Interpro parser. Different to the other parsers in two respects. 1) does not...

Interpro parser. Different to the other parsers in two respects. 1) does not create the dependent xrefs.   2) inserts data into a new table which stores the mapping from interpro to pfam.

misc-scripts/xref_mapping/XrefParser/InterproParser.pm

+package XrefParser::InterproParser;
+  
+use strict;
+use POSIX qw(strftime);
+use File::Basename;
+  
+use XrefParser::BaseParser;
+  
+use vars qw(@ISA);
+@ISA = qw(XrefParser::BaseParser);
+ 
+my $xref_sth ;
+my $dep_sth;
+  
+ 
+  
+# --------------------------------------------------------------------------------
+# Parse command line and run if being run directly
+  
+if (!defined(caller())) {
+  
+  if (scalar(@ARGV) != 1) {
+    print "\nUsage: InterproParser.pm file\n\n";
+    exit(1);
+  }
+  
+  run(@ARGV);
+}
+  
+ 
+sub run {
+  my $self = shift if (defined(caller(1)));
+  my $file = shift;
+ 
+  my $source_id = shift;
+  my $species_id = shift;
+
+  print STDERR "source = $source_id\tspecies = $species_id\n";
+  if(!defined($source_id)){
+    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
+    print "source id is $source_id \n";
+  }
+  if(!defined($species_id)){
+    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
+    print "species id is $species_id \n";
+  }
+
+  my $dir = dirname($file);
+ 
+  my %short_name;
+  my %description;
+  my %pfam;
+    
+  open (SHORT, $dir."/short_name.dat") || die "Can't open hugo interpro file $dir/short_name.dat\n";
+#IPR000001       Kringle
+#IPR000002       Fizzy
+#IPR000003       RtnoidX_receptor
+
+  while(<SHORT>){
+    chomp;
+    my ($interpro, $name) = split(/\t/,$_);
+    $short_name{$interpro} = $name;
+  }
+  close SHORT;
+
+  
+  my $count = 0;
+
+  open (LONG, $dir."/protein2interpro.dat") || 
+    die "Can't open interpro file  $dir/protein2interpro.dat\n";
+  #O00050  PF03184 166     377     IPR004875       CENP-B protein
+  #O00050  PF05225 15      60      IPR007889       Helix-turn-helix, Psq
+  #O00050  PF06465 448     500     IPR009463       Protein of unknown function DUF10
+  #  0        1     2       3        4               5
+
+  while (<LONG>) {
+    chomp;
+    my @array = split(/\t/,$_);
+    my $hgnc = $array[0];
+    $description{$array[4]} = $array[5];
+    $pfam{$array[4]} = $array[1];
+  }
+  close (LONG);
+
+  my $add_interpro_sth =  XrefParser::BaseParser->dbi->prepare
+    ("INSERT INTO interpro (interpro, pfam) VALUES(?,?)");
+
+  foreach my $interpro (keys %short_name){
+    $count++;
+#    print $short_name{$interpro}."\t".$interpro."\t".$description{$interpro}.
+#      "\t".$pfam{$interpro}."\n";
+    XrefParser::BaseParser->add_xref($interpro,'',$short_name{$interpro},
+				     $description{$interpro},$source_id,$species_id);
+    if(defined($pfam{$interpro})){
+      $add_interpro_sth->execute($interpro,$pfam{$interpro});
+    }
+    else{
+      print "No pfam for $interpro\n";
+    }
+       
+  }
+  print "$count xref successfully loaded.\n";
+#  die "not ready yet\n";
+  
+  
+}
+
+sub new {
+
+  my $self = {};
+  bless $self, "XrefParser::InterproParser";
+  return $self;
+
+}
+ 
+1;
+    
+