add gene search

diff --git a/gene_search b/gene_search
new file mode 100755 (executable)
index 0000000..7f1ed28
--- /dev/null
+++ b/gene_search
@@ -0,0 +1,132 @@
+#! /usr/bin/perl
+# , 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 2011 by Don Armstrong <don@donarmstrong.com>.
+# $Id: perl_script 1825 2011-01-02 01:53:43Z don $
+
+
+use warnings;
+use strict;
+
+use Getopt::Long;
+use Pod::Usage;
+
+use Bio::DB::EUtilities;
+
+use Encode qw(encode_utf8);
+use Term::ANSIColor qw(:constants);
+use Text::Wrap;
+
+
+=head1 NAME
+
+pubmed_search - 
+
+=head1 SYNOPSIS
+
+ pubmed_search [options] [searchterms]
+
+ 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);
+
+my %options = (debug           => 0,
+              help            => 0,
+              man             => 0,
+              color           => 1,
+              org_mode        => 0,
+              );
+
+GetOptions(\%options,
+          'color|c!',
+          'org_mode|org-mode',
+          'debug|d+','help|h|?','man|m');
+
+pod2usage() if $options{help};
+pod2usage({verbose=>2}) if $options{man};
+
+$DEBUG = $options{debug};
+
+my @USAGE_ERRORS;
+if (not @ARGV) {
+    push @USAGE_ERRORS,"You must pass something";
+}
+
+pod2usage(join("\n",@USAGE_ERRORS)) if @USAGE_ERRORS;
+
+my $search = Bio::DB::EUtilities->new(-eutil => 'esearch',
+                                      -email => 'don@donarmstrong.com',
+                                      -db    => 'gene',
+                                      -term => join(' ',@ARGV),
+                                      -retmax => 1000,
+                                     );
+my @ids = $search->get_ids();
+# print scalar(@ids)." results:\n";
+exit 0 unless @ids;
+my $esummary = Bio::DB::EUtilities->new(-eutil => 'efetch',
+                                       -email => 'don@donarmstrong.com',
+                                       -db    => 'gene',
+                                       -id  => \@ids,
+                                       -retmode => 'xml',
+                                      );
+#print $esummary->get_Response()->content();
+use XML::LibXML;
+my $xml = XML::LibXML->load_xml(string => $esummary->get_Response()->content());
+for my $gene ($xml->findnodes('Entrezgene-Set/Entrezgene')) {
+    # print $article->toString;
+    my ($locus) = $gene->findnodes('.//Gene-ref_locus');
+    my ($desc) = $gene->findnodes('.//Gene-ref_desc');
+    my ($summary) = $gene->findnodes('.//Entrezgene_summary');
+    if ($options{org_mode}) {
+       print "* ";
+    }
+    print BOLD GREEN if $options{color};
+    print $locus->textContent();
+    print ": ";
+    print RESET if $options{color};
+    print BOLD CYAN if $options{color};
+    print encode_utf8($desc->textContent())."\n";
+    print RESET if $options{color};
+    print BOLD MAGENTA if $options{color};
+    if (defined $summary) {
+       if ($options{org_mode}) {
+           print "** Summary\n";
+       }
+       $summary = $summary->textContent();
+       $summary =~ s/^\s*//mg;
+       $summary = encode_utf8($summary);
+       print wrap('','',$summary);
+       print "\n\n";
+       print RESET if $options{color};
+    }
+}
+
+__END__