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