bin/loci_gene_model_match.pl

   1 #!/usr/bin/env perl
   2 use strict;
   3 use warnings;
   4 use English;
   5 use Carp;
   6 use FindBin;
   7 use Getopt::Std;
   8
   9 use Data::Dumper;
  10
  11 use Bio::FeatureIO;
  12
  13 use CXGN::ITAG::Release;
  14
  15 sub usage {
  16   my $message = shift || '';
  17   $message = "Error: $message\n" if $message;
  18   die <<EOU;
  19 $message
  20 Usage:
  21   $FindBin::Script
  22
  23   Script to get some stuff or something. (Naama should rewrite this)
  24
  25   Options:
  26
  27     none yet
  28
  29 EOU
  30 }
  31 sub HELP_MESSAGE {usage()}
  32
  33 our %opt;
  34 getopts('',\%opt) or usage();
  35
  36 my ($curr_pipeline) = CXGN::ITAG::Release->find();
  37 $curr_pipeline or die 'no current ITAG pipeline found in base dir '.CXGN::ITAG::Release->releases_root_dir;
  38
  39 my $annotation_file = $curr_pipeline->get_file_info('combi_genomic_gff3')->{file};
  40
  41 open my $loci_matches, "grep ITAG_sgn_loci $annotation_file |"
  42   or die "$! running grep on $annotation_file";
  43
  44 while (my $line = <$loci_matches> ) {
  45   chomp $line;
  46   my ($seq,$source,$type,$start,$end,$score,$dir,$phase,$attrs) = split /\s+/,$line,9;
  47   next unless $source eq 'ITAG_sgn_loci';
  48   my %attrs = map split(/(?<=[^\\])=/,$_), split(/(?<=[^\\]);/,$attrs);
  49   print "got match for $attrs{Name} on $seq from $start to $end\n";
  50 }
  51