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/tools/filters/CreateInterval.pl

https://bitbucket.org/cistrome/cistrome-harvard/
Perl | 19 lines | 8 code | 7 blank | 4 comment | 2 complexity | e7aec02da073f3895673723f89b3eefe MD5 | raw file
 1#! /usr/bin/perl -w
 2
 3# Accepts chrom, start, end, name, and strand
 4# If strand is void sets it to plus
 5# CreateInterval.pl $chrom $start $end $name $strand $output
 6
 7my $strand = "+";
 8
 9die "Not enough arguments\n" unless @ARGV == 6;
10
11open OUT, ">$ARGV[5]" or die "Cannot open $ARGV[5]:$!\n";
12
13$strand = "-" if $ARGV[4] eq "minus";
14$ARGV[3] =~ s/\s+/_/g;
15$ARGV[3] =~ s/\t+/_/g;
16
17print OUT "$ARGV[0]\t$ARGV[1]\t$ARGV[2]\t$ARGV[3]\t0\t$strand\n";
18close OUT;
19