Mercurial > repos > earlhaminst > hcluster_sg_parser

annotate hcluster_sg_parser.pl @ 0:dbc49bd1a3e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
1 #!/usr/bin/perl
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
2 #
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
3 use strict;
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
4 use warnings;
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
5 # A simple perl parser to convert hcluster_sg 3-column output into list of ids in separate files
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
6 # hcluster_sg_parser.pl <file>
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
7
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
8 my $file1 = $ARGV[0];
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
9 open my $fh1, '<', $file1;
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
10
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
11 while (my $line = <$fh1>) {
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
12 chomp $line;
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
13 my @row = split(/\t/, $line);
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
14
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
15 my $cluster_id = $row[0];
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
16 my $id_list = $row[2];
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
17 # Change commas to newlines
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
18 $id_list =~ s/\,/\n/g;
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
19
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
20 my $outfile = $cluster_id."_output.txt";
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
21 open(my $fh, '>', $outfile) or die "Could not open file '$outfile' for writing: $!";
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
22 print $fh $id_list;
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
23 close $fh;
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
24 }
dbc49bd1a3e9 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 75c6b4d9bd23cdd5f8e5626b1b01f2abba32c274-dirty
earlhaminst
parents:
diff changeset
25 close $fh1;