IKMC_get_data.pl

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#!/ebi/extserv/bin/perl/bin/perl
# See the NOTICE file distributed with this work for additional information
# regarding copyright ownership.
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
#      http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
 
# an example script demonstrating the use of BioMart webservice
 
 
#
# NOTE this could have implemented in the parser itself but the data is needed
# for the simple features so
#
use strict;
use warnings;
 
use LWP::UserAgent;
 
 
 my $xml = (<<XXML);
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "1" count = "" datasetConfigVersion = "0.6" >
  
  <Dataset name = "dcc" interface = "default" >
    <Attribute name = "mgi_accession_id" />
    <Attribute name = "marker_symbol" />
    <Attribute name = "vector_available" />
    <Attribute name = "escell_available" />
    <Attribute name = "mouse_available" />
    <Attribute name = "ensembl_gene_id" />
    </Dataset>
</Query>
XXML
 
open (OUT,">ensembl_ikmc_initial.txt");
 
my $path="http://www.i-dcc.org/biomart/martservice?";
my $request = HTTP::Request->new("POST",$path,HTTP::Headers->new(),'query='.$xml."\n");
my $ua = LWP::UserAgent->new;
 
my $response;
 
$ua->request($request,
         sub{
         my($data, $response) = @_;
         if ($response->is_success) {
             print OUT "$data";
         }
         else {
             warn ("Problems with the web server: ".$response->status_line);
         }
         },1000);
 
close OUT;
 
my %symbols;
my %ensembl_ids;
my %status;
 
open (IN,"ensembl_ikmc_initial.txt");
#nb [9] is now cell_line_bg and [10] is backcross
while (<IN>){
    my @line = split(/\t/,$_);
    chop $line[5];
    my $mgi_id = $line[0];
    $symbols{$mgi_id}=$line[1];
    $ensembl_ids{$mgi_id}=$line[5];
    $status{$mgi_id} = 1 if ($status{$mgi_id} eq '');
 
    if ($status{$mgi_id} < 4 && $line[4] == 1){
    $status{$mgi_id} = 4;
    }
    elsif ($status{$mgi_id} < 3 && $line[3] == 1){
    $status{$mgi_id} = 3;
    }
    elsif ($status{$mgi_id} < 2 && $line[2] == 1){
    $status{$mgi_id} = 2;
    }
 
}
close IN;
 
open (OUT,">ensembl_ikmc_xref.txt");
foreach my $mgi_id(keys %symbols){
    my $description;
    $description = 'No products available yet' if $status{$mgi_id} == 1;
    $description = 'Vector available' if $status{$mgi_id} == 2;
    $description = 'ES cells available' if $status{$mgi_id} == 3;
    $description = 'Mice available' if $status{$mgi_id} == 4;
 
    print OUT "$mgi_id\t$symbols{$mgi_id}\t$description\t$ensembl_ids{$mgi_id}\n";
}
close OUT;