--- /dev/null
+#! /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 @csv_fields = qw(name hits rzscore refseq location alias database terms description function);
+
+my %genes;
+
+for my $file_name (@ARGV) {
+ my $file = new IO::File $file_name, 'r' or die "Unable to open file $file_name $!";
+ while (<$file>) {
+ next if /^"Name"/;
+ my @gene = map {s/^\"//; s/\"$//; $_;} split /(?<=\")\,(?=\")/, $_;
+ $genes{$gene[NAME]}{name} = $gene[NAME];
+ $genes{$gene[NAME]}{database}{$gene[DBNAME]}++;
+ $genes{$gene[NAME]}{hits}++;
+ $genes{$gene[NAME]}{terms}{$gene[KEYWORD]}++;
+ add_unique_parts($genes{$gene[NAME]},'refseq',$gene[REFSEQ]);
+ add_if_better($genes{$gene[NAME]},'description',$gene[DESCRIPTION]);
+ add_if_better($genes{$gene[NAME]},'location',$gene[LOCATION]);
+ add_unique_parts($genes{$gene[NAME]},'function',split(/; /, $gene[FUNCTION]));
+ add_unique_parts($genes{$gene[NAME]},'alias', split(/; /, $gene[ALIAS]));
+ }
+}
+
+print join(',',map {qq("$_")} @csv_fields),qq(\n);
+for my $gene (keys %genes) {
+ $genes{$gene}{rzscore} = scalar keys %{$genes{$gene}{terms}};
+ next if $genes{$gene}{rzscore} == 1 and exists $genes{$gene}{terms}{antigen};
+ $genes{$gene}{rzscore} -= 1 if exists $genes{$gene}{terms}{antigen};
+ print STDOUT join (',',
+ map {s/"//g; qq("$_")}
+ map {
+ my $value = $_;
+ if (ref $value eq 'HASH') {
+ join('; ',map {qq($_:$$value{$_})} keys %$value);
+ }
+ elsif (ref $value eq 'ARRAY') {
+ join('; ', @$value);
+ }
+ else {
+ $value;
+ }
+ } @{$genes{$gene}}{@csv_fields}
+ ), qq(\n);
+}
+
+
+sub add_unique_parts{
+ my ($hr,$key,@values) = @_;
+ if (not defined $$hr{key}) {
+ $$hr{$key} = [@values];
+ }
+ else {
+ my %temp_hash;
+ @temp_hash{@{$$hr{$key}}} = (1) x scalar @{$$hr{$key}};
+ $temp_hash{@values} = (1) x scalar @values;
+ $$hr{$key} = [keys %temp_hash];
+ }
+}
+
+sub add_if_better{
+ my ($hash, $key, $value) = @_;
+ if (not defined $$hash{$key}) {
+ $$hash{$key} = $value;
+ }
+ elsif (length $$hash{$key} < length $value and $value !~ /^NO\s+(LOCATION|DESCRIPTION)+$/) {
+ $$hash{$key} = $value;
+ }
+}
+
+
+
+
+__END__