From: Don Armstrong <don@donarmstrong.com>
Date: Mon, 27 Aug 2007 22:29:47 +0000 (+0000)
Subject: move get_ncbi_results
X-Git-Url: https://git.donarmstrong.com/?p=function2gene.git;a=commitdiff_plain;h=2f7bfa126e44399e0d7c3f3b755afbe895ac6e3a

move get_ncbi_results

git-svn-id: file:///srv/svn/function2gene/trunk@6 a0738b58-4706-0410-8799-fb830574a030
---

diff --git a/bin/get_ncbi_results b/bin/get_ncbi_results
new file mode 100755
index 0000000..c104356
--- /dev/null
+++ b/bin/get_ncbi_results
@@ -0,0 +1,172 @@
+#! /usr/bin/perl
+
+# get_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
+
+  get_ncbi_results [options]
+
+get_ncbi_results - Retrieve search results from NCBI using parameters
+passed on stdin.
+
+=head1 SYNOPSIS
+
+
+ Options:
+  --format, -f format of search results to return [default xml]
+  --database, -b database to search for results [default gene]
+  --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_ncbi_results -f xml -b gene -D ./results/ -n '${search}_name.xml' < search_parameters
+
+Will pretty much do what you want
+
+=cut
+
+
+
+use vars qw($DEBUG $REVISION);
+
+BEGIN{
+     ($REVISION) = q$LastChangedRevision: 1$ =~ /LastChangedRevision:\s+([^\s]+)/;
+     $DEBUG = 0 unless defined $DEBUG;
+}
+
+use IO::File;
+use URI::ParamMunge;
+use LWP::UserAgent;
+
+# XXX parse config file
+
+my %options = (debug    => 0,
+	       help     => 0,
+	       man      => 0,
+	       format   => 'xml',
+	       database => 'gene',
+	       dir      => '.',
+	       name     => 'ncbi_${search}_results.$format',
+	       terms    => '-',
+	       pubmed_site => 'http://www.ncbi.nlm.nih.gov',
+	       pubmed_search_url  => '/entrez/query.fcgi?db=gene&cmd=search&term=12q24*+AND+homo[Orgn]&doptcmdl=Brief&dispmax=1000',
+	       pubmed_get_url     => '/entrez/query.fcgi?db=gene&cmd=Text&dopt=XML',
+	      );
+
+GetOptions(\%options,'format|f=s','database|b=s','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}: $!";
+}
+
+my $ua = new LWP::UserAgent(agent=>"DA_get_ncbi_results/$REVISION");
+
+#For every term
+while (<$terms>) {
+     # Get uids to retrieve
+     chomp;
+     my $search = $_;
+     my $format = $options{format};
+     my $url = uri_param_munge($options{pubmed_site}.$options{pubmed_search_url},
+			       {term => $search,
+				db   => $options{database},
+			       },
+			      );
+     my $request = HTTP::Request->new('GET', $url);
+     my $response = $ua->request($request);
+     $response = $response->content;
+     my @gene_ids = $response =~ m/\[GeneID\:\s+(\d+)\]/g;
+
+     my $file_name = eval qq("$options{name}") or die $@;
+     my $xml_file = new IO::File "$options{dir}/$file_name", 'w' or die "Unable to open $options{dir}/$file_name: $!";
+
+     # Get XML file
+     my @current_ids;
+     while (@current_ids = splice(@gene_ids,0,20)) {
+	  $url = uri_param_munge($options{pubmed_site}.$options{pubmed_get_url},
+				 {dopt => uc($options{format}),
+				  db   => $options{database},
+				 },
+				) .'&' . join('&',map {qq(uid=$_)} @current_ids);
+	  $request = HTTP::Request->new('GET', $url);
+	  $response = $ua->request($request);
+	  $response = $response->content;
+	  # For some dumb reason, they send us xml with html
+	  # entities. Ditch them.
+	  #$response = decode_entities($response);
+	  $response =~ s/\&gt;/>/gso;
+	  $response =~ s/\&lt;/</gso;
+	  $response =~ s/&quot;/"/gso;
+
+	  # They also affix a <pre> and suffix a </pre> ditch them.
+	  $response =~ s/^\s*<pre>//gso;
+	  $response =~ s#</pre>\s*$##gso;
+
+	  $response =~ s#<\?xml[^>]+>##gso;
+	  $response =~ s#<!DOCTYPE[^>]+>##gso;
+
+	  print {$xml_file} $response;
+	  sleep 10;
+     }
+     undef $xml_file;
+}
+
+
+
+
+
+
+__END__
diff --git a/bin/get_ncbi_xml_results b/bin/get_ncbi_xml_results
deleted file mode 100755
index c104356..0000000
--- a/bin/get_ncbi_xml_results
+++ /dev/null
@@ -1,172 +0,0 @@
-#! /usr/bin/perl
-
-# get_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
-
-  get_ncbi_results [options]
-
-get_ncbi_results - Retrieve search results from NCBI using parameters
-passed on stdin.
-
-=head1 SYNOPSIS
-
-
- Options:
-  --format, -f format of search results to return [default xml]
-  --database, -b database to search for results [default gene]
-  --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_ncbi_results -f xml -b gene -D ./results/ -n '${search}_name.xml' < search_parameters
-
-Will pretty much do what you want
-
-=cut
-
-
-
-use vars qw($DEBUG $REVISION);
-
-BEGIN{
-     ($REVISION) = q$LastChangedRevision: 1$ =~ /LastChangedRevision:\s+([^\s]+)/;
-     $DEBUG = 0 unless defined $DEBUG;
-}
-
-use IO::File;
-use URI::ParamMunge;
-use LWP::UserAgent;
-
-# XXX parse config file
-
-my %options = (debug    => 0,
-	       help     => 0,
-	       man      => 0,
-	       format   => 'xml',
-	       database => 'gene',
-	       dir      => '.',
-	       name     => 'ncbi_${search}_results.$format',
-	       terms    => '-',
-	       pubmed_site => 'http://www.ncbi.nlm.nih.gov',
-	       pubmed_search_url  => '/entrez/query.fcgi?db=gene&cmd=search&term=12q24*+AND+homo[Orgn]&doptcmdl=Brief&dispmax=1000',
-	       pubmed_get_url     => '/entrez/query.fcgi?db=gene&cmd=Text&dopt=XML',
-	      );
-
-GetOptions(\%options,'format|f=s','database|b=s','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}: $!";
-}
-
-my $ua = new LWP::UserAgent(agent=>"DA_get_ncbi_results/$REVISION");
-
-#For every term
-while (<$terms>) {
-     # Get uids to retrieve
-     chomp;
-     my $search = $_;
-     my $format = $options{format};
-     my $url = uri_param_munge($options{pubmed_site}.$options{pubmed_search_url},
-			       {term => $search,
-				db   => $options{database},
-			       },
-			      );
-     my $request = HTTP::Request->new('GET', $url);
-     my $response = $ua->request($request);
-     $response = $response->content;
-     my @gene_ids = $response =~ m/\[GeneID\:\s+(\d+)\]/g;
-
-     my $file_name = eval qq("$options{name}") or die $@;
-     my $xml_file = new IO::File "$options{dir}/$file_name", 'w' or die "Unable to open $options{dir}/$file_name: $!";
-
-     # Get XML file
-     my @current_ids;
-     while (@current_ids = splice(@gene_ids,0,20)) {
-	  $url = uri_param_munge($options{pubmed_site}.$options{pubmed_get_url},
-				 {dopt => uc($options{format}),
-				  db   => $options{database},
-				 },
-				) .'&' . join('&',map {qq(uid=$_)} @current_ids);
-	  $request = HTTP::Request->new('GET', $url);
-	  $response = $ua->request($request);
-	  $response = $response->content;
-	  # For some dumb reason, they send us xml with html
-	  # entities. Ditch them.
-	  #$response = decode_entities($response);
-	  $response =~ s/\&gt;/>/gso;
-	  $response =~ s/\&lt;/</gso;
-	  $response =~ s/&quot;/"/gso;
-
-	  # They also affix a <pre> and suffix a </pre> ditch them.
-	  $response =~ s/^\s*<pre>//gso;
-	  $response =~ s#</pre>\s*$##gso;
-
-	  $response =~ s#<\?xml[^>]+>##gso;
-	  $response =~ s#<!DOCTYPE[^>]+>##gso;
-
-	  print {$xml_file} $response;
-	  sleep 10;
-     }
-     undef $xml_file;
-}
-
-
-
-
-
-
-__END__