New parser for AedesGenBank xrefs

misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm

+package XrefParser::AedesGenBankParser;
+
+use strict;
+use File::Basename;
+
+use XrefParser::BaseParser;
+
+use vars qw(@ISA);
+@ISA = qw(XrefParser::BaseParser);
+
+#Aedes GenBank protein - because not yet in UniProt
+#>EAT48991.1
+#MGKSKAHRIKGLTGPKMSLGDQITEGRVSKKPKAPKIRLRAEEEEFVDSRTTKKILQQAR
+#KQQAELNLLDDSFGPSLAESAAAASVGKRRHRLGDAASSDESDEEYREEADVDGQDFFDD
+#IKINEEDERALEMFQNKDGVKTRTLADLIMDKITEKQTEIQTQFSDTGSLKMEEIDPRVR
+
+sub run {
+
+  my ($self, $file, $source_id, $species_id) = @_;
+  my $cpt = 0 ;
+
+  next if (/^File:/);   # skip header
+
+  my @xrefs;
+
+  local $/ = "\n>";
+
+  if(!open(FILE,"<".$file)){
+    print "Could not open $file\n";
+    return 1;
+  }
+  while (<FILE>) {
+
+    my $xref;
+
+    my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
+    #print "My header is -$header-\n" ;
+    #print "My sequence is -$sequence-\n" ;
+
+    if ($header eq "") {
+      $header = "Aedes_GenBank".$cpt ;
+      print STDERR "One sequence with a random name ... \n" ;
+      $cpt++ ;
+    }
+
+    # deconstruct header - just use first part
+    #my ($accession, $description) = split /\|/, $header;  #if description
+    my $accession = $header;                               #if no description
+
+
+
+    # make sequence into one long string
+    $sequence =~ s/\n//g;
+
+    # build the xref object and store it
+    #print "ACCESSION & LABEL are $accession\n" ;
+    #print "SEQUENCE is $sequence\n" ;
+    #print "SOURCE_ID is $source_id\n" ;
+    #print "SPECIES_ID is $species_id\n" ;
+    #print "SEQUENCE_TYPE is peptide!\n";
+    #print "STATUS is experimental!\n" ;
+
+    $xref->{ACCESSION}     = $accession;
+    $xref->{LABEL}         = $accession;
+    #$xref->{DESCRIPTION}   = $description;
+    $xref->{SEQUENCE}      = $sequence;
+    $xref->{SOURCE_ID}     = $source_id;
+    $xref->{SPECIES_ID}    = $species_id;
+    $xref->{SEQUENCE_TYPE} = 'peptide';
+    $xref->{STATUS}        = 'experimental';
+
+    push @xrefs, $xref;
+
+  }
+
+  close (FILE);
+
+  print scalar(@xrefs) . " AedesGenBank xrefs succesfully parsed\n";
+
+  XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs);
+
+  print "Done\n";
+  return 0;
+}
+
+
+sub new {
+
+  my $self = {};
+  bless $self, "XrefParser::AedesGenBankParser";
+  return $self;
+
+}
+
+1;