Script that can fix InParanoid sqltable files that have incorrect gene ids

svn path=/; revision=608

diff --git a/interactome_scripts/fix_sqltable_files.pl b/interactome_scripts/fix_sqltable_files.pl
new file mode 100755 (executable)
index 0000000..e83ad65
--- /dev/null
+++ b/interactome_scripts/fix_sqltable_files.pl
@@ -0,0 +1,29 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+if(-e "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl") {
+       require "$ENV{HOME}/scripts/jaiswallab/interactome_scripts/find_species.pl";
+}elsif(-e "$ENV{HOME}/bin/find_species.pl") {
+       require "$ENV{HOME}/bin/find_species.pl";
+}
+
+my $in_file = $ARGV[0];
+my $out_file = $ARGV[1];
+
+open(INFILE, "$in_file");
+open(OUTFILE, ">$out_file");
+
+while(<INFILE>) {
+       my $line = $_;
+       chomp $line;
+       
+       my ($clust_id, $bit_score, $file, $score, $gene) = split(/\t/, $line);
+       my $species = find_species($file);
+       my $new_gene = find_gene($gene, $species);
+       print OUTFILE "$clust_id\t$bit_score\t$file\t$score\t$new_gene\n";
+}
+close(INFILE);
+close(OUTFILE);
+