Trims an "out_table" file in accordance with a specific set of organisms

Author: sahrendt0

parseByTax.pl

@@ -0,0 +1,66 @@
+#!/usr/bin/perl
+# Script: parseByTax.pl
+# Description: Trims an "out_table" file in accordance with a specific set of organisms 
+# Author: Steven Ahrendt
+# email: [email protected]
+# Date: 04.02.2014
+##################################
+use warnings;
+use strict;
+use Getopt::Long;
+use Data::Dumper;
+
+#####-----Global Variables-----#####
+my $input;
+my ($help,$verb);
+my %out_table;
+my @orgs = qw(Amac Bden Cang Clat Gpro Hpol OrpC PirE Rall Spun);
+
+GetOptions ('i|input=s' => \$input,
+            'h|help'   => \$help,
+            'v|verbose' => \$verb);
+my $usage = "Usage: parseByTax.pl -i input\n";
+die $usage if $help;
+die "No input.\n$usage" if (!$input);
+
+#####-----Main-----#####
+open(my $fh,"<",$input) or die "Can't open $input: $!\n";
+my $lc = 0;
+my @gene_names;
+while (my $line = <$fh>)
+{
+  chomp $line;
+  my @data = split(/\t/,$line);
+  if($lc == 0)
+  {
+    @gene_names = @data;
+  }
+  else
+  {
+    for(my $i=1;$i<scalar(@gene_names); $i++)
+    {
+      $out_table{$data[0]}{$gene_names[$i]} = $data[$i];
+    }
+  }
+  $lc++;
+}
+close($fh);
+
+#print Dumper \%out_table;
+
+print join("\t",@gene_names),"\n";
+shift @gene_names;
+foreach my $org (@orgs)
+{
+  print $org,"\t";
+  foreach my $gene (@gene_names)
+  {
+    print $out_table{$org}{$gene},"\t";
+  }
+  print "\n";
+}
+
+warn "Done.\n";
+exit(0);
+
+#####-----Subroutines-----#####