add get and parse uniprot results

[function2gene.git] / bin / get_uniprot_results

diff --git a/bin/get_uniprot_results b/bin/get_uniprot_results
new file mode 100755 (executable)
index 0000000..680e850
--- /dev/null
+++ b/bin/get_uniprot_results
@@ -0,0 +1,147 @@
+#! /usr/bin/perl
+
+# get_uniprot_results retreives files of search results from uniprot,
+# 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 2008 by Don Armstrong <don@donarmstrong.com>.
+
+
+use warnings;
+use strict;
+
+
+use Getopt::Long;
+use Pod::Usage;
+
+=head1 NAME
+
+  get_uniprot_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
+
+  get_uniprot_results -D ./uniprot_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 $DEBUG;
+}
+
+use IO::File;
+use URI;
+use WWW::Mechanize;
+use Time::HiRes qw(usleep);
+
+# XXX parse config file
+
+my %options = (debug    => 0,
+              help     => 0,
+              man      => 0,
+              dir      => '.',
+              name     => '${search}_results_uniprot',
+              terms    => '-',
+              uniprot_site => 'http://ca.expasy.org',
+              uniprot_search_url  => '/cgi-bin/sprot-search-ful?S=on&T=on',
+             );
+
+GetOptions(\%options,'name|n=s',
+          'terms|t=s','dir|D=s','debug|d+','help|h|?','man|m');
+
+pod2usage() if $options{help};
+pod2usage({verbose=>2}) if $options{man};
+
+$DEBUG = $options{debug};
+
+if (not -d $options{dir}) {
+     die "$options{dir} does not exist or is not a directory";
+}
+
+#open search terms file
+my $terms;
+if ($options{terms} eq '-') {
+     $terms = \*STDIN;
+}
+else {
+     $terms = new IO::File $options{terms}, 'r' or die "Unable to open file $options{terms}: $!";
+}
+
+#For every term
+while (<$terms>) {
+     # Get uids to retrieve
+     chomp;
+     s/\r$//g;
+     my $search = $_;
+     my $dir_name = eval qq("$options{name}") or die $@;
+     if (not -d "$options{dir}/$dir_name") {
+         mkdir("$options{dir}/$dir_name") or die "Unable to make directory $options{dir}/$dir_name $!";
+     }
+     my $uri = URI->new($options{uniprot_site}.$options{uniprot_search_url});
+     $uri->query_form($uri->query_form(),
+                     SEARCH => $search,
+                    );
+     my $url = $uri->as_string;
+     my $mech = WWW::Mechanize->new(agent=>"DA_get_uniprot_results/$REVISION");
+     print "retreived $url\n";
+     $mech->get($url);
+     my @links = $mech->find_all_links(text_regex=>qr/_HUMAN/);
+     for my $gene_link (@links) {
+         my $gene_url = $gene_link->url_abs->as_string;
+         print STDERR "saving $gene_url\n";
+         $mech->get($gene_url);
+         $mech->follow_link(text_regex => qr/View\s*entry\s*in\s*raw\s*text\s*format/);
+         my $cleaned_url = $gene_url;
+         $cleaned_url =~ s{http://}{}g;
+         $cleaned_url =~ s/[^\w]//g;
+         eval {
+              $mech->save_content($options{dir}.'/'.$dir_name.'/'.$cleaned_url);
+         };
+         if ($@) {
+              warn $@;
+         }
+     }
+}
+
+
+
+
+
+
+__END__