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1 #!/usr/bin/env perl
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2
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3 use strict;
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4 use warnings;
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5
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6 ##################################################################
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7 # Select genes that are associated with the diseases listed in the
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8 # disease ontology.
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9 # ontology: http://do-wiki.nubic.northwestern.edu/index.php/Main_Page
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10 # gene associations by FunDO: http://projects.bioinformatics.northwestern.edu/do_rif/
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11 # Sept 2010, switch to doLite
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12 # input: build outfile sourceFileLoc.loc term or partial term
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13 ##################################################################
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14
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15 if (!@ARGV or @ARGV < 3) {
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16 print "usage: disease_ontology_gene_selector.pl build outfile.txt sourceFile.loc [list of terms]\n";
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17 exit;
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18 }
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19
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20 my $build = shift @ARGV;
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21 my $out = shift @ARGV;
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22 my $in = shift @ARGV;
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23 my $term = shift @ARGV;
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24 $term =~ s/^'//; #remove quotes protecting from shell
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25 $term =~ s/'$//;
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26 my $data;
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27 open(LOC, $in) or die "Couldn't open $in, $!\n";
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28 while (<LOC>) {
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29 chomp;
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30 if (/^\s*#/) { next; }
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31 my @f = split(/\t/);
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32 if ($f[0] eq $build) {
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33 if ($f[1] eq 'disease associated genes') {
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34 $data = $f[2];
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35 }
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36 }
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37 }
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38 close LOC or die "Couldn't close $in, $!\n";
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39 if (!$data) {
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40 print "Error $build not found in $in\n";
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41 exit;
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42 }
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43 if (!defined $term) {
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44 print "No disease term entered\n";
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45 exit;
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46 }
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47
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48 #start with just fuzzy term matches
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49 open(OUT, ">", $out) or die "Couldn't open $out, $!\n";
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50 open(FH, $data) or die "Couldn't open data file $data, $!\n";
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51 $term =~ s/\s+/|/g; #use OR between words
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52 while (<FH>) {
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53 chomp;
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54 my @f = split(/\t/); #chrom start end strand geneName geneID disease
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55 if ($f[6] =~ /($term)/i) {
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56 print OUT join("\t", @f), "\n";
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57 }elsif ($term eq 'disease') { #print all with disease
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58 print OUT join("\t", @f), "\n";
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59 }
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60 }
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61 close FH or die "Couldn't close data file $data, $!\n";
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62 close OUT or die "Couldn't close $out, $!\n";
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63
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64 exit;
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