12/parse_hmmscan.pl

#!/usr/bin/perl -w

use strict;

print "protname\tlen\tdomname\tbegin\tend\n";

open(IN, 'clotting.tab') or die "could not open file\n";
while (<IN>) {
    unless (/^\#/) {    # avoid all lines beginning
                        # with the '#' character
        my @columns  = split(/ +/);
        my $domname  = $columns[0];
        my $protname = $columns[3];
        $protname    =~ s/.*\|//;
        my $len      = $columns[5];
        my $evalue   = $columns[12];
        my $begin    = $columns[17];
        my $end      = $columns[18];
        if ( $evalue < 1e-5 ) {
            print "$protname\t$len\t$domname\t$begin\t$end\n";
        }
    }
}
close IN;