Mercurial > repos > earlhaminst > hcluster_sg_parser

comparison hcluster_sg_parser.pl @ 0:dbc49bd1a3e9 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
author earlhaminst
date Mon, 12 Dec 2016 07:12:23 -0500
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-1:000000000000 0:dbc49bd1a3e9
1 #!/usr/bin/perl
2 #
3 use strict;
4 use warnings;
5 # A simple perl parser to convert hcluster_sg 3-column output into list of ids in separate files
6 # hcluster_sg_parser.pl <file>
7
8 my $file1 = $ARGV[0];
9 open my $fh1, '<', $file1;
10
11 while (my $line = <$fh1>) {
12 chomp $line;
13 my @row = split(/\t/, $line);
14
15 my $cluster_id = $row[0];
16 my $id_list = $row[2];
17 # Change commas to newlines
18 $id_list =~ s/\,/\n/g;
19
20 my $outfile = $cluster_id."_output.txt";
21 open(my $fh, '>', $outfile) or die "Could not open file '$outfile' for writing: $!";
22 print $fh $id_list;
23 close $fh;
24 }
25 close $fh1;