add gene to alases

diff --git a/gene_to_aliases b/gene_to_aliases
new file mode 100755 (executable)
index 0000000..563512f
--- /dev/null
+++ b/gene_to_aliases
@@ -0,0 +1,122 @@
+#! /usr/bin/perl
+# gene_to_aliases takes a list of genes and returns their aliases,
+# and is released under the terms of the GPL version 2, or any later
+# version, at your option. See the file README and COPYING for more
+# information.
+# Copyright 2009 by Don Armstrong <don@donarmstrong.com>.
+# $Id: perl_script 1432 2009-04-21 02:42:41Z don $
+
+
+use warnings;
+use strict;
+
+use Getopt::Long;
+use Pod::Usage;
+
+=head1 NAME
+
+gene_to_aliases - take a list of genes and return aliases
+
+=head1 SYNOPSIS
+
+ [options]
+
+ Options:
+  --debug, -d debugging level (Default 0)
+  --help, -h display this help
+  --man, -m display manual
+
+=head1 OPTIONS
+
+=over
+
+=item B<--debug, -d>
+
+Debug verbosity. (Default 0)
+
+=item B<--help, -h>
+
+Display brief usage information.
+
+=item B<--man, -m>
+
+Display this manual.
+
+=back
+
+=head1 EXAMPLES
+
+
+=cut
+
+
+use vars qw($DEBUG);
+
+use WWW::Mechanize;
+use URI::Escape;
+
+my %options = (debug           => 0,
+              help            => 0,
+              man             => 0,
+              );
+
+GetOptions(\%options,
+          'debug|d+','help|h|?','man|m');
+
+pod2usage() if $options{help};
+pod2usage({verbose=>2}) if $options{man};
+
+$DEBUG = $options{debug};
+
+my @USAGE_ERRORS;
+# if (1) {
+#      push @USAGE_ERRORS,"You must pass something";
+# }
+
+pod2usage(join("\n",@USAGE_ERRORS)) if @USAGE_ERRORS;
+
+my @genes;
+while (<>) {
+    chomp;
+    next unless length $_;
+    push @genes,$_;
+}
+
+my $m = WWW::Mechanize->new(autocheck => 0);
+
+for my $gene (@genes) {
+    my $url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&retmax=1&term='.
+       uri_escape($gene.'[Symbol] AND Homo[Orgn]');
+    my $content = get_loop($url);
+    my @id = $content =~
+       m|<Id>(\d+)</Id>|gis;
+    if (not @id) {
+       print $gene,qq(\n);
+       next;
+    }
+    $content = get_loop('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&retmax=1&retmode=xml&id='.$id[0]);
+    my @syn = $content =~
+       m{<(?:Gene|Prot)-ref_(?:syn|name)_E>([^<]+)</(?:Gene|Prot)-ref_(?:syn|name)_E>}g;
+    print join("\t",$gene,@syn),qq(\n);
+    print $content if $DEBUG;
+}
+sub get_loop {
+    my $url = shift;
+    my $counter = 0;
+    my $content='';
+ LOOP: {do {
+        if ($m->get($url
+                        )) {
+            $content = $m->content;
+            last;
+        }
+        $counter++;
+        sleep 10;
+    } while ($counter < 100);
+    }
+    return $content;
+}
+
+
+
+__END__