Mercurial > repos > brasset_jensen > srnapipe

annotate lib/sRNAPipe/subgroups.pm @ 64:967512924317 draft

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planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
author brasset_jensen
date Mon, 28 Jan 2019 11:57:15 -0500
parents
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64
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
diff changeset
1 package sRNAPipe::subgroups;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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3 use strict;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
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4 use warnings;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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5 use Exporter;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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6 our @ISA = qw( Exporter );
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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7 our @EXPORT_OK = qw( &subgroups );
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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9 use POSIX;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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10 use File::Copy;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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11 use FindBin;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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12 use lib "$FindBin::Bin/../lib";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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13 use sRNAPipe::align qw ( get_hash_alignment );
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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15 sub subgroups
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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16 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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17 my ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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18 my (@files, $sum, $pie, $repar, %ismapped, %isjunk, %repartition, @junk_ref, @all_ref );
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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20 srand();
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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21 print $report "----------------------------\n";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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22 print $report "Create subgroups:\nfastq_in: $fin\ndirectory_out: $dir\nmismatches: $mis\nmismatches TE: $mis_TE\n";
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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24 mkdir $dir;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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25 $dir = $dir.'/' unless $dir =~ /(.*)\/$/;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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27 my $accept_miRNas = $dir.'miRNAs.fastq';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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28 my $reject_miRNAs = $dir.'miRNAs_rejected.fastq';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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29 my $sam_miRNAs = $dir.'miRNAs.sam';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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30 my @tmp = get_hash_alignment($miRNAs, $mis, 1, 1, $accept_miRNas, $reject_miRNAs, $fin, $proc, 'miRNAs',$sam_miRNAs, $report);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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31 my $mi = $tmp[0]; my $sam = '';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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32 $repartition{'miRNAs'} = $mi;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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35 my $reject_rRNAs = $dir.'rRNAs_rejected.fastq';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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36 if ( $rRNAs eq 'None')
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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37 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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38 move($reject_miRNAs,$reject_rRNAs);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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39 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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40 else
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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41 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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42 $sam = new String::Random;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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43 $sam = $sam->randpattern("CCcccccc");
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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44 @tmp = get_hash_alignment($rRNAs, $mis, 0, 1, 'NA', $reject_rRNAs, $reject_miRNAs, $proc, 'rRNAs', $sam, $report);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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45 $repartition{'rRNAs'} = $tmp[0];
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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46 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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47 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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49 my $reject_tRNAs = $dir.'rRNAs_rejected.fastq';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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50 if ( $rRNAs eq 'None')
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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51 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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52 move($reject_rRNAs,$reject_tRNAs);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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53 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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54 else
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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55 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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56 $sam = new String::Random;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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57 $sam = $sam->randpattern("CCcccccc");
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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58 @tmp = get_hash_alignment($tRNAs, $mis, 0, 1, 'NA', $reject_tRNAs, $reject_rRNAs, $proc, 'tRNAs', $sam, $report);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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59 $repartition{'tRNAs'} = $tmp[0];
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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60 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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61 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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64 my $bonafide = $dir.'bonafide_reads.fastq';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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65 if ( $rRNAs eq 'None')
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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66 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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67 move($reject_tRNAs,$bonafide);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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68 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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69 else
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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70 {
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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71 $sam = new String::Random;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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72 $sam = $sam->randpattern("CCcccccc");
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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73 @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report);
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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74 $repartition{'snRNAs'} = $tmp[0];
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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75
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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76 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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77 }
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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78 my $bo = $tmp[1];
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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79
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80 my $sam_transcripts = $dir.'transcripts.sam';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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81 my $reject_transcripts = $dir.'rejected_transcripts.fastq';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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82 @tmp = get_hash_alignment($transcripts, $mis, 0, 1, 'NA', $reject_transcripts, $bonafide, $proc, 'transcripts', $sam_transcripts, $report, $dir.'transcripts.fai');
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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83 $repartition{'transcripts'} = $tmp[0];
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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84
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85
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86 my $sam_TEs = $dir.'TEs.sam';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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87 my $reject_TEs = $dir.'rejected.fastq';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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88 @tmp = get_hash_alignment($TE, $mis_TE, 0, 1, 'NA', $reject_TEs, $reject_transcripts, $proc, 'TEs', $sam_TEs, $report, $dir.'TEs.fai' );
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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89 $repartition{'TEs'} = $tmp[0] ; $repartition{'others'} = $tmp[1];
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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90 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
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91 unlink $reject_transcripts;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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92 unlink $reject_rRNAs;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
brasset_jensen
parents:
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93 unlink $reject_miRNAs;
967512924317 planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
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94 unlink $reject_tRNAs;
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95
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96 #create repartition
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97 my $pi = fastqSubgroups($bonafide, $dir, $min_si, $max_si, $min_pi, $max_pi );
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98
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99 open (my $re, '>'.$dir.'repartition.txt') || die "cannot open $dir repartition.txt $!\n";
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100 print $re "type\tnumber\tpercentage\n";
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101 $sum += $_ foreach values %repartition;
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102 foreach my $k ( sort keys %repartition )
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103 {
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104 my $prct = 0;
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105 $prct = $repartition{$k} / $sum * 100 if $sum != 0;
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106 print $re "$k\t$repartition{$k}\t"; printf $re "%.2f\n",$prct;
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107 }
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108 return ( $bo, $mi, $pi);
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109 }
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110
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111 sub fastqSubgroups
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112 {
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113 my ( $fastq, $output_directory, $min_si, $max_si, $min_pi, $max_pi ) = @_;
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114 my $fastq_siRNA = $output_directory."siRNAs.fastq";
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115 my $fastq_piRNA = $output_directory."piRNAs.fastq";
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116
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117 open my $fic, '<', $fastq || die "cannot open input file $! \n";
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118 open my $si, '>', $fastq_siRNA || die "cannot open siRNA.fastq $! \n";
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119 open my $pi, '>', $fastq_piRNA || die "cannot open piRNA.fastq $! \n";
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120
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121 my ($length, $cmp, $type, $siRNA_number, $miRNA_h_number, $piRNA_number, $not_pi_number) = (0,0,0,0,0,0,0);
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122 my (@fastq) =(); my $seq_name;
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123 my $out;
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124 while(<$fic>)
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125 {
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126 chomp $_;
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127 $cmp++;
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128 if ($cmp == 1)
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129 {
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130 die "file do not contain a @ at line $cmp\n" unless ($_ =~ /^\@/ );
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131 $type = 0; @fastq = ();
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132 if ($_ =~ /^\@(.*)\s.*/) { $seq_name = $1;}
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133 elsif ($_ =~ /^\@(.*)/) {$seq_name = $1;}
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134 push(@fastq,$_);
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135 }
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136 elsif ($cmp == 2)
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137 {
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138 #die "unrecognized symbol at line $cmp\n" unless $_ =~ /[atcgATCGnN]+/;
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139 push(@fastq,$_);
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140 $length = length($_);
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141 $type = 0;
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142 if ( $length >= $min_si && $length <= $max_si )
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143 {
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144 $type = 2;
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145 $siRNA_number++;
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146 }
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147 if ($length >= $min_pi && $length <= $max_pi )
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148 {
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149 $type += 4;
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150 $piRNA_number++;
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151 }
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152 }
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153 elsif ($cmp == 3 )
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154 {
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155 die "file do not contain a + at line $cmp\n" unless $_ =~ /^\+/;
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156 push(@fastq,$_);
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157 }
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158 elsif ($cmp == 4 )
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159 {
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160 push(@fastq,$_);
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161 $cmp = 0;
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162 if ($type != 0)
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163 {
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164 if ($type & 4 ) { foreach my $t (@fastq) { print $pi $t."\n";} }
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165 if ($type & 2 ) { foreach my $t (@fastq) { print $si $t."\n";} }
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166 }
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167 }
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168 }
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169 close $fic;
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170 close $si; close $pi;
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171 return ($piRNA_number);
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172 }
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173
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174 1;