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#!/usr/bin/perl |
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use strict; |
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my $usage=q/ |
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gff_add_CDS.pl <gff_w_CDS.gff> <gff_input..> |
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|
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Adds the CDS records from a GFF file to another GFF input |
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which presumably lacks it (or if the input already has CDS |
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records, they will be discarded). |
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/; |
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my %cdsdata; # CDSParent => [ "CDSseg1_data", "CDSseg2_data", ..] |
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|
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#loads the CDS data |
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my $cdsfile=shift(@ARGV); |
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my $cdscount; |
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open(CDSGFF, $cdsfile) || die ("Error opening CDS file $cdsfile\n"); |
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while (<CDSGFF>) { |
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my @t=split('\t'); |
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next unless $t[2] eq 'CDS'; |
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chomp($t[8]); |
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my ($p)=($t[8]=~m/\bParent=([^;]+)/); |
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die("Error parsing Parent for CDS segment at $_\n") unless $p; |
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$t[8]=~s/\bParent=[^;]+;?//; |
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push(@{$cdsdata{$p}}, join("\t",@t[2..8])); |
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$cdscount++; |
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} |
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close CDSGFF; |
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|
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#print STDERR "..loaded $cdscount CDS segments..\n"; |
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|
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while (<>) { |
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my @t=split('\t'); |
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print $_; |
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if ($t[2] eq 'mRNA') { |
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# print CDS data here, if found |
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my ($id)=($t[8]=~m/\bID=([^;]+)/); |
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my $cds=$cdsdata{$id}; |
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unless ($cds) { |
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#search for the special "acc" attribute we may store there for Drupal |
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my ($acc)=($t[8]=~m/\bacc=([^;]+)/); |
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$cds=$cdsdata{$acc}; |
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} |
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if ($cds) { |
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foreach my $cdseg (@$cds) { |
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#$cdseg.="Parent=$id" |
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# unless ($cdseg=~s/\t([^\t]+)$/\tParent=$id;$1/); |
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$cdseg=~s/\t([^\t]*)$/\tParent=$id;$1/; |
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print join("\t",@t[0..1],$cdseg)."\n"; |
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} |
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} |
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} |
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} |
