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annotate orthologs/ucsb_hamster/lib/run_genewise.pm @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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1 package run_genewise;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 use strict;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 $ENV{'WISECONFIGDIR'} = "/home/osiris/galaxy-dist/tools/osiris/orthologs/ucsb_hamster/lib/wisecfg";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 # this module runs genewise on a DNA sequence and a protein sequence
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 # and then allows to parse this result.
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 # the constructor creates an object containing a reference to an array
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 # containing the file content
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 1;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 sub new {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 my $self_tmp = [];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 my $self;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 my ($class, $dna, $prot, $path) = @_;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 if (!defined $path) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 $path = '/tmp';
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 $dna =~ s/R/N/g; #Added by THO -- genewise crashed with 'R' in dna sequence
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 $dna =~ s/S/N/g; #Added by THO -- genewise crashed with 'R' in dna sequence
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 $dna =~ s/W/N/g; #Added by THO -- genewise crashed with 'R' in dna sequence
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 $dna =~ s/D/N/g; #Added by THO -- genewise crashed with 'R' in dna sequence
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 $dna =~ s/K/N/g; #Added by THO -- genewise crashed with 'R' in dna sequence
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 $dna =~ s/Y/N/g; #Added by THO -- genewise crashed with 'R' in dna sequence
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 $dna =~ s/B/N/g; #Added by THO -- genewise crashed with 'R' in dna sequence
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 $dna =~ s/V/N/g; #Added by THO -- genewise crashed with 'R' in dna sequence
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 $dna =~ s/M/N/g; #Added by THO -- genewise crashed with 'R' in dna sequence
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 # the file names
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 my $protname = 'protein';
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 my $dnaname = 'dna';
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29
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 ## print the two sequences to default path /tmp/
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 open (DNA, ">$path/dna.fa") or die "could not open $path/dna.fa for writing\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 print DNA ">$dnaname\n$dna";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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33 close DNA;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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34 open (PROTEIN, ">$path/prot.fa") or die "could not open $path/prot.fa for writing\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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35 print PROTEIN ">$protname\n$prot";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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36 close PROTEIN;
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37
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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38 ## run genewise on the two sequences
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 `echo \$WISECONFIGDIR`;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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40
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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41 # $self_tmp = [`.\/genewise -trans -cdna -pep -sum $path/prot.fa $path/dna.fa`];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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42 #THO--For Galaxy run Genewise in the path
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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43 $self_tmp = [`genewise -trans -cdna -pep -sum $path/prot.fa $path/dna.fa`];
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44 for (my $i = 0; $i < @$self_tmp; $i++) {
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45 $self_tmp->[$i] =~ s/\s{1,}$//;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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46 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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47 $self->{gw} = $self_tmp;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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48 $self->{nt_seq} = $dna;
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49 $self->{prot_seq} = $prot;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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50 $self->{protname} = $protname;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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51 $self->{dnaname} = $dnaname;
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52 $self->{gw_count} = @$self_tmp;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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53 $self->{get_indel} = 1; ## per default the indel-part is recovererd, rather than masked by 'N'. See code for details
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54 $self->{indels} = _GetIndels($self_tmp);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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55 bless ($self, $class);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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56 return $self;}
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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57 #################
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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58 ## sub score extract the score for the alignment
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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59 sub score {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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60 my $self = shift;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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61 my $score;
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62 for (my $i = 0; $i < $self->{gw_count}; $i ++) {
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63 if ($self->{gw}->[$i] =~ /^(\d{1,}\.{0,1}\d{0,}).*/) {
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64 $score = $1;
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65 last;
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66 }
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67 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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68 return ($score);
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69 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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70 ##################
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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71 sub protein {
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72 my $self = shift;
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73 my $gw = $self->{gw};
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74 my $prot = '';
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75 for (my $i = 0; $i < @$gw; $i++) {
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76 if ($gw->[$i] =~ />.*\.pep/) { #the protein seq starts
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77 my $count = 1;
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78 while ($gw->[$i+$count] ne '//') {
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79 my $protpart = $gw->[$i+$count];
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80 chomp $protpart;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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81 $prot .= $protpart;
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82 $count ++;
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83 }
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84 }
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85 elsif (length $prot > 0) {
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86 last;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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87 }
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88 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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89 return($prot);
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90 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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91 ##################
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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92 sub translation {
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93 my $self = shift;
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94 my $finish = 0;
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95 my $translated_seq = '';
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96 my @transtmp;
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97
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98 ## step 1: extract the relevant info from the genewise output
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99
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100 for (my $i = 0; $i < $self->{gw_count}; $i++) {
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101 if ($self->{gw}->[$i] =~ />.*.tr/) {# a translated bit starts
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102 while ($self->{gw}->[$i] !~ '//') {
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103 push @transtmp, $self->{gw}->[$i];
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104 $i++;
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105 }
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106 last; # end the for loop since nothing left to be done
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107 }
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108 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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109
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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110 ## step two: get the sequences
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111 my $count = -1;
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112 my $trans;
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113 for (my $i = 0; $i < @transtmp; $i++) {
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114 if ($transtmp[$i] =~ />/) {
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115 $count++;
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116 $trans->[$count]->{seq} = ''; # initialize
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117 if ($transtmp[$i] =~ /.*\[([0-9]{1,}):([0-9]{1,})\].*/) {
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118 $trans->[$count]->{start} = $1;
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119 $trans->[$count]->{end} = $2;
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120 }
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121 }
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122 else {
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parents:
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123 $trans->[$count]->{seq} .= $transtmp[$i];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
124 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
125 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
126
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
127 ## step 3: connect the fragments
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
128 if (@$trans == 1) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
129 $translated_seq = $trans->[0]->{seq};
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
130 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
131 else {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
132 for (my $i = 0; $i < @$trans; $i++) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
133 $translated_seq .= $trans->[$i]->{seq};
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
134 if ($i < (@$trans - 1)) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
135 my $missing = $trans->[$i+1]->{start} - $trans->[$i]->{end} -1;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
136 $translated_seq .= 'X';
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
137 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
138 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
139 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
140 return($translated_seq);
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
141 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
142
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
143 ##################
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
144 sub codons {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
145 my $self = shift;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
146 my $finish = 0;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
147 my $codon_seq = '';
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
148 my @transtmp;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
149
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
150 ## step 1: extract the relevant info from the genewise output
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
151 for (my $i = 0; $i < $self->{gw_count}; $i++) {
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
152 if ($self->{gw}->[$i] =~ />.*sp$/) {# the codons set starts
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
153 while ($self->{gw}->[$i] !~ '//') {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
154 push @transtmp, $self->{gw}->[$i];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
155 $i++;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
156 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
157 last; # end the for loop since nothing left to be done
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
158 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
159 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
160
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
161 ## step two: get the sequences
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
162 my $count = -1;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
163 my $trans;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
164 for (my $i = 0; $i < @transtmp; $i++) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
165 if ($transtmp[$i] =~ />/) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
166 $count++;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
167 $trans->[$count]->{seq} = ''; # initialize
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
168 if ($transtmp[$i] =~ /.*\[([0-9]{1,}):([0-9]{1,})\].*/) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
169 $trans->[$count]->{start} = $1;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
170 $trans->[$count]->{end} = $2;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
171 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
172 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
173 else {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
174 $transtmp[$i] =~ tr/a-z/A-Z/;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
175 $trans->[$count]->{seq} .= $transtmp[$i];
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
176 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
177 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
178
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
179 ## step 3: connect the fragments
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
180 if ( @$trans == 1) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
181 $codon_seq = $trans->[0]->{seq};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
182 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
183 else {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
184 for (my $i = 0; $i < @$trans; $i++) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
185 $codon_seq .= $trans->[$i]->{seq};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
186 if ($i < (@$trans - 1)) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
187 my $indel = '';
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
188 my $missing = $trans->[$i+1]->{start} - $trans->[$i]->{end} -1;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
189
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
190 ## now decide whether the nts that did not got translated are masked by
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
191 ## 'N' or whether they will be represented as lower case letters
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
192 if ($self->{get_indel}) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
193 $indel = substr($self->{nt_seq}, $trans->[$i]->{end}, $missing);
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
194 $indel =~ tr/A-Z/a-z/;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
195 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
196 else {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
197 $indel = 'N' x $missing;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
198 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
199 ## now append gap characters until the frame is recovered. Not that the gap
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
200 ## characters are added to the end of the indel-part. Thus, the codons are
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
201 ## not considered.
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
202 while (length($indel)%3 != 0) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
203 $indel .= '-';
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
204 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
205
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
206 $codon_seq .= $indel;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
207 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
208 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
209 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
210 return ($codon_seq);
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
211 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
212 ###########################
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
213 sub protein_borders {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
214 my $self = shift;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
215 my $gw = $self->{gw};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
216 for (my $i = 0; $i < @$gw; $i++) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
217 if ($gw->[$i] =~ /Bits.*introns$/) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
218 my ($start, $end) = $gw->[$i+1] =~ /.*$self->{protname}\s{1,}([0-9]{1,})\s{1,}([0-9]{1,}).*/;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
219 return($start, $end);
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
220 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
221 else {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
222 die "no protein-start and end could not be determnined. Check genewise command\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
223 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
224 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
225 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
226 ##########################
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
227 sub cdna_borders {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
228 my $self = shift;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
229 my $gw = $self->{gw};
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
230 for (my $i = 0; $i < @$gw; $i++) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
231 if ($gw->[$i] =~ /Bits.*introns$/) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
232 my ($start, $end) = $gw->[$i+1] =~ /.*$self->{dnaname}\s{1,}([0-9]{1,})\s{1,}([0-9]{1,}).*/;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
233 return($start, $end);
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
234 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
235 else {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
236 die "no cdna-start and end could not be determnined. Check genewise command\n";
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
237 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
238 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
239 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
240 ##########################
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
241 sub _GetIndels {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
242 my $gw = shift;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
243 my $indel;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
244 for (my $i = 0; $i < @$gw; $i++) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
245 if ($gw->[$i] =~ /Bits/) {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
246 $indel = $gw->[$i+1] =~ /.*([0-9]{1,})/;
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
247 return($indel);
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
248 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
249 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
250 }