Script to request a batch of IDs from the nameserver, any domain Vari…

…ation/Gene/Strain. Returns a stub acefile with some generic tags and origin info.

scripts/GENEACE/get_NS_ids.pl

@@ -0,0 +1,196 @@
+#!/usr/bin/env perl
+#
+# a script to batch request variation ids based on lists of public_names
+# Last change by $Author: mh6 $ on $Date: 2015-03-31 10:16:20 $
+# usage: perl get_NS_ids.pl -species elegans -user me -pass me < file containing varId_pubId_per_line
+
+
+use lib $ENV{CVS_DIR};
+use lib "$ENV{CVS_DIR}/NAMEDB/lib";
+
+use NameDB_handler;
+use Wormbase;
+use Storable;
+use Getopt::Long;
+use IO::File;
+use strict;
+
+
+my ($PASS,$USER, $DB); # mysql ones
+my $DOMAIN;
+
+my ($wormbase, $debug, $test, $store, $species,$infile,$outfile,$nocheck, 
+    $ace_file_template, $input_is_public_names, $input_is_other_names, $input, $output,$public);
+
+GetOptions (
+    "debug=s"   => \$debug,   # send log emails only to one user
+    "test"      => \$test,    # run against the test database on utlt-db
+    "store:s"   => \$store,   # if you want to pass a Storable instead of recreating it
+    "species:s" => \$species, # elegans/briggsae/whateva .. needed for logging
+    "user:s"	=> \$USER,    # mysql username
+    "pass:s"	=> \$PASS,    # mysql password
+    'nocheck'   => \$nocheck, # don't check public_names
+    'input:s'   => \$input,   # File containing new public_names for new Variations
+    "output:s"  => \$output,  # File to capture the new WBVar and name associations
+    'acetemplate=s' => \$ace_file_template, #unknown template file that is also printed along with the IDs retrieved by the script
+    'public'    => \$public,   # The file only contains public_names so these should be used (This should be used for all types unless Variation with other names).
+    'domain:s'  => \$DOMAIN, # specify Gene, Variation, Feature or Strain to retrieve this type of ID.
+    )||die(@!);
+
+die "Species option is mandatory\n" unless $species; # need that for NameDB to fetch the correct regexps
+die "No domain specified which is mandatory\n" unless $DOMAIN; # need that for NameDB to assign correct ID type
+#die "Must specify -public if domain isn't Variation\n" unless (($public) && ($DOMAIN ne "Variation"));
+if ( $store ) {
+  $wormbase = retrieve( $store ) or croak("Can't restore wormbase from $store\n");
+} else {
+  $wormbase = Wormbase->new( -debug    => $debug,
+                             -test     => $test,
+                             -organism => $species
+      );
+}
+
+# establish log file.
+my $log = Log_files->make_build_log($wormbase);
+
+$DB = $wormbase->test ? 'test_wbgene_id;utlt-db:3307' : 'nameserver_live;web-wwwdb-core-02:3449';
+
+my $db = NameDB_handler->new($DB,$USER,$PASS,$wormbase->wormpub . '/DATABASES/NameDB');
+$db->setDomain($DOMAIN);
+
+# there should be *only* one public_name per line in the input_file
+# like:
+# abc123
+# abc234
+
+if (defined $ace_file_template) {
+  my $tmp_str = "";
+
+  open(my $atfh, $ace_file_template) 
+      or $log->log_and_die("Could not open $ace_file_template for reading\n");
+  while(<$atfh>) {
+    /\S/ and $tmp_str .= $_;
+  }
+
+  $ace_file_template = $tmp_str;
+}
+
+my @entries;
+open (OUT, ">$output") or $log->log_and_die("Could not open $output for reading\n");
+open (IN, "<$input") or $log->log_and_die("Could not open $input for reading\n");
+while (<IN>) {
+    chomp;
+    s/\"//g;
+    my @names;
+
+#should the -public flag be set??
+#    unless (/\S+\s+\S+/) {
+#        
+#    }
+#    if (/\S+\s+\S+/) {
+#        print "File appears to contain multiple name attributes, assuming that is intended";
+#    }
+
+    unless ($public){      
+        @names = split(/\s+/, $_);
+    }
+    else {
+        @names = $_;
+    }
+    if (scalar(@names) == 2 or scalar(@names) == 1) {
+        push @entries, \@names,
+    } else {
+        $log->log_and_die("Bad line:$_\n");
+    }
+}
+
+      foreach my $entry (@entries) {
+          my ($public_name, $other_name);
+          if ($public) {
+              ($public_name, $other_name) = @$entry;
+          }
+          else {
+              ($other_name, $public_name) = @$entry;
+          }
+          if (not $nocheck and defined $public_name and not defined &_check_name($public_name)) {
+              next;
+          }
+
+          my $id = $db->idCreate;
+
+          $public_name = $id if not defined $public_name;
+
+          $db->addName($id,'Public_name'=>$public_name);
+
+          print OUT "\n$DOMAIN : \"$id\"\n";
+          print OUT "Public_name \"$public_name\"\n";
+          print OUT "Other_name \"$other_name\"\n" if (defined $other_name);
+          print OUT "Live\nRemark \"Batch $DOMAIN object requested via get_NS_ids.pl\"\n";              
+          if (defined $ace_file_template) {
+              print OUT "$ace_file_template\n";
+          }
+      }
+$log->mail;
+
+# small function to check the variation public_name for sanity
+sub _check_name {
+  my $name = shift;
+  my $var = $db->idGetByTypedName('Public_name'=>$name)->[0];
+  if($var) {  
+    print STDERR "ERROR: $name already exists as $var\n";
+    return undef;
+  }
+  return 1;
+}
+
+__END__
+
+=pod
+
+=head1 NAME - get_variation_ids.pl
+
+=head1 DECRIPTION
+
+This script takes a list of submitter-supplied variation names  and generates new WBVar identifiers in the name server, 
+writing the results to the given output file. 
+
+The input file is expected to contain a list of submitter-supplied variation names, one per line. Optionally, each 
+line may also contain an additional name, which is added to the NameDB as the public name. If no second name is 
+defined, the generated WBVar identifier will be used as the public name
+
+By default, the script will refuse to create new WBVar identifiers for public names that already exist in the
+database; this behaviour can be switched off with the -nocheck option. 
+
+-head1 OUTPUT
+
+The default output is a 3-column table of 
+
+WBVarid<tab>Public name<tab>Submitter-supplied name
+
+However, if the -acetemplate  option is used, Ace format can be generated (see -acetemplate below). With Ace format, 
+the submitter-supplied name is used to populate the Other_name tag. 
+
+
+=head1 USAGE EXAMPLES
+
+get_variation_ids.pl -species briggsae input_id_-user me -pass me input file.txt -output output_id_file.txt
+
+get_variation_ids.pl -species elegans -user me -pass me -acetemplate wild_template.ace -input input_id_file.txt -output output_file.ace
+
+=head1 OPTIONS
+
+-species      WormBase species name, required for logging (defaults to elegans)
+
+-user         MySQL NameDB account user name
+
+-pass         MySQL NameDB account password
+
+-acetemplate  Takes the file name of a file containing Ace template format which will be printed to the end of the results to create a fuller entry.
+ 
+-nocheck      Do not check for public name clashes
+
+-input        Takes the file name that you have generated as input
+
+-output       Takes the name of a file that the results from the nameserver are written to. 
+
+=cut
+