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root/gclib/scripts/gff_add_CDS.pl
Revision: 24
Committed: Tue Jul 26 21:46:39 2011 UTC (8 years, 1 month ago) by gpertea
File size: 1401 byte(s)
Log Message:
Line File contents
1 #!/usr/bin/perl
2 use strict;
3 my $usage=q/
4 gff_add_CDS.pl <gff_w_CDS.gff> <gff_input..>
5
6 Adds the CDS records from a GFF file to another GFF input
7 which presumably lacks it (or if the input already has CDS
8 records, they will be discarded).
9 /;
10 my %cdsdata; # CDSParent => [ "CDSseg1_data", "CDSseg2_data", ..]
11
12 #loads the CDS data
13 my $cdsfile=shift(@ARGV);
14 my $cdscount;
15 open(CDSGFF, $cdsfile) || die ("Error opening CDS file $cdsfile\n");
16 while (<CDSGFF>) {
17 my @t=split('\t');
18 next unless $t[2] eq 'CDS';
19 chomp($t[8]);
20 my ($p)=($t[8]=~m/\bParent=([^;]+)/);
21 die("Error parsing Parent for CDS segment at $_\n") unless $p;
22 $t[8]=~s/\bParent=[^;]+;?//;
23 push(@{$cdsdata{$p}}, join("\t",@t[2..8]));
24 $cdscount++;
25 }
26 close CDSGFF;
27
28 #print STDERR "..loaded $cdscount CDS segments..\n";
29
30 while (<>) {
31 my @t=split('\t');
32 print $_;
33 if ($t[2] eq 'mRNA') {
34 # print CDS data here, if found
35 my ($id)=($t[8]=~m/\bID=([^;]+)/);
36 my $cds=$cdsdata{$id};
37 unless ($cds) {
38 #search for the special "acc" attribute we may store there for Drupal
39 my ($acc)=($t[8]=~m/\bacc=([^;]+)/);
40 $cds=$cdsdata{$acc};
41 }
42 if ($cds) {
43 foreach my $cdseg (@$cds) {
44 #$cdseg.="Parent=$id"
45 # unless ($cdseg=~s/\t([^\t]+)$/\tParent=$id;$1/);
46 $cdseg=~s/\t([^\t]*)$/\tParent=$id;$1/;
47 print join("\t",@t[0..1],$cdseg)."\n";
48 }
49 }
50 }
51 }

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