Parser for IPI .fasta files.

misc-scripts/xref_mapping/XrefParser/IPIParser.pm

+package XrefParser::IPIParser;
+
+use strict;
+use File::Basename;
+
+use XrefParser::BaseParser;
+
+use vars qw(@ISA);
+@ISA = qw(XrefParser::BaseParser);
+
+# IPI file format: fasta, e.g.
+# >IPI:IPI00000005.1|SWISS-PROT:P01111|TREMBL:Q15104|REFSEQ_NP:NP_002515|ENSEMBL:ENSP00000261444 Tax_Id=9606 Transforming protein N-Ras
+# MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
+# QEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDL
+# PTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYRMKKLNSSDDGTQG
+# CMGLPCVVM
+
+sub run {
+
+  my $self = shift;
+  my $file = shift;
+  my $source_id = shift;
+  my $species_id = shift;
+
+  my @xrefs;
+
+  local $/ = "\n>";
+
+  open(IPI,"<".$file) || die "Could not open $file\n";
+
+  my $species_tax_id = $self->get_taxonomy_from_species_id($species_id);
+
+  while (<IPI>) {
+
+    my $xref;
+
+    my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
+
+    # deconstruct header
+    my @header = split /\|/, $header;
+    my ($ipi) = $header[0] =~ /^IPI:(IPI(\d)+(\.\d+)?)/ or warn("Can't deduce IPI identifier from " .  $header[0]);
+    my ($ipi_ac, $ipi_ver) = $ipi =~ /(IPI\d+)\.(\d+)/;
+
+    my ($tax_id, $description) = $header[-1] =~ /.*Tax_Id=(\d+)\s+(.*)/;
+
+    # only interested in species with the taxonomy ID were looking for
+    next if ($tax_id != $species_tax_id);
+
+    # note currently we ignore all the other cross-references in the IPI file
+
+    # make sequence into one long string
+    $sequence =~ s/\n//g;
+
+    # build the xref object and store it
+    $xref->{ACCESSION}     = $ipi_ac;
+    $xref->{VERSION}       = $ipi_ver;
+    $xref->{LABEL}         = $ipi;
+    $xref->{DESCRIPTION}   = $description;
+    $xref->{SEQUENCE}      = $sequence;
+    $xref->{SOURCE_ID}     = $source_id;
+    $xref->{SPECIES_ID}    = $species_id;
+    $xref->{SEQUENCE_TYPE} = 'peptide';
+    $xref->{STATUS}        = 'experimental';
+
+    #print "IPI: $ipi tax: $tax_id desc: $description\n";
+
+    push @xrefs, $xref;
+
+  }
+
+  print scalar(@xrefs) . " IPI xrefs succesfully parsed\n";
+
+  XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs);
+  print "Done\n";
+
+}
+
+
+sub new {
+
+  my $self = {};
+  bless $self, "XrefParser::IPIParser";
+  return $self;
+
+}
+
+1;