Gets all PFAM IDs associated with a gene ID for a given organism

Author: sahrendt0

getPFAM.pl

@@ -0,0 +1,53 @@
+#!/usr/bin/perl
+# Script: getPFAM.pl
+# Description: Gets all PFAM IDs associated with a gene ID for a given organism
+# Author: Steven Ahrendt
+# email: [email protected]
+# Date: 04.04.2014
+##################################
+use warnings;
+use strict;
+use lib '/rhome/sahrendt/Scripts';
+use Getopt::Long;
+use BCModules;
+use Data::Dumper;
+
+#####-----Global Variables-----#####
+my $input;
+my ($help,$verb);
+my (%pfam,$pfamFile,$spec);
+
+GetOptions ('i|input=s' => \$input,
+            'h|help'   => \$help,
+            'v|verbose' => \$verb);
+my $usage = "Usage: getPFAM.pl -i input\n";
+die $usage if $help;
+die "No input.\n$usage" if (!$input);
+
+#####-----Main-----#####
+$spec = (split(/\./,$input))[0];
+$pfamFile = "$spec\_pfam_to_genes.txt";
+%pfam = indexPFAM($pfamFile);
+open(my $fh, "<", $input) or die "Can't open $input: $!\n";
+while(my $line = <$fh>)
+{
+  chomp $line;
+  print $line,"\t";
+  my $id = (split(/\|/,$line))[1];
+  $id =~ s/T\d$//;
+  if(exists $pfam{$id})
+  {
+    for(my $i=0;$i < scalar @{$pfam{$id}{PFAM_ACC}}; $i++)
+    {
+      print @{$pfam{$id}{PFAM_ACC}}[$i],";";
+    }
+  }
+  print "\n";
+}
+close($fh);
+#print Dumper \%pfam;
+
+warn "Done.\n";
+exit(0);
+
+#####-----Subroutines-----#####