contigs {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
431 if( @_ != 1 )
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
432 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
433 print "Usage: hash_contigs contigs_file";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
434 exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
435 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
436 my $contigs_file = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
437 if( $contigs_file =~ /\.gz$/ )
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
438 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
439 open(CONTIGS, $contigs_file, "gunzip -c $contigs_file |" ) or die "Cant open contigs file: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
440 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
441 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
442 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
443 open( CONTIGS, $contigs_file) or die "Cant open contigs file: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
444 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
445
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
446 my %contigs_hash; # hash to store contig names and sequences
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
447 my $contigName;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
448
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
449
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
450 while (<CONTIGS>) ##add error checking...
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
451 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
452 if (/^>(\S+)/) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
453 $contigName=$1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
454 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
455 else {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
456 chomp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
457 $contigs_hash{$contigName} .= $_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
458 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
459 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
460 close(CONTIGS);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
461 #tdo
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
462 ## check if qual exists
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
463 my %contigs_qual_hash;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
464
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
465
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
466 if (-r "$contigs_file.qual" or -r "$contigs_file.qual.gz") {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
467 if( -r "$contigs_file.qual.gz" )
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
468 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
469 open(CONTIGS, "$contigs_file.qual.gz", "gunzip -c $contigs_file.qual.gz |" ) or die "Cant open contigs file: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
470 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
471 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
472 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
473 open( CONTIGS, "$contigs_file.qual" ) or die "Cant open contigs file: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
474 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
475
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
476
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
477 while (<CONTIGS>) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
478 if (/^>(\S+)/) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
479 $contigName=$1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
480 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
481 else {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
482 chomp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
483 $contigs_qual_hash{$contigName} .= $_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
484 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
485 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
486
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
487 } # end tdo # end if exist
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
488
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
489
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
490 return (\%contigs_hash,\%contigs_qual_hash);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
491 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
492 #######################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
493 ##############################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
494 ### it gets a delta name
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
495 sub getMummerComparison{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
496 my $deltaName = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
497
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
498
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
499 ### transform the delta file to coords
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
500 my $call ="show-coords -H -T -q $deltaName > $deltaName.coords ";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
501 !system(" $call") or die "Problems doing the show-coords comparison: $call $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
502
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
503
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
504 ### willh old results
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
505 my %h;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
506
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
507 ### has as index the postion with the max hits
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
508 my %h_max;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
509 my $tmp=0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
510 my $tmp_index;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
511 my $key='';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
512 my $is_promer =0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
513 if ($deltaName =~/^promer/)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
514 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
515 $is_promer =1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
516 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
517
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
518 open (F,"$deltaName.coords") or die "Problem in getComparisonFile to open file $deltaName.coords\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
519 my @File=<F>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
520 my @a;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
521 @a=split(/\s+/,$File[0]);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
522 $tmp=$a[5];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
523 $tmp_index=$a[0];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
524 if ($is_promer ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
525 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
526 $key=$a[12]; ## nucmer: $key = $a[8]
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
527 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
528 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
529 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
530 $key = $a[8];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
531 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
532
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
533 foreach (@File) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
534 @a=split(/\s+/);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
535
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
536 if ($is_promer ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
537 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
538 push @{ $h{$a[12]}}, "$a[12]\t$a[11]\t$a[7]\t$a[5]\t0\t0\t$a[2]\t$a[3]\t$a[0]\t$a[1]\t1\t$a[5]\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
539 if ($key eq $a[12] and $a[5]>$tmp)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
540 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
541 $tmp=$a[5]; # length
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
542 $tmp_index=$a[0]; # position reference
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
543 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
544 elsif ($key ne $a[12]) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
545 ### here possible bugg...
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
546 $h_max{$tmp_index}=$key;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
547 $key=$a[12];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
548 $tmp=$a[5]; # length
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
549 $tmp_index=$a[0]; # position reference
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
550
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
551 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
552 } #end if
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
553 #else i.e. if nucmer
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
554 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
555 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
556 push @{ $h{$a[8]}}, "$a[8]\t$a[6]\t$a[6]\t$a[5]\t0\t0\t$a[2]\t$a[3]\t$a[0]\t$a[1]\t1\t$a[5]\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
557 if ($key eq $a[8] and $a[5]>$tmp)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
558 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
559 $tmp=$a[5]; # length
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
560 $tmp_index=$a[0]; # position reference
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
561 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
562 elsif ($key ne $a[8]) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
563 ### here possible bugg...
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
564 $h_max{$tmp_index}=$key;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
565 $key=$a[8];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
566 $tmp=$a[5]; # length
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
567 $tmp_index=$a[0]; # position reference
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
568
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
569 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
570 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
571
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
572 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
573 $h_max{$tmp_index}=$key;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
574 # print Dumper %h_max;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
575
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
576 return (\%h,\%h_max);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
577 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
578 ##################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
579 ###########################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
580 sub writeBinContigs2Ref{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
581 my $nameBin = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
582 my $name = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
583
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
584 open (F, "$nameBin") or die "Couldn't find file $nameBin: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
585
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
586 my @ar;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
587
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
588 my $count=0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
589
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
590 while (<F>) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
591 push @ar, $_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
592 $count++;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
593 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
594 #### sa4: added error checking:- if file is empty
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
595 if (scalar(@ar) < 1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
596 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
597 print "No contigs in unusedcontigs file\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
598 $count = 0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
599
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
600 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
601 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
602 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
603 open (F, "> $name.notMapped.contigs.tab") or die "Couldn't write file $name.tab: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
604 print F doArt(\@ar);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
605 close(F);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
606 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
607 return $count;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
608
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
609 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
610
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
611
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
612 ##############################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
613 sub doArt{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
614 my ($ref) = @_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
615
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
616
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
617 ## hash of array with all positions of the contig
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
618 my %Pos;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
619
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
620 ## Hash with note of result line of nucmer
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
621 my %lines;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
622
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
623 foreach (@$ref) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
624 chomp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
625 my @ar=split(/\t/);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
626 push @{ $Pos{$ar[12]}}, "$ar[0]..$ar[1]";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
627 $lines{$ar[12]} .= "FT $_\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
628 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
629
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
630 my $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
631
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
632 foreach my $contig (keys %lines) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
633
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
634 if (scalar(@{ $Pos{$contig} } >1)) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
635 my $tmp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
636
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
637 foreach (@{ $Pos{$contig} }) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
638 $tmp.="$_,";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
639 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
640 $tmp =~ s/,$//g; # get away last comma
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
641 $res .= "FT contig join($tmp)\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
642 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
643 else {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
644 $res .= "FT contig $Pos{$contig}[0]\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
645 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
646 $res .= "FT /systematic_id=\"$contig\"\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
647 $res .= "FT /note=\"Contig $contig couldn't map perfectly.\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
648 $res .= $lines{$contig};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
649 $res .= "FT \"\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
650
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
651 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
652
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
653 return $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
654 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
655
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
656 ##########################################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
657 #---------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
658 sub makeN #creates a string of Ns
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
659 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
660 my $n = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
661 my $Ns= "N";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
662 for (my $i =1; $i < $n; $i+=1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
663 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
664 $Ns = $Ns."N";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
665 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
666 return $Ns;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
667 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
668
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
669 ###########################################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
670 ## reverse complement a sequence
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
671 #---------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
672 sub revComp {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
673 my $dna = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
674 my $revcomp = reverse($dna);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
675
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
676 $revcomp =~ tr/ACGTacgt/TGCAtgca/;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
677
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
678 return $revcomp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
679 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
680
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
681 ################################################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
682 ### function to visualize rep. regions in Reference genome.
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
683 sub findRepeats
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
684 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
685 my $reference = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
686 my $name = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
687 my $path_prog = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
688
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
689 # get path
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
690 my ($path_coords) = $path_prog;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
691
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
692 $path_coords =~ s/nucmer/show-coords/;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
693
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
694 my $call = "$path_prog --maxmatch -c 100 -b 40 -p $name.repeats -l 25 $reference $reference &> /dev/null ";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
695 !system("$call") or die "Problems doing the nucmer comparison: $call $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
696 $call ="$path_coords -r -c -l $name.repeats.delta > $name.repeats.coords ";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
697 !system(" $call") or die "Problems doing the show-coords comparison: $call $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
698
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
699 my @Res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
700 open (F, "$name.repeats.coords" ) or die "Problems to open file $reference.repeats.coords: Is MUMmer installed correctly and inserted in the PATH environment variable? ($!)\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
701 $_=<F>; $_=<F>; $_=<F>; $_=<F>;$_=<F>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
702 while (<F>) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
703 my @ar = split(/\s+/);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
704 if (!($ar[1] == $ar[4] or $ar[2] == $ar[5] or $ar[7] > 100000)) { # to exclude self alignment
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
705
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
706 foreach ($ar[1]..$ar[2]) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
707 $Res[($_-1)]++;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
708 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
709 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
710 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
711
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
712 ### write the result to the plot file
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
713
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
714 my $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
715 foreach (@Res){
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
716 if (defined($_)) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
717 $res .= "$_\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
718 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
719 else {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
720 $res .= "0\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
721 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
722 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
723
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
724 open (F, "> $name.Repeats.plot") or die "Couldn't open file $name.plot to write: $! \n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
725 print F $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
726 close(F);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
727
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
728 ### delete files
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
729 unlink("$name.repeats.delta");
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
730 unlink("$name.repeats.coords");
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
731 unlink("$name.repeats.cluster");
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
732 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
733
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
734 ################################################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
735 # reverse a list of qualities
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
736 #------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
737 sub reverseQual{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
738 my $str = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
739
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
740 $str =~ s/\s+$//g;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
741
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
742 my @ar = split(/\s/,$str);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
743 my $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
744
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
745 for (my $i=(scalar(@ar)-1);$i>=0;$i--) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
746 $res.="$ar[$i] ";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
747 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
748 return $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
749 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
750
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
751 ##############################################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
752 # ----------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
753 sub getPosCoords{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
754 my $ref_ar = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
755 my $contig = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
756
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
757 my $offset = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
758 my $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
759 # print Dumper $$ref_ar{$contig};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
760 foreach (@{$$ref_ar{$contig}}) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
761 print "in getPos Coords: $_\n";;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
762
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
763 my @ar=split(/\t/);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
764 $ar[6]+=$offset;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
765 $ar[7]+=$offset;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
766 $res .= join("\t",@ar);;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
767 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
768
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
769 return $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
770
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
771 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
772 #############################################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
773 # -----------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
774 sub getPosCoordsTurn{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
775 my $ref_ar = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
776 my $contig = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
777
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
778 my $offset = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
779
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
780
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
781 my $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
782
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
783 # print Dumper $$ref_ar{$contig};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
784 foreach (@{$$ref_ar{$contig}}) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
785 my @ar=split(/\t/);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
786 my $tmp_8=$ar[8];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
787 my $tmp_9=$ar[9];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
788
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
789 $ar[8]=$ar[6]+$offset;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
790 $ar[9]=$ar[7]+$offset;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
791 $ar[6]=$tmp_8;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
792 $ar[7]=$tmp_9;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
793
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
794 ## change query subject
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
795
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
796 $res .= join("\t",@ar);;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
797 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
798
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
799 return $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
800
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
801 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
802
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
803 ############################################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
804 #------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
805 sub printStats{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
806
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
807 my ($num_fortillingcontigs,$num_notsetTilling,$num_mapped, $num_contigs, $num_inComparisoncontigs, $ref_len, $total_bases_mpd) = @_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
808 $num_fortillingcontigs=$num_notsetTilling+$num_mapped;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
809 my $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
810 $res.= "Short statistics of run.\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
811 $res.= "$num_contigs\t\tcontigs entered to be mapped against the reference.\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
812 $res.= sprintf("$num_inComparisoncontigs\t%0.2f \%\tmade a hit against the reference to the given parameter (-s -d etc)\n",($num_inComparisoncontigs*100/$num_contigs));
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
813 $res.= sprintf("$num_fortillingcontigs\t%0.2f \%\twere considered for the tilling graph (-s -d etc)\n",($num_fortillingcontigs*100/$num_contigs));
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
814 $res.= sprintf("$num_mapped\t%0.2f \%\tare mapped in the tilling graph (-s -d etc)\n",($num_mapped*100/$num_contigs));
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
815 $res.= sprintf("\nCoverage: The reference is $ref_len long. Up to $total_bases_mpd bp (%0.2f \%) are covered by the contigs (This doesn't mean that these regions are really similar...)\n",($total_bases_mpd*100/$ref_len));
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
816
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
817 print $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
818
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
819 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
820 ##################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
821 #### Do Tiling
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
822 #----------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
823 sub doTiling {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
824
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
825 my ($mummer_tiling, $path_toPass, $path_dir,$reference, $query_file, $choice, $prefix,$mlfas, $fasta_bin, $avoid_Ns, $ref_len, $gaps_2file, $ref_inline, $add_bin_2ps, $pick_primer, $flank, $chk_uniq, $run_blast) = @_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
826
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
827 ### these are also defined in the main script.... to be changed!!
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
828 my ($num_contigs , $num_inbincontigs, $avg_cont_size,$num_overlaps , $num_gaps,
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
829 $num_mapped,$total_bases_mpd,$p_ref_covered,$num_ambigus,$num_inComparisoncontigs,
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
830 $num_fortillingcontigs,$num_notsetTilling)= (0,0,0,0,0,0,0,0,0,0,0,0);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
831
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
832 my ($href, $ref_contigs_qual) = hash_contigs($query_file);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
833 my $qualAvailable=0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
834 my %contigs_hash = %{$href};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
835 my @c_keys = keys %contigs_hash;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
836 $num_contigs = scalar(@c_keys);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
837 my @cont_lens;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
838 my (@ids ,$id, $id_len);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
839 my (@Rs, @Re, @G, @Len, @cov, @pid, @orient, @Cid);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
840 my (@Ps, @Pe);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
841 my ($total);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
842 my $g; #define gap size between contigs
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
843 my $tiling_gap; #gap size from tiling graph
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
844 open (TIL, $mummer_tiling) or die "Could not open $mummer_tiling: $!";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
845 while (<TIL>)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
846 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
847 chomp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
848 if ($_ =~/^>/)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
849 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
850 my $line = substr $_, 1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
851 my @splits = split /\s+/, $line;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
852 $id = $splits[0];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
853 push @ids, $id;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
854 $id_len= $splits[1];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
855 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
856 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
857 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
858 my @splits = split /\s+/, $_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
859 push @Rs, $splits[0];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
860 push @Re, $splits[1];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
861 push @G, $splits[2];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
862 push @Len, $splits[3];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
863 push @cov, $splits[4];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
864 push @pid, $splits[5];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
865 push @orient, $splits[6];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
866 push @Cid, $splits[7];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
867 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
868
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
869 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
870 close (TIL);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
871 if (scalar(@Rs) != scalar(@Re))
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
872 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
873 print "ERROR: unequal array size\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
874 exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
875 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
876 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
877 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
878 $total = scalar(@Rs);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
879 $num_mapped = scalar(@Rs);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
880 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
881 my $ref_loc = $reference; # get locations of reference and query files
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
882 my $qry_loc = $query_file;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
883 my $dif_dir =0; #assume query and reference are in the working directory
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
884 my @splits_reference = split (/\//, $reference);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
885 my $new_reference_file = $splits_reference[(scalar(@splits_reference)-1)];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
886 my @splits_query = split (/\//, $query_file);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
887 my $new_query_file = $splits_query[(scalar(@splits_query)-1)];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
888 if ($prefix eq "")
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
889 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
890 $prefix = $new_query_file."_".$new_reference_file;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
891 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
892 #-------------------------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
893 #define file handles for output files and open files to write output
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
894 #-------------------------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
895 my ($seqFH,$tabFH,$binFH,$crunchFH, $gapFH, $mlFH, $dbinFH, $avoidNFH);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
896 open ($seqFH, '>', $prefix . '.fasta') or die "Could not open file $prefix.fasta for write: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
897 open ($tabFH, '>', $prefix . '.tab') or die "Could not open file $prefix.tab for write: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
898 open ($binFH, '>', $prefix . '.bin') or die "Could not open file $prefix.bin for write: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
899 open ($crunchFH, '>', $prefix . '.crunch') or die "Could not open file $prefix.crunch for write: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
900 open ($gapFH, '>', $prefix . '.gaps') or die "Could not open file $prefix.gaps for write: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
901 if ($mlfas ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
902 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
903 open ($mlFH, '>', $prefix . '.contigs.fas') or die "Could not open file $prefix.contigs.fas for write: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
904 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
905 if ($fasta_bin ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
906 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
907 open ($dbinFH, '>', $prefix . '.contigsInbin.fas') or die "Could not open file $prefix.contigsInbin.fas for write: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
908 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
909 if ($avoid_Ns ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
910 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
911 open ($avoidNFH, '>', $prefix .'.NoNs.fasta') or die "Could not open file $prefix.NoNs.fasta for write: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
912 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
913 #-------------------------------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
914 # Writing tiling graph and generating a pseudomolecule
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
915 # Note use use ps for pseudomolecule
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
916 #@Ps = start of ps, and @Pe = end of ps
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
917 my $ps_start =1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
918 $Ps[0] = 1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
919 $Pe[0] = $Ps[0] + $Len[0] -1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
920 my $tmp_qual;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
921 my $tmp_nqual;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
922 my $tmp_seq ="";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
923 my $tmp_nseq ="";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
924 print "Total contigs = $total \n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
925
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
926 #------------------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
927 # The 'for loop' loops over each contig in the Tiling output
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
928 #Writing to file is done for each contig to speed up the process
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
929 #This part could potentially be a separate subroutine
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
930
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
931 print $tabFH "ID ",$id, "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
932 print $seqFH ">", "ordered_", $id, "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
933 for (my $i=1; $i <= $total; $i+=1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
934 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
935 my $covv =sprintf("%.0f",$cov[$i -1]); #ROUNDING
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
936 my $pidd = sprintf("%.0f", $pid[$i -1]);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
937 my ($contig_coord, $color, $contig_seq);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
938 my $contig_qual='';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
939 $tiling_gap = $G[$i -1];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
940 if ($tiling_gap <= 5){ #insert 100Ns for overlaps and gaps of size less than or equal to 5bp
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
941 $g = 99; # default gap size to
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
942 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
943 else{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
944 $g = $tiling_gap;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
945 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
946 if (defined($Len[$i]))
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
947 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
948 $Ps[$i] = $Pe[$i-1] +$g +1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
949 $Pe[$i] = $Ps[$i] + $Len[$i] -1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
950 $total_bases_mpd+=$Len[$i];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
951 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
952
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
953 if ($Rs[$i -1] <0) #check if a reference starting position is less than 0
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
954 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
955 $Rs[$i -1] =1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
956 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
957
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
958 if($orient[$i-1] eq "+")
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
959 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
960 $contig_coord = $Ps[$i -1]."..".$Pe[$i-1];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
961 $color = 4;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
962 $contig_seq = $contigs_hash{$Cid[$i-1]};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
963 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
964 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
965 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
966 $contig_coord = "complement(".$Ps[$i -1]."..".$Pe[$i-1].")";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
967 $color =3;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
968 $contig_seq = revComp($contigs_hash{$Cid[$i-1]}); #REVERSE COMPLEMENT A SEQUENCE
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
969
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
970 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
971 push (@cont_lens, length($contig_seq));
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
972
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
973 # tdo
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
974 if (defined($$ref_contigs_qual{$Cid[$i-1]})) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
975 ## flag to know, that the qual exists
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
976 $qualAvailable=1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
977 $contig_qual = $$ref_contigs_qual{$Cid[$i-1]};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
978 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
979 $tmp_qual .= $contig_qual;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
980 $tmp_seq .= $contig_seq;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
981 if ($avoid_Ns ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
982 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
983 $tmp_nseq.= $contig_seq;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
984 #tdo
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
985 $tmp_nqual .= $contig_qual;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
986 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
987 if ($mlfas ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
988 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
989 my $head = $Cid[$i-1];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
990 my $multifasta_seq = write_Fasta_headers ($contig_seq,$head);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
991 print $mlFH $multifasta_seq;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
992 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
993 if ($Re[$i -1] > $ref_len)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
994 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
995 $Re[$i -1] = $ref_len -1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
996 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
997 if ($Pe[$i -1] > length($tmp_seq))
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
998 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
999 $Pe[$i -1] = length($tmp_seq);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1000 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1001
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1002 #-----------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1003 print $crunchFH $covv, " ", $pidd, " ", $Ps[$i -1], " ", $Pe[$i -1], " ", $Cid[$i -1], " ", $Rs[$i -1], " ", $Re[$i-1], " ", "unknown NONE\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1004
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1005 #WRITE FEATURE FILE
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1006 print $tabFH "FT contig ",$contig_coord, "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1007 print $tabFH "FT ", "/systematic_id=\"", $Cid[$i-1],"\"","\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1008 print $tabFH "FT ", "/method=\"", "mummer\"", "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1009 print $tabFH "FT ", "/Contig_coverage=\"",$cov[$i -1], "\"", "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1010 print $tabFH "FT ", "/Percent_identity=\"",$pid[$i -1], "\"", "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1011 if ($tiling_gap > 1) #WRITE GAP LOCATIONS AND SIZE TO FILE
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1012 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1013 my $gap_start = $Pe[$i -1] +1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1014 my $gap_end = "";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1015 if (defined $Ps[$i])
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1016 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1017 $gap_end = $Ps[$i] -1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1018 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1019 my $ref_start = $Re[$i -1] +1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1020 my $ref_end;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1021 if (defined $Rs[$i])
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1022 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1023 $ref_end =$Rs[$i]-1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1024 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1025 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1026 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1027 $ref_end = "END";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1028 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1029 print $gapFH "Gap\t",$tiling_gap, "\t", $gap_start, "\t", $gap_end, "\t", $ref_start, "\t", $ref_end,"\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1030 if ($gaps_2file ne "" && $ref_start < $ref_len)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1031 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1032 my $ref_gapsFH;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1033 open ($ref_gapsFH, '>', $gaps_2file.'.Gaps_onRef') or die "Could not open file $gaps_2file.Gaps_onRef for write: $!\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1034 my $gapOnref = substr ($ref_inline, $ref_start, $g);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1035 print $ref_gapsFH ">",$g,"_",$ref_start, "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1036 my $file_toPrint = write_Fasta ($gapOnref);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1037 print $ref_gapsFH $file_toPrint;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1038 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1039 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1040 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1041 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1042 $color = 5;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1043 print $tabFH "FT ", "/Overlapping=\"", "YES\"", "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1044 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1045 my $ns = makeN($g);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1046 $tmp_seq = $tmp_seq.$ns;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1047 #tdo
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1048 for (1..length($ns)) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1049 $tmp_qual .= "0 ";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1050 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1051 print $tabFH "FT ", "/colour=\"",$color, "\"", "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1052 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1053 #------------------------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1054 #tdo
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1055 my @Quality_Array;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1056 if ($qualAvailable) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1057 @Quality_Array = split(/\s/,$tmp_qual);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1058 my $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1059 foreach (@Quality_Array) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1060 $res .= "$_\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1061 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1062 ## get name
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1063 my @splits_query = split (/\//, $query_file);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1064 $new_query_file = $splits_query[(scalar(@splits_query)-1)];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1065 open (F,"> $new_query_file.qual.plot") or die "problems\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1066 print F $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1067 close(F);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1068 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1069 ##WRITE PSEUDOMOLECULE WITHOUT 'N's
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1070 #--------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1071 if ($avoid_Ns ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1072 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1073 print $avoidNFH ">", "ordered_", $id, "without 'N's","\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1074 my $toWrite = write_Fasta ($tmp_nseq);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1075 print $avoidNFH $toWrite;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1076 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1077 ####################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1078 #WRITE CONTIGS WITH NO HIT TO FILE #
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1079 #################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1080 my %Cids;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1081
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1082 foreach(@Cid)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1083 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1084 chomp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1085 $Cids{$_} = 1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1086 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1087 my @contigs_2bin = ();
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1088 my %h_contigs_2bin;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1089
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1090 foreach (@c_keys)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1091 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1092 push(@contigs_2bin, $_) unless exists $Cids{$_};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1093
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1094 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1095 foreach(@contigs_2bin)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1096 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1097 $h_contigs_2bin{$_}=1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1098
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1099 print $binFH "$_ \n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1100
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1101 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1102 $num_inbincontigs= scalar(@contigs_2bin);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1103
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1104 ########
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1105 # WRITE PSEUDOMOLECULE TO FILE
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1106 #----------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1107 my $new_seq = $tmp_seq;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1108 my $prev_len = length($tmp_seq);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1109 my $total_len = $prev_len;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1110 foreach (@contigs_2bin)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1111 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1112 chomp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1113 #my $binseq = $contigs_hash{$contigs_2bin[$i]};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1114 my $l = length ($contigs_hash{$_});
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1115 $total_len +=$l;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1116 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1117 if ($add_bin_2ps ==1) #appending unmapped contigs to pseudomolecule
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1118 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1119
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1120 for (my $i =0; $i < scalar(@contigs_2bin); $i+=1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1121 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1122 my $binseq = $contigs_hash{$contigs_2bin[$i]};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1123 $new_seq .=$contigs_hash{$contigs_2bin[$i]};
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1124 my $len_current_contig = length($binseq);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1125 my $start = $prev_len +1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1126 my $end = $start + $len_current_contig -1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1127 my $col = 7;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1128 if ($start > $total_len)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1129 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1130 $start = $total_len;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1131 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1132 if ($end >$total_len)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1133 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1134 $end = $total_len;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1135 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1136 my $co_cord = $start."..".$end;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1137 my $note = "NO_HIT";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1138 print $tabFH "FT contig ",$co_cord, "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1139 print $tabFH "FT ", "/systematic_id=\"", $contigs_2bin[$i],"\"","\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1140 print $tabFH "FT ", "/method=\"", "mummer\"", "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1141 print $tabFH "FT ", "/colour=\"",$col, "\"", "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1142 print $tabFH "FT ", "/", $note, "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1143 $prev_len= $end;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1144 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1145 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1146 my $to_write = write_Fasta ($new_seq);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1147 print $seqFH $to_write;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1148 ########
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1149 #WRITE CONTIGS IN BIN TO FILE #
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1150 #------------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1151 if ($fasta_bin ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1152 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1153 foreach(@contigs_2bin)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1154 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1155 print $dbinFH ">", $_, "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1156 my $to_write = write_Fasta($contigs_hash{$_});
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1157 print $dbinFH $to_write;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1158 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1159 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1160 #unlink ("$choice.delta");
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1161 #unlink ("$choice.filtered.delta");
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1162 #unlink ("$choice.cluster");
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1163 #unlink ("$choice.tiling");
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1164 #PRINT FINAL MESSAGE
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1165 print " FINISHED CONTIG ORDERING\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1166 print "\nTo view your results in ACT\n\t\t Sequence file 1: $new_reference_file\n\t\t Comparison file 1: $prefix.crunch\n\t\t Sequence file 2: $prefix.fasta\n
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1167 \t\tACT feature file is: $prefix.tab\n
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1168 \t\tContigs bin file is: $prefix.bin\n
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1169 \t\tGaps in pseudomolecule are in: $prefix.gaps\n\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1170
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1171 #Run tblastx....
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1172 if ($run_blast ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1173 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1174 print "Running tblastx on contigs in bin...\nThis may take several minutes ...\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1175 my $formatdb = 'formatdb -p F -i' ;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1176 # my @formating = `
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1177 !system("$formatdb $new_reference_file") or die "ERROR: Could not find 'formatdb' for blast\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1178 my $blast_opt = 'blastall -m 9 -p tblastx -d ';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1179 my $contigs_inBin = $prefix.'.contigsInbin.fas';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1180 # my @bigger_b = `
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1181 !system("$blast_opt $new_reference_file -i $contigs_inBin -o blast.out") or die "ERROR: Could not find 'blastall' , please install blast in your working path (other dir==0)\n$blast_opt $new_reference_file -i $contigs_inBin -o blast.out\n \n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1182 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1183
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1184
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1185 if ($pick_primer == 1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1186 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1187 print " DESIGNING PRIMERS FOR GAP CLOSURE...\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1188 my $qq = "$prefix.fasta";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1189 pickPrimers($qq, $reference, $flank, $path_toPass, $chk_uniq,$qualAvailable,@Quality_Array);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1190 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1191 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1192
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1193
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1194 #------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1195 sub write_Fasta {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1196 my $sequence = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1197 my $fasta_seq ="";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1198 my $length = length($sequence);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1199 if ($length <= 60)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1200 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1201 $fasta_seq = $sequence ;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1202 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1203 elsif ($length> 60 )
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1204 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1205 for (my $i =0; $i < $length; $i+=60)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1206 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1207 my $tmp_s = substr $sequence, $i, 60;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1208 $fasta_seq .= $tmp_s."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1209 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1210 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1211
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1212 return $fasta_seq;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1213 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1214
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1215 sub write_Fasta_headers {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1216 my $sequence = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1217 my $header = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1218 my $fasta_seq =">$header\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1219 my $length = length($sequence);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1220 if ($length <= 60)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1221 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1222 $fasta_seq.= $sequence ;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1223 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1224 elsif ($length> 60 )
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1225 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1226 for (my $i =0; $i < $length; $i+=60)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1227 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1228 my $tmp_s = substr $sequence, $i, 60;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1229 $fasta_seq .= $tmp_s."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1230 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1231 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1232
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1233 return $fasta_seq;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1234 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1235
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1236 #---------------------------------------------- END OF CONTIG ORDERING SUBROUTINES----------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1237
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1238 #----------------------------------------------- PRIMER DESIGN ---------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1239 sub pickPrimers
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1240 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1241 #$ps = pseudo molecule,$rf = reference, $flan = flanking region size
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1242 my ($ps,$rf, $flan, $passed_path, $chk_uniq,$qualAvailable, @Quality_Array);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1243 if (@_==4){
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1244 ($rf,$ps, $flan, $chk_uniq) = @_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1245 print "Primers without ordering..\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1246 print $rf;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1247 $passed_path = "nucmer";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1248 $qualAvailable =0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1249 @Quality_Array = [];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1250 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1251 else #(@_ == 7)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1252 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1253 ($ps,$rf, $flan, $passed_path, $chk_uniq, $qualAvailable, @Quality_Array) = @_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1254 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1255
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1256 my $dna='';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1257 my @gappedSeq;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1258 my $records='';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1259 my @sequence;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1260 my $input='';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1261 #tdo
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1262 my @gappedQual;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1263 #my $quality='';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1264 my $path_toPass = $passed_path;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1265 my @fasta;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1266 my $query='';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1267 my @exc_regions;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1268 my $ch_name;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1269 #my $flank = $flan;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1270 open (FH, $rf) or die "Could not open reference file\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1271 open (FH2, $ps) or die "Could not open query/pseudomolecule file\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1272 my $ref; #print ".... ", $rf; exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1273 my @r = <FH>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1274 my @qry = <FH2>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1275 my $dn = join ("", @qry);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1276 $ref = join ("", @r);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1277 $dna = Fasta2ordered ($dn);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1278 #check if primer3 is installed
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1279 my $pr3 = "primer3_core";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1280 my ($pr3_path, $pr3_Path, $pr3_path_dir) = checkProg ($pr3);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1281 #my @check_prog = `which primer3_core`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1282 open (PRI, '>primer3.summary.out') or die "Could not open file for write\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1283
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1284 #
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1285
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1286 #print $ref; exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1287 #PARSING FOR PRIMER3 INPUT
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1288 my ($opt,$min,$max,$optTemp,$minTemp,$maxTemp,$flank,$lowRange,$maxRange,$gcMin,$gcOpt,$gcMax,$gclamp,$exclude,$quality) = getPoptions($qualAvailable);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1289 my ($gap_position,@positions, %seq_hash);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1290
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1291 my $exc1 = $flank -$exclude; #start of left exclude
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1292 print "Please wait... extracting target regions ...\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1293 #regular expression extracts dna sequence before and after gaps in sequence (defined by N)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1294 while($dna=~ /([atgc]{$flank,$flank}N+[atgc]{$flank,$flank})/gi)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1295 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1296 $records= $1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1297 push (@gappedSeq, $records);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1298 $gap_position = index($dna, $records);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1299 push @positions, $gap_position;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1300 $seq_hash{$gap_position}=$records;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1301 #dna
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1302 if ($qualAvailable) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1303 my $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1304 for (my $nn=($gap_position-1); $nn <= ($gap_position-1+length($records)-1); $nn++) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1305 $res.="$Quality_Array[$nn] ";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1306 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1307 push @gappedQual, $res;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1308 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1309 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1310 #loop prints out primer targets into a file format accepted by primer3
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1311 my $count=1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1312 my $identify='';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1313 my $seq_num = scalar @gappedSeq;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1314 my $name= " ";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1315
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1316 my ($totalp, @left_name, @right_name, @left_seq, @right_seq);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1317
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1318 my ($leftP_names, $rightP_names, $leftP_seqs, $rightP_seqs, $leftP_start, $leftP_lens, $rightP_ends, $rightP_lens,$left_Exclude,$right_Exclude, $primers_toExc, $prod_size)=
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1319 ("","","","","","","","","","", "", "");
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1320
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1321 print $seq_num, " gaps found in target sequence\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1322 print "Please wait...\nLooking for primers...\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1323 print "Running Primer3 and checking uniquness of primers...\nCounting left and right primer hits from a nucmer mapping (-c 15 -l 15)\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1324
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1325 for (my $i=0; $i<$seq_num; $i+=1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1326 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1327 $identify = $count++;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1328 if (defined $ch_name)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1329 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1330 $name = $ch_name;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1331 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1332 my $len = length($gappedSeq[$i]);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1333 my $exc2 = $len - $flank;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1334 open(FILE, '>data') or die "Could not open file\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1335 #tdo
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1336 my $qual='';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1337 if ($qualAvailable) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1338 $qual="PRIMER_SEQUENCE_QUALITY=$gappedQual[$i]\nPRIMER_MIN_QUALITY=$quality\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1339 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1340
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1341 #WARNING: indenting the following lines may cause problems in primer3
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1342 print FILE "PRIMER_SEQUENCE_ID=Starting_Pos $positions[$i]
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1343 SEQUENCE=$gappedSeq[$i]
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1344 PRIMER_OPT_SIZE=$opt
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1345 PRIMER_MIN_SIZE=$min
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1346 PRIMER_MAX_SIZE=$max
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1347 PRIMER_OPT_TM=$optTemp
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1348 PRIMER_MIN_TM=$minTemp
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1349 PRIMER_MAX_TM=$maxTemp
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1350 PRIMER_NUM_NS_ACCEPTED=1
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1351 PRIMER_PRODUCT_SIZE_RANGE=$lowRange-$maxRange
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1352 PRIMER_MIN_GC=$gcMin
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1353 PRIMER_GC_CLAMP =$gclamp
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1354 PRIMER_OPT_GC_PERCENT=$gcOpt
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1355 PRIMER_MAX_GC=$gcMax
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1356 PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=$exc1,$exclude $exc2,$exclude
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1357 ".$qual."Number To Return=1
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1358 =\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1359 close FILE;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1360
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1361 #runs primer3 from commandline
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1362
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1363 ################# NOTE: PRIMER3 SHOULD BE IN YOUR WORKING PATH #########
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1364
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1365 my @Pr3_output = `$pr3_path -format_output <data`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1366 #print $positions[$i], "\t", $i, " ", $path_toPass, " ", $rf, $exc1, " ",$exc2, "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1367 my $fil = join (":%:", @Pr3_output);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1368 my ($uniq_primer, $string,$left_nm,$right_nm,$left_sq, $right_sq,$left_strt,$left_ln, $right_End,$right_ln,$primers_toExclude, $product_size)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1369 = check_Primers ($fil, $positions[$i], $i,$path_toPass, $rf, $exc1, $exc2);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1370
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1371 print PRI $string;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1372 if ($uniq_primer ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1373 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1374 $leftP_names.=$left_nm."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1375 $rightP_names.=$right_nm."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1376 $leftP_seqs.=$left_sq."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1377 $rightP_seqs.=$right_sq."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1378 $leftP_start.=$left_strt."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1379 $leftP_lens.=$left_ln."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1380 $rightP_ends.=$right_End."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1381 $rightP_lens.=$right_ln."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1382 $left_Exclude.=$exc1."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1383 $right_Exclude.=$exc2."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1384 $prod_size.=$product_size."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1385 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1386 if ($primers_toExclude ne "")
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1387 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1388 $primers_toExc.= $primers_toExclude; #."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1389 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1390
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1391 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1392 write_Primers ($leftP_names, $rightP_names, $leftP_seqs, $rightP_seqs, $leftP_start, $leftP_lens, $rightP_ends, $rightP_lens,$primers_toExc,$left_Exclude,$right_Exclude, $prod_size);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1393 #write_Primers (@left_name, @right_name, @left_seq, @right_seq,@left_start, @left_len, @right_end, @right_len, @left_exclude, @right_exclude, $primers_toExclude);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1394
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1395 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1396
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1397 #checks the uniqueness of primers
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1398 #input an array with promer3 output for each gap
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1399 sub check_Primers
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1400 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1401
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1402 my ($fil, $position, $index,$path_toPass, $rf, $exc1, $exc2) = @_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1403 my @Pr3_output = split /:%:/, $fil;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1404 my ($left_name, $right_name, $left_seq, $right_seq, $left_start,$left_len,$right_end,$right_len,$left_exclude,$right_exclude) = ("", "", "", "", "", "", "", "", "", "");
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1405 my $primers_toExclude ="";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1406 my $product_size ="";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1407 my $string ="";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1408 my $uniq_primer = 0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1409 $string.="=========================================================================================\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1410 $string.="Primer set for region starting at ".$position."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1411
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1412 if (defined $Pr3_output[5] && defined $Pr3_output[6])
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1413 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1414 if ($Pr3_output[5]=~ /LEFT PRIMER/)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1415 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1416 # print $Pr3_output[5];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1417 #check uniquness of primer against the genome
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1418 my @splits_1 = split (/\s+/, $Pr3_output[5]);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1419 my $left_primer = $splits_1[8];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1420 my $left_st = $splits_1[2];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1421 my $left_length = $splits_1[3];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1422
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1423 my @splits_2 = split (/\s+/, $Pr3_output[6]);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1424 my $right_primer = $splits_2[8];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1425 my $right_st = $splits_2[2];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1426 my $right_length = $splits_2[3];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1427
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1428 open (QRY_1, '>./left_query'); # open a file for left primers
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1429 print QRY_1 ">left_01\n"; #
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1430 print QRY_1 $left_primer,"\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1431 open (QRY_2, '>./right_query');
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1432 print QRY_2 ">right_01\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1433 print QRY_2 $right_primer,"\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1434
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1435 my ($left_count, $right_count);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1436 #if ($chk_uniq eq "nucmer")
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1437 #{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1438 my $options = "-c 15 --coords -l 15 ";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1439 my $rq = "right_query";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1440 my $lq = "left_query";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1441 my (@right_ps, @left_ps);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1442 # print $path_toPass, "\t", $options, "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1443
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1444
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1445 my @Rrun = `$path_toPass $options -p R $rf $rq &> /dev/null`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1446 print ".";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1447 my $f1 = "R.coords";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1448 open (RP, $f1) or die "Could not open file $f1 while checking uniqueness of right primer\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1449 while (<RP>)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1450 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1451 chomp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1452 if ($_ =~ /right_01$/)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1453 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1454 push @right_ps, $_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1455 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1456 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1457 close (RP);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1458 my @Lrun = `$path_toPass $options -p L $rf $lq &> /dev/null`;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1459 print ".";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1460 my $f2 = "L.coords";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1461 open (LQ, $f2) or die "Could not open file $f2\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1462 while (<LQ>)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1463 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1464 chomp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1465 if ($_ =~ /left_01$/)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1466 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1467 push @left_ps, $_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1468 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1469 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1470 close (LQ);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1471 $right_count = scalar (@right_ps);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1472 $left_count = scalar(@left_ps);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1473 #check if a primer is not in the excluded region::
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1474 my $primer_NearEnd =0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1475 if ($left_st > $exc1 || $right_st < $exc2)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1476 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1477 $primer_NearEnd = 1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1478 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1479
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1480 if ($left_count < 2 && $right_count<2 && $primer_NearEnd ==0)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1481 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1482 $string.=$left_count."\t".$Pr3_output[5]."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1483 $string.=$right_count."\t".$Pr3_output[6]."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1484 $string.="***************************** PRIMER3 OUTPUT **************************\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1485 foreach (@Pr3_output) {$string.=$_;}
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1486
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1487 my @prod_size_split = split /\s+/, $Pr3_output[10];
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1488
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1489 $product_size = substr($prod_size_split[2], 0, -1);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1490 $left_name = $position;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1491 $right_name = $position;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1492 my $lp_uc = uc ($left_primer);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1493 my $rp_uc = uc($right_primer);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1494 #print $left_count, "..", $right_count, "\t";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1495 $left_seq = $lp_uc;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1496 $right_seq= $rp_uc;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1497
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1498 $left_start= $left_st;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1499 $left_len = $left_length;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1500
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1501 $right_end = $right_st;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1502 $right_len = $right_length;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1503
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1504 $left_exclude = $exc1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1505 $right_exclude =$exc2;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1506 $uniq_primer =1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1507 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1508 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1509 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1510 if ($primer_NearEnd ==1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1511 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1512 $string.="One of the oligos is near the end of a contig\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1513 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1514 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1515 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1516 $string.="Primer set not unique\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1517 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1518 $primers_toExclude.=">L.".$position."\n".$left_primer."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1519 $primers_toExclude.=">R.".$position."\n".$right_primer."\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1520 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1521
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1522 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1523 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1524 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1525 $string.="No Primers found\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1526 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1527 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1528
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1529 return ($uniq_primer, $string,$left_name,$right_name,$left_seq, $right_seq,$left_start,$left_len, $right_end,$right_len,$primers_toExclude, $product_size);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1530
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1531
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1532 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1533
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1534 ###------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1535 # Writes primers and their regions to file
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1536 sub write_Primers {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1537 my ($leftP_names, $rightP_names, $leftP_seqs, $rightP_seqs, $leftP_start, $leftP_lens, $rightP_ends, $rightP_lens,$primers_toExclude,$left_Exclude,$right_Exclude, $product_sizes) = @_;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1538 my (@left_name, @right_name, @left_seq, @right_seq, @left_start, @left_len, @right_end, @right_len, @left_exclude, @right_exclude, @product_size);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1539
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1540 #open files to read
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1541 @left_name = split /\n/, $leftP_names;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1542 @right_name= split /\n/, $rightP_names;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1543 @left_seq = split /\n/, $leftP_seqs;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1544 @right_seq = split /\n/, $rightP_seqs;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1545
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1546 @left_start = split /\n/, $leftP_start;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1547 @left_len = split /\n/, $leftP_lens;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1548 @right_end = split/\n/, $rightP_ends;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1549 @right_len = split /\n/, $rightP_lens;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1550 @left_exclude = split /\n/, $left_Exclude;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1551 @right_exclude = split /\n/,$right_Exclude;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1552 @product_size = split /\n/, $product_sizes;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1553
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1554 my $primers_withSize ="";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1555 open (SEN, '>sense_primers.out') or die "Could not open file for write\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1556 open (ASEN, '>antiSense_primers.out') or die "Could not open file for write\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1557 open (REG_1, '>sense_regions.out') or die "Could not open file for write\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1558 open (REG_2, '>antiSense_regions.out') or die "Could not open file for write\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1559
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1560 if ($primers_toExclude ne "")
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1561 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1562 open (PEX, '>primers_toExclude.out') or die "Could not open file for write\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1563 print PEX $primers_toExclude;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1564 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1565
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1566
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1567 my $totalp = scalar (@left_name);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1568
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1569 #print $totalp, "\n"; exit;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1570
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1571 my $well_pos;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1572 my $max_plates = ceil($totalp/96);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1573 #print "MAX Ps ", $max_plates, "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1574 my $plate=1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1575 my $sen ="";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1576 my $asen ="";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1577 my $plate_counter =0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1578 my $wells = 96;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1579 for (my $index =0; $index < $totalp; $index += $wells)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1580 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1581 my $do = $index;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1582 my $upper_bound= $index + $wells;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1583 if ($upper_bound > $totalp)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1584 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1585 $upper_bound = $totalp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1586 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1587
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1588 for (my $j=$index; $j <= ($upper_bound-1); $j+=1)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1589 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1590 my $i = $j;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1591 if ($j < 96)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1592 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1593 $well_pos = get_WellPosition ($j);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1594 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1595 else
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1596 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1597 $well_pos = get_WellPosition ($j - $wells)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1598 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1599
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1600 #$primers_withSize.=$product_size[$i]."\t"."Plate_".$plate. "\t\tS.".$i."\tS.".$left_name[$i]."\t".
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1601 print SEN "Plate_".$plate, "\t\t","S.", $i, "\tS.", $left_name[$i], "\t", $left_seq[$i], "\t\t+", "\t", $well_pos, "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1602 print ASEN "Plate_".$plate, "\t\t","AS.", $i, "\tAS.", $right_name[$i], "\t", $right_seq[$i], "\t\t-","\t", $well_pos,"\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1603 print REG_1 "Plate_".$plate, "\t\t","S.", $i, "\t", $left_start[$i], "\t", $left_len[$i], "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1604 print REG_2 "Plate_".$plate, "\t\t","AS.", $i, "\t", $right_end[$i], "\t",$right_len[$i], "\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1605
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1606 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1607 $plate +=1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1608 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1609
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1610 #delete tmp. files
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1611 #my $rm = "rm -f";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1612 system ("rm -f data left_query right_query R.delta R.cluster R.coords L.delta L.cluster L.coords");
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1613 print "\nPRIMER DESIGN DONE\n\n";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1614 # end of primer design program
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1615 }#//
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1616 #####
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1617 # returns a well position for oligos
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1618 sub get_WellPosition{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1619
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1620 my $j = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1621 my $well_pos;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1622 if ($j < 12)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1623 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1624 $well_pos = "a".($j+1);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1625 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1626 elsif ($j>11 && $j<24) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1627 $well_pos = "b". (($j+1) -12);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1628 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1629 elsif ($j>23 && $j<36) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1630 $well_pos = "c". (($j+1) -24);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1631 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1632 elsif ($j>35 && $j<48) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1633 $well_pos = "d". (($j+1) - 36);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1634 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1635 elsif($j>47 && $j<60) {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1636 $well_pos = "e". (($j+1) -48);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1637 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1638 elsif ($j>59 && $j<72)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1639 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1640 $well_pos = "f". (($j+1) - 60);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1641 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1642 elsif ($j>71 && $j< 84)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1643 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1644 $well_pos = "g". (($j+1) - 72);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1645 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1646 elsif ($j>83 && $j<96)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1647 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1648 $well_pos = "h". (($j+1) - 84);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1649 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1650 return $well_pos;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1651 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1652
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1653
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1654 ####################################################################
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1655 #get options for primer design
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1656 #----------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1657 sub getPoptions{
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1658
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1659 my $qualAvailable = shift;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1660 #### USER INPUTS ##########
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1661 #ask for optimum primer size
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1662 print "\nEnter Optimum Primer size (default 20 bases):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1663 my $opt=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1664 chomp $opt;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1665 if($opt eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1666 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1667 $opt = 20;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1668 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1669 #ask for minimum primer size
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1670 print "\nEnter Minimum Primer size (default 18 bases):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1671 my $min=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1672 chomp $min;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1673 if($min eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1674 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1675 $min = 18;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1676 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1677 #ask for maximum primer size
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1678 print "\nEnter Maximum Primer size (default 27 bases):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1679 my $max= <STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1680 chomp $max;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1681 if($max eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1682 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1683 $max= 27;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1684 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1685 #ask for optimum primer temperature
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1686 print "\nEnter Optimum melting temperature (Celcius) for a primer oligo (default 60.0C):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1687 my $optTemp=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1688 chomp $optTemp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1689 if($optTemp eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1690 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1691 $optTemp = 60.0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1692 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1693 #ask for minimum primer temperature
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1694 print "\nEnter Minimum melting temperature (Celcius) for a primer oligo (default 57.0C):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1695 my $minTemp=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1696 chomp $minTemp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1697 if($minTemp eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1698 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1699 $minTemp = 57.0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1700 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1701 #ask for maximum primer temperature
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1702 print "\nEnter Maximum melting temperature (Celcius) for a primer oligo (default 63.0C):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1703 my $maxTemp=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1704 chomp $maxTemp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1705 if($maxTemp eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1706 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1707 $maxTemp = 63.0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1708 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1709 print "\nEnter flanking region size (default 1000 bases): ";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1710 my $flank=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1711 chomp $flank;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1712 if ($flank eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1713 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1714 $flank = 1000;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1715 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1716 #ask for primer product range
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1717 print "\nEnter minimum product size produced by primers (default =flanking size):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1718 my $lowRange=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1719 chomp $lowRange;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1720 if($lowRange eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1721 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1722 $lowRange = $flank;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1723 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1724 print "\nEnter maxmimum product size produced by primers (default 7000):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1725 my $maxRange=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1726 chomp $maxRange;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1727 if($maxRange eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1728 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1729 $maxRange = 7000;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1730 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1731 #ask for minimum GC content in primers
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1732 print "\nEnter minimum GC content in primers (default 20%):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1733 my $gcMin=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1734 chomp $gcMin;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1735 if($gcMin eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1736 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1737 $gcMin = 20.0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1738 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1739 #ask for optimum GC content in primers
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1740 print "\nEnter optimum GC content in primers (default 50%):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1741 my $gcOpt=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1742 chomp $gcOpt;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1743 if($gcOpt eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1744 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1745 $gcOpt = 50.0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1746 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1747 #ask for maximum GC content in primers
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1748 print "\nEnter maximum GC content in primers (default 80%):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1749 my $gcMax=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1750 chomp $gcMax;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1751 if($gcMax eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1752 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1753 $gcMax = 80.0;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1754 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1755 print "\nEnter GC clamp (default 1):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1756 my $gclamp=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1757 chomp $gclamp;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1758 if($gclamp eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1759 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1760 $gclamp = 1;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1761 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1762 print "\nEnter size of region to exclude at the end of contigs (default 100 bases):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1763 my $exclude=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1764 chomp $exclude;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1765 if ($exclude eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1766 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1767 $exclude = 100;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1768 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1769
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1770
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1771 #tdo
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1772 my $quality='';
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1773 if ($qualAvailable)
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1774 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1775
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1776 print "\nEnter minimum quality for primer pick (default 40):";
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1777 $quality=<STDIN>;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1778 chomp $quality;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1779 if($quality eq '')
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1780 {
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1781 $quality = 40;
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1782 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1783 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1784
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1785
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1786 return ($opt,$min,$max,$optTemp,$minTemp,$maxTemp,$flank,$lowRange,$maxRange,$gcMin,$gcOpt,$gcMax,$gclamp,$exclude, $quality);
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1787
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1788 }
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1789 ###############
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1790 #-----------------------------------------------------END of PRIMER DESIGN ----------------------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1791 #-----------------------------------------------------END OF ABACAS -----------------------------------------------------------------------
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1792
a1fdc6925620 "planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
nml
parents:
diff changeset
1793