IKMC parser

misc-scripts/xref_mapping/XrefParser/IKMCParser.pm

+package XrefParser::IKMCParser;
+
+use strict;
+
+use base qw( XrefParser::BaseParser );
+
+# This parser will read Direct Xrefs from a simple tab-delimited file.
+# The columns of the file should be the following:
+#
+# 1)    Accession ID
+# 2)    label
+# 3)    source type
+# 4)    stable_id
+#
+
+sub new {
+    my $proto = shift;
+
+    my $class = ref $proto || $proto;
+    my $self = bless {}, $class;
+
+    return $self;
+}
+
+sub run {
+    my $self = shift;
+
+    my $source_id = shift;
+    my $species_id = shift;
+    my $files_ref  = shift;
+    my $rel_file   = shift;
+    my $verbose = shift;
+    
+    my $filename = @{$files_ref}[0];
+
+    my $file_io = $self->get_filehandle($filename);
+    if ( !defined($file_io) ) {
+        return 1;
+    }
+
+    my $parsed_count = 0;
+
+    printf( STDERR "source = %d\t species = %d, file is %s\n",
+            $source_id, $species_id, $filename );
+
+    my %type2id;
+    foreach my $t ("ES cells available", "Vector available", "No products available yet", "Mice available"){
+      my $ikmc = "IKMC_".$t;
+      $ikmc =~ s/ /_/g;
+      $type2id{$t}  = XrefParser::BaseParser->get_source_id_for_source_name($ikmc);
+      print $ikmc."\t".$type2id{$t}."\n";
+      if(!defined( $type2id{$t})){
+	die  "Could not get source id for $ikmc\n";
+      }
+    }	
+
+
+    while ( defined( my $line = $file_io->getline() ) ) {
+        chomp $line;
+
+        my ( $accession, $label, $source_type, $ensembl_id)
+          = split( /\t/, $line );
+
+        if ( !defined($accession)) {
+            printf( "Line %d contains  has less than one column.\n",
+                    1 + $parsed_count );
+            print("The parsing failed\n");
+            return 1;
+        }
+
+        my $type        = 'gene';
+        $label       ||= $accession;
+
+	my $source_id = $type2id{$source_type};
+        ++$parsed_count;
+
+        my $xref_id =
+          XrefParser::BaseParser->get_xref( $accession, $source_id, $species_id );
+
+        if ( !defined($xref_id) || $xref_id eq '' ) {
+            $xref_id =
+              XrefParser::BaseParser->add_xref(
+                                   $accession,   undef,   $label,
+                                   '', $source_id, $species_id, "DIRECT"
+              );
+        }
+        XrefParser::BaseParser->add_direct_xref( $xref_id, $ensembl_id,
+                                                 $type, $accession );
+    } ## end while ( defined( my $line...
+
+    printf( "%d direct xrefs succesfully parsed\n", $parsed_count );
+
+    $file_io->close();
+
+    print "Done\n";
+
+    return 0;
+} ## end sub run
+
+1;