add mutt alias which executes neomutt if that exists

[bin.git] / gene_search

diff --git a/gene_search b/gene_search
index 7f1ed28a2e8902284c67abdd558c706e6785a118..9d1a3e2fab087226623323cf75e561c06ce87122 100755 (executable)
--- 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};