add bin files for search routines

[function2gene.git] / bin / parse_ncbi_results

diff --git a/bin/parse_ncbi_results b/bin/parse_ncbi_results
new file mode 100755 (executable)
index 0000000..51d339d
--- /dev/null
+++ b/bin/parse_ncbi_results
@@ -0,0 +1,198 @@
+#! /usr/bin/perl
+
+# parse_ncbi_results retreives files of search results from ncbi,
+# 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 2004 by Don Armstrong <don@donarmstrong.com>.
+
+# $Id: ss,v 1.1 2004/06/29 05:26:35 don Exp $
+
+
+use warnings;
+use strict;
+
+
+use Getopt::Long;
+use Pod::Usage;
+
+=head1 NAME
+
+  parse_ncbi_results [options]
+
+=head1 SYNOPSIS
+
+
+ Options:
+  --dir, -D directory to stick results into [default .]
+  --name, -n file naming scheme [default ${search}_results.$format]
+  --terms, -t file of search terms [default -]
+  --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 useage information.
+
+=item B<--man, -m>
+
+Display this manual.
+
+=back
+
+=head1 EXAMPLES
+
+  parse_ncbi_results -D ./ncbi_results/ -n '${search}_name.html' < search_parameters
+
+Will pretty much do what you want
+
+=cut
+
+
+
+use vars qw($DEBUG $REVISION);
+
+BEGIN{
+     ($REVISION) = q$LastChangedRevision: 1$ =~ /LastChangedRevision:\s+([^\s]+)/;
+     $DEBUG = 0 unless defined $DEBUG;
+}
+
+use XML::Parser::Expat;
+use IO::File;
+
+# XXX parse config file
+
+my %options = (debug    => 0,
+              help     => 0,
+              man      => 0,
+              dir      => '.',
+              keyword  => undef,
+             );
+
+GetOptions(\%options,'keyword|k=s','debug|d+','help|h|?','man|m');
+
+
+pod2usage() if $options{help};
+pod2usage({verbose=>2}) if $options{man};
+
+$DEBUG = $options{debug};
+
+# CSV columns
+use constant {NAME        => 0,
+             REFSEQ      => 1,
+             LOCATION    => 2,
+             ALIAS       => 3,
+             FUNCTION    => 4,
+             DESCRIPTION => 5,
+             KEYWORD     => 6,
+             DBNAME      => 7,
+             FILENAME    => 8,
+            };
+
+my $current_gene = undef;
+my $keyword = undef;
+my $file_name = undef;
+my ($within_GO,$mrna_ref_seq) = 0,0;
+
+sub tag_start{
+     my ($expat, $element, %attr) = @_;
+
+     local $_ = lc $element;
+     if ($_ eq 'entrezgene') {
+         $current_gene = [];
+         $$current_gene[KEYWORD] = $keyword;
+         $$current_gene[DBNAME] = 'ncbi';
+         $$current_gene[FILENAME] = $file_name;
+     }
+}
+
+sub tag_content {
+     my ($expat, $string) = @_;
+
+     return unless defined $current_gene;
+
+     local $_ = lc $expat->current_element;
+
+     if ($_ eq 'gene-ref_locus') {
+         $$current_gene[NAME] = $string;
+     }
+     elsif ($_ eq 'gene-ref_maploc') {
+         $$current_gene[LOCATION] = $string;
+     }
+     elsif ($_ eq 'gene-ref_desc') {
+         push @{$$current_gene[ALIAS]}, $string;
+     }
+     elsif ($_ eq 'prot-ref_name_e' or $_ eq 'gene-ref_syn_e') {
+         push @{$$current_gene[ALIAS]}, $string;
+     }
+     elsif ($_ eq 'entrezgene_summary') {
+         $$current_gene[DESCRIPTION] = $string;
+     }
+     elsif ($_ eq 'gene-commentary_heading') {
+         $within_GO = 0;
+         $mrna_ref_seq = 0;
+         $within_GO = 1 if $string =~ /GeneOntology/;
+         $mrna_ref_seq = 1 if $string =~ /mRNA Sequence/i;
+     }
+     elsif ($_ eq 'other-source_anchor') {
+         return unless $within_GO;
+         push @{$$current_gene[FUNCTION]}, $string;
+     }
+     elsif ($_ eq 'gene-commentary_accession') {
+         return unless $expat->within_element('Gene-commentary_products');
+         $$current_gene[REFSEQ] ||= $string;
+     }
+}
+
+sub tag_stop {
+     my ($expat, $element) = @_;
+
+     local $_ = lc $element;
+     if ($_ eq 'entrezgene') {
+         # If current_gene is defined, output the current gene information
+         if (defined $current_gene and @$current_gene) {
+              $$current_gene[NAME] ||= ${$$current_gene[ALIAS]}[1] if defined $$current_gene[ALIAS];
+              for (qw(NAME REFSEQ LOCATION ALIAS
+                      FUNCTION DESCRIPTION KEYWORD DBNAME
+                      FILENAME)) {
+                   $$current_gene[eval "$_"] ||= "NO $_";
+              }
+              print STDOUT join(',', map {$_ = join('; ', @$_) if ref $_; qq("$_");} @$current_gene),qq(\n);
+              undef $current_gene;
+         }
+     }
+}
+
+my $parser = new XML::Parser::Expat;
+$parser->setHandlers('Start' => \&tag_start,
+                    'End'   => \&tag_stop,
+                    'Char'  => \&tag_content
+                   );
+
+for (@ARGV) {
+     $file_name = $_;
+     ($keyword) = $options{keyword} || $file_name =~ m#(?:^|/)([^\/]+?)[\s-]+AND[\s\-].+_results.xml$#;
+     print STDOUT join(",", map {qq("$_");} qw(Name RefSeq Location Alias Function Description Keyword DBName Filename)),qq(\n);
+     my $file = new IO::File $file_name, 'r' or die "Unable to open file $file_name $!";
+
+     $parser->parse($file);
+
+     undef $file;
+}
+
+
+
+
+
+
+__END__