Perl script to combine multiple columns from the protraits table to a single categorical traitType for FENNEC

extract_protraits.pl

#!/usr/bin/perl

# USAGE: perl extract_traits.pl <ProTraits_binaryIntegrated_File> <columns ...> 
# EXAMPLE: perl extract_traits.pl ProTraits_binaryIntegratedPr0.90.txt 275 276 277 292 >oxygenreq.tsv

use strict;
use warnings;

my $file = shift(@ARGV);
my @columns = @ARGV;

open IN, "<$file" or die "$!";
my $header = <IN>;
chomp $header;
my @header = split(/\t/, $header);

while(<IN>){
	chomp;
	my @row = split(/\t/, $_);
	foreach my $col (@columns){
		print "$row[1]\t$header[$col-1]\t\t\t\n" if($row[$col-1] eq "1");
	}
}

close IN or die "$!";