script to get data file.

misc-scripts/mouse_knockouts/IKMC_get_data.pl

+#!/ebi/extserv/bin/perl/bin/perl
+# 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 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;