Check-in before shutdown; draft parser for Gareth Wilson's Affy data. Very much a work in progress!

misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm

+package XrefParser::WilsonAffyParser;
+
+use strict;
+
+use XrefParser::BaseParser;
+
+use vars qw(@ISA);
+@ISA = qw(XrefParser::BaseParser);
+my $xref_sth ;
+my $dep_sth;
+my $syn_sth;
+
+
+
+sub run {
+
+  my ($self, $file, $source_id, $species_id) = @_;
+
+  my @xrefs = $self->create_xrefs($source_id, $species_id, $file);
+
+  # upload
+  XrefParser::BaseParser->upload_xref_object_graphs(@xrefs);
+
+}
+
+sub create_xrefs {
+
+  my ($self, $source_id, $species_id, $file) = @_;
+
+  my ($count, $noseq, $direct) = (0,0,0);
+
+  $| = 1; # don't buffer
+
+  my @xrefs;
+
+  open(FILE,"<".$file) || die "Could not open $file\n";
+
+  <FILE>; # skip first line
+
+  while (<FILE>) {
+
+    #last if ($count > 200);
+    my $xref;
+
+    my @fields = split /\t/;
+
+    # first field (probe_set) is accession
+    my $acc = $fields[0];
+    chomp($acc);
+    $acc =~ s/\"//g;
+
+
+    # get linked accession (may be RefSeq or EMBL or ensembl)
+    my $target = $fields[2];
+    chomp($target);
+    $target =~ s/\"//g;
+
+    # Create direct xrefs for mappings to Ensembl transcripts
+    if ($target =~ /ENSGALT/) {
+
+      # remove version if present
+      ($target) = $target =~ /([^.]*)\.([^.]*)/;
+
+      # add xref - not we're assuming it doesn't already exist;
+      # may need to check like in CCDS parser
+      my $xref_id = $self->add_xref($acc, 0, $acc, "", $source_id, $species_id);
+      $self->add_direct_xref($xref_id, $target, "transcript", "");
+      $direct++;
+
+    } else {
+
+      # fetch sequence for others (EMBL ESTs and RefSeqs - pfetch will handle these)
+      system ("pfetch -q $target > seq.txt");
+      open(SEQ, "<seq.txt");
+      my $seq = <SEQ>;
+      chomp($seq);
+      close(SEQ);
+
+      if ($seq && $seq !~ /no match/) {
+
+	$xref->{ACCESSION} = $acc;
+	$xref->{SEQUENCE} = $seq;
+	$xref->{LABEL} = $acc;
+	$xref->{SOURCE_ID} = $source_id;
+	$xref->{SPECIES_ID} = $species_id;
+	$xref->{SEQUENCE_TYPE} = 'dna';
+	$xref->{STATUS} = 'experimental';
+
+	# Add description noting where the mapping came from
+	$xref->{DESCRIPTION} = $target . " used as mapping target";
+
+	#print $xref->{ACCESSION} . " " . $target . " " . $? . "\n";
+
+	$count++;
+
+	print "$count " if ($count % 100 == 0);
+
+	push @xrefs, $xref;
+
+      } else {
+
+	print "Couldn't get sequence for $target\n";
+	$noseq++;
+
+      }
+
+    }
+
+  }
+
+  close(FILE);
+
+  print "\n\nParsed $count primary xrefs.\n";
+  print "Couldn't get sequence for $noseq primary_xrefs\n" if ($noseq);
+  print "Added $direct direct xrefs.\n";
+
+  return \@xrefs;
+
+}
+
+sub new {
+
+  my $self = {};
+  bless $self, "XrefParser::WilsonAffyParser";
+  return $self;
+
+}
+
+1;