X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=gene_search;h=9d1a3e2fab087226623323cf75e561c06ce87122;hb=56c8d8b286ae38e170ce915472f9aa86fabf9fee;hp=7f1ed28a2e8902284c67abdd558c706e6785a118;hpb=c9645f6b18d502c7a599e60b772faf2914ccab98;p=bin.git

diff --git a/gene_search b/gene_search
index 7f1ed28..9d1a3e2 100755
--- a/gene_search
+++ b/gene_search
@@ -63,11 +63,15 @@ my %options = (debug           => 0,
 	       man             => 0,
 	       color           => 1,
 	       org_mode        => 0,
+	       symbol          => 0,
+	       organism        => 'Homo sapiens',
 	       );
 
 GetOptions(\%options,
 	   'color|c!',
-	   'org_mode|org-mode',
+	   'org_mode|org-mode!',
+	   'symbol|s!',
+	   'organism|o=s',
 	   'debug|d+','help|h|?','man|m');
 
 pod2usage() if $options{help};
@@ -82,10 +86,15 @@ if (not @ARGV) {
 
 pod2usage(join("\n",@USAGE_ERRORS)) if @USAGE_ERRORS;
 
+my $term = join(' ',@ARGV);
+if ($options{symbol}) {
+    $term = join(' OR ',map {'('.$_.'[Preferred Symbol] AND '.$options{organism}.'[Orgn])'} @ARGV);
+}
+
 my $search = Bio::DB::EUtilities->new(-eutil => 'esearch',
 				       -email => 'don@donarmstrong.com',
 				       -db    => 'gene',
-				       -term => join(' ',@ARGV),
+				       -term => $term,
 				       -retmax => 1000,
 				      );
 my @ids = $search->get_ids();
@@ -97,14 +106,18 @@ my $esummary = Bio::DB::EUtilities->new(-eutil => 'efetch',
 					-id  => \@ids,
 					-retmode => 'xml',
 				       );
-#print $esummary->get_Response()->content();
+#print $esummary->get_Response()->content() if $DEBUG;
 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;
+    print $gene->toString if $DEBUG;
     my ($locus) = $gene->findnodes('.//Gene-ref_locus');
     my ($desc) = $gene->findnodes('.//Gene-ref_desc');
     my ($summary) = $gene->findnodes('.//Entrezgene_summary');
+    my ($idiogram) = $gene->findnodes('.//Gene-ref_maploc');
+    next unless defined $idiogram;
+    my ($start) = $gene->findnodes('.//Gene-commentary_seqs/Seq-loc/Seq-loc_int/Seq-interval/Seq-interval_from');
+    my ($stop) = $gene->findnodes('.//Gene-commentary_seqs/Seq-loc/Seq-loc_int/Seq-interval/Seq-interval_to');
     if ($options{org_mode}) {
 	print "* ";
     }
@@ -112,6 +125,9 @@ for my $gene ($xml->findnodes('Entrezgene-Set/Entrezgene')) {
     print $locus->textContent();
     print ": ";
     print RESET if $options{color};
+    print "(".$idiogram->textContent();
+    print " ".$start->textContent().":";
+    print $stop->textContent().") ";
     print BOLD CYAN if $options{color};
     print encode_utf8($desc->textContent())."\n";
     print RESET if $options{color};