wormBase stuff added

misc-scripts/xref_mapping/XrefParser/BaseParser.pm

@@ -260,6 +260,52 @@ sub get_source_id_for_source_name {
   return $source_id;
 
 }
+
+sub get_valid_xrefs_for_dependencies{
+  my ($self, $dependent_name, @reverse_ordered_source_list) = @_;
+
+  my %dependent_2_xref;
+
+
+  my $sql = "select source_id from source where name =?";
+  my $sth = dbi()->prepare($sql);
+  my @dependent_sources;
+  $sth->execute($dependent_name);
+  while(my @row = $sth->fetchrow_array()){
+    push @dependent_sources,$row[0];
+  }
+
+  my @sources;
+  foreach my $name (@reverse_ordered_source_list){
+    $sth->execute($name);
+    while(my @row = $sth->fetchrow_array()){
+      push @sources,$row[0];
+    }
+  }
+  $sth->finish;
+
+  $sql  = "select d.dependent_xref_id, x2.accession ";
+  $sql .= "  from dependent_xref d, xref x1, xref x2 ";
+  $sql .= "    where x1.xref_id = d.master_xref_id and";
+  $sql .= "          x1.source_id=? and ";
+  $sql .= "          x2.xref_id = d.dependent_xref_id and";
+  $sql .= "          x2.source_id=? ";
+  
+  my $sth = dbi()->prepare($sql);
+  foreach my $d (@dependent_sources){
+    foreach my $s (@sources){
+       $sth->execute($s,$d);
+       while(my @row = $sth->fetchrow_array()){
+	 $dependent_2_xref{$row[1]} = $row[0];
+       }
+     }
+  }
+
+  return \%dependent_2_xref;
+}
+
+
+
 sub get_valid_codes{
   my ($self,$source_name,$species_id) =@_;
   my %valid_codes;

misc-scripts/xref_mapping/XrefParser/GOParser.pm

@@ -31,6 +31,7 @@ sub run {
   my $file = shift;
   my $source_id = shift;
   my $species_id = shift;
+  my %wrongtype;
 
   if(!defined($source_id)){
     $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
@@ -42,13 +43,15 @@ sub run {
 
   my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
   my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
+  my %worm;
+  my $wormset;
 
   my $count  = 0;
 
   open(GO,"<".$file) || die "Could not open $file\n";
 
   my $taxon_line = "taxon:".$species_id;
-
+  my $miss =0;
   while (<GO>) {
     if(/$taxon_line/){
       chomp;
@@ -73,8 +76,28 @@ sub run {
 	  $count++;
 	}
       }
-      else{
-	print STDERR "unknown type ".$array[0]."\n";
+      elsif($array[0] =~ /^WB$/){
+#WB      CE20707 ZYG-9           GO:0008017      WB:WBPaper00003099|PMID:9606208 ISS             F                       protein  taxon:6239      20030829        WB
+	if(!defined($wormset)){
+	  $wormset = 1;
+	  %worm = %{XrefParser::BaseParser->get_valid_xrefs_for_dependencies
+	      ('wormbase_transcript','Uniprot/SPTREMBL','RefSeq_peptide',
+	       'Uniprot/SWISSPROT')};
+	}
+	if(defined($worm{$array[2]})){
+	  XrefParser::BaseParser->add_to_xrefs($worm{$array[2]},$array[4],'',$array[4],'',$array[6],$source_id,$species_id);
+	  $count++;
+	}
+	else{
+	  $miss++;
+	  if($miss < 10){
+	    print "miss: ".$array[2]."\n";
+	  }
+	}
+      }
+      elsif(!defined($wrongtype{$array[0]})){
+	print STDERR "WARNING: unknown type ".$array[0]."\n";
+	$wrongtype{$array[0]} = 1;
       }
     }
   }

misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm

@@ -81,7 +81,17 @@ sub create_xrefs {
     $type = 'dna';
     $source_id = $dna_source_id;
 
-  } else{
+  } elsif($file =~ /RefSeq_dna/){
+
+    $type = 'dna';
+    $source_id = $dna_source_id;
+
+  } elsif($file =~ /RefSeq_protein/){
+
+    $type = 'peptide';
+    $source_id = $peptide_source_id;
+
+  }else{
     die "Could not work out sequence type & source for $file\n";
   }
 
@@ -145,6 +155,7 @@ sub create_xrefs {
       my @LocusIDline = $entry =~ /db_xref=.LocusID:(\d+)/g;
       my @EntrezGeneIDline = $entry =~ /db_xref=.GeneID:(\d+)/g;
       my @mimline = $entry =~ /db_xref=.MIM:(\d+)/g;
+      my @wormline = $entry =~ /db_xref=\"WormBase:(\S+)\"/g;
 
       foreach my $ll (@LocusIDline) {
 	my %dep;
@@ -153,6 +164,21 @@ sub create_xrefs {
 	$dep{ACCESSION} = $ll;
 	push @{$xref->{DEPENDENT_XREFS}}, \%dep;
       }
+      foreach my $ll (@wormline) {
+	my %dep;
+	$dep{SOURCE_ID} = $dependent_sources{'wormbase_transcript'};
+	$dep{LINKAGE_SOURCE_ID} = $source_id;
+	$dep{ACCESSION} = $ll;
+	push @{$xref->{DEPENDENT_XREFS}}, \%dep;
+	if($ll =~ /(\S+\.\d+)/){
+	  my $temp = $1;
+	  my %dep2;
+	  $dep2{SOURCE_ID} = $dependent_sources{'wormbase_gene'};
+	  $dep2{LINKAGE_SOURCE_ID} = $source_id;
+	  $dep2{ACCESSION} = $temp;
+	  push @{$xref->{DEPENDENT_XREFS}}, \%dep2;
+	}
+      }
       foreach my $ll (@EntrezGeneIDline) {
 	my %dep;
 	$dep{SOURCE_ID} = $dependent_sources{EntrezGene};

misc-scripts/xref_mapping/XrefParser/UniProtParser.pm

@@ -224,12 +224,8 @@ sub create_xrefs {
       my @dep_lines = split /\n/, $deps;
     foreach my $dep (@dep_lines) {
       if ($dep =~ /^DR\s+(.+)/) {
-#	print $dep."\n";
 	my ($source, $acc, @extra) = split /;\s*/, $1;
-#	print "source is $source \n";
-#	print "acc is $acc \n";
 	if (exists $dependent_sources{$source}) {
-#	  print "EXISTS\n";
 	  # create dependent xref structure & store it
 	  my %dep;
 	  $dep{SOURCE_NAME} = $source;
@@ -238,7 +234,6 @@ sub create_xrefs {
 	  $dep{ACCESSION} = $acc;
 	  push @{$xref->{DEPENDENT_XREFS}}, \%dep; # array of hashrefs
 	  if($dep =~ /EMBL/){
-#	    print "prtein_id is ".$extra[0]."\n";
 	    my ($protein_id) = $extra[0];
 	    if($protein_id ne "-"){
 	      my %dep2;
@@ -250,6 +245,39 @@ sub create_xrefs {
 	    }
 	  }
 	}
+	elsif($source =~ /WormPep/){
+	  #DR   WormPep; F35D6.1b; CE28299.
+	  my %dep;
+	  $dep{SOURCE_NAME} = 'wormbase_transcript';
+	  $dep{LINKAGE_SOURCE_ID} = $xref->{SOURCE_ID};
+	  $dep{SOURCE_ID} = $dependent_sources{'wormbase_transcript'};
+	  $dep{ACCESSION} = $acc;
+	  push @{$xref->{DEPENDENT_XREFS}}, \%dep; # array of hashrefs
+
+	  my $gene;
+	  if($acc =~ /(\S+\.\d+)/){
+	    $gene = $1;
+	    my %dep2;
+	    $dep2{SOURCE_NAME} = 'wormbase_gene';
+	    $dep2{LINKAGE_SOURCE_ID} = $xref->{SOURCE_ID};
+	    $dep2{SOURCE_ID} = $dependent_sources{'wormbase_gene'};
+	    $dep2{ACCESSION} = $gene;
+	    push @{$xref->{DEPENDENT_XREFS}}, \%dep2; # array of hashrefs
+	  }
+
+	  my %dep3;
+	  my $worm_id ;
+	  if($extra[0] =~ /([^.]+)/){
+	    $worm_id = $1;
+	  }
+	  $dep3{SOURCE_NAME} = 'wormpep_id';
+	  $dep3{LINKAGE_SOURCE_ID} = $xref->{SOURCE_ID};
+	  $dep3{SOURCE_ID} = $dependent_sources{'wormpep_id'};
+	  $dep3{ACCESSION} = $worm_id;
+	  push @{$xref->{DEPENDENT_XREFS}}, \%dep3; # array of hashrefs
+
+#	  print $worm_id."\t".$gene."\t".$acc."\n";
+	}
       }
     }