Mercurial > repos > pjbriggs > motif_tools

comparison CountUniqueIDs.pl @ 3:b4e22d2d7fa7 draft

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Add missing Perl scripts from previous uploads.
author pjbriggs
date Mon, 09 Apr 2018 04:45:06 -0400
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2:96a4ee27b08a 3:b4e22d2d7fa7
1 #! /usr/bin/perl -w
2
3 use strict;
4
5 #### Read thru a GFF file of motifs return the number of unique ids
6 #### Ian Donaldson Sept 2008
7
8 #### Usage
9 unless(@ARGV == 2) {
10 die("USAGE: $0 | GFF file | Output file\n\n");
11 }
12
13 #### Ready output file
14 open(GFF, "<$ARGV[0]") or die("Could not open GFF file!!\n\n");
15 open(OUTPUT, ">$ARGV[1]") or die("Could not open output file!!\n\n");
16
17 #### Hash to hold ids
18 my %id_hash = ();
19
20 #### Work thru GFF file
21 while(defined(my $gff_line = <GFF>)) {
22 if($gff_line =~ /(^#|^\s)/) { next }
23
24 my @gff_line_bits = split(/\t/, $gff_line);
25
26 my $id = $gff_line_bits[0];
27
28 $id_hash{$id}=1;
29 }
30
31 my @all_keys = sort(keys(%id_hash));
32
33 my $elements = scalar(@all_keys);
34
35 #print OUTPUT "There are $elements unique sequences in the file\n";
36 print OUTPUT "$elements non-redundant sequences\n";
37
38 #### Close files
39 close(GFF);
40 close(OUTPUT);
41
42 exit;