MIM now generates GENE_MAP and MORBID_MAP xrefs

misc-scripts/xref_mapping/XrefParser/BaseParser.pm

@@ -1139,6 +1139,26 @@ sub add_to_xrefs{
 
 }
 
+sub add_to_syn_for_mult_sources{
+  my ($self, $acc, $sources, $syn) = @_;
+
+  if(!defined($add_synonym_sth)){
+    $add_synonym_sth =  $dbi->prepare("INSERT INTO synonym VALUES(?,?)");
+  }
+  my $found =0;
+  foreach my $source_id (@$sources){
+    my $xref_id = $self->get_xref($acc, $source_id);
+    if(defined($xref_id)){
+      $add_synonym_sth->execute($xref_id, $syn) || die "$dbi->errstr \n $xref_id\n $syn\n";
+      $found =1;
+    }
+  }
+#  if(!$found){
+#    die "Could not find acc $acc in xref table for sources".join(", ",@$sources)."\n";
+#  }
+}
+
+
 sub add_to_syn{
   my ($self, $acc, $source_id, $syn) = @_;
 

misc-scripts/xref_mapping/XrefParser/MIMParser.pm

@@ -10,7 +10,6 @@ use vars qw(@ISA);
 @ISA = qw(XrefParser::BaseParser);
 
 
-
 # --------------------------------------------------------------------------------
 # Parse command line and run if being run directly
 
@@ -29,21 +28,77 @@ sub run {
 
   my $self = shift if (defined(caller(1)));
   my $file = shift;
-  my $source_id = shift;
+  my $general_source_id = shift;
   my $species_id = shift;
   my %old_to_new;
   my %removed;
-
-  if(!defined($source_id)){
-    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
+  my $source_id;
+  my @sources;
+  if(!defined($general_source_id)){
+    $general_source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
   }
   if(!defined($species_id)){
     $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
   }
+  push @sources, $general_source_id;
+ 
 
+  my %genemap;
+  my %morbidmap;
+  my $gene_source_id = XrefParser::BaseParser->get_source_id_for_source_name("GENE_MAP");
+  push @sources, $gene_source_id;
+  my $morbid_source_id =  XrefParser::BaseParser->get_source_id_for_source_name("MORBID_MAP");
+  push @sources, $morbid_source_id;
 
-  local $/ = "*RECORD*";
+  print "sources are:- ".join(", ",@sources)."\n";
+  if(!open(MIM,"<MIM/genemap")){
+    print  "ERROR: Could not open MIM/genemap\n";
+    return 1; # 1 is an error
+  }
+    
+  #Each entry is a list of fields, separated by the '|' character. 
+  #The fields are, in order :
   
+  #1  - Numbering system, in the format  Chromosome.Map_Entry_Number
+  #2  - Month entered
+  #3  - Day     "
+  #4  - Year    "
+  #5  - Location
+  #6  - Gene Symbol(s)
+  #7  - Gene Status (see below for codes)
+  #8  - Title
+  #9  - 
+  #10 - MIM Number
+  #11 - Method (see below for codes)
+  #12 - Comments
+  #13 -
+  #14 - Disorders
+  #15 - Disorders, cont.
+  #16 - Disorders, cont
+  #17 - Mouse correlate
+  #18 - Reference  }
+
+  while(<MIM>){
+    my @array = split (/\|/, $_);
+    $genemap{$array[9]} = 1; # array starts at 0 so 10 - 1.
+  }
+  close MIM;
+  
+  if(!open(MIM,"<MIM/morbidmap")){
+    print  "ERROR: Could not open MIM/morbidmap\n";
+    return 1; # 1 is an error
+  }
+
+  while(<MIM>){
+    my @array = split (/\|/, $_);
+    $morbidmap{$array[2]} = 1;
+  }
+  close MIM;
+
+
+
+  local $/ = "*RECORD*";
+
   if(!open(MIM,"<".$file)){
     print  "ERROR: Could not open $file\n";
     return 1; # 1 is an error
@@ -58,7 +113,29 @@ sub run {
     my $description = undef;
     if(/\*FIELD\*\s+NO\n(\d+)/){
       $number = $1;
-    }
+      if(defined($morbidmap{$number})){
+	$source_id = $morbid_source_id;
+      }
+      elsif(defined($genemap{$number})){
+	$source_id = $gene_source_id;
+      }
+      else{
+	if(/\*FIELD\*\sTI\n([\^\#\%\+\*]*)\d+(.*)\n/){
+	  if($1 eq "^"){
+	    if(/\*FIELD\*\sTI\n[\^]\d+ MOVED TO (\d+)/){
+	      $old_to_new{$number} = $1;
+	    }
+	    else{
+	      $removed{$number} = 1;
+	      $removed_count++;
+	    }
+	    next;
+	  }
+	}
+	next;
+#	$source_id = $general_source_id; 
+      }
+   }
     if($number==0){
       die "ERROR $_";
     }
@@ -93,7 +170,7 @@ sub run {
       $new = $old_to_new{$new};
     }
     if(!defined($removed{$new})){
-      $self->add_to_syn($new,$source_id,$old);
+      $self->add_to_syn_for_mult_sources($new, \@sources, $old);
       $syn_count++;
     }
   }
@@ -102,6 +179,8 @@ sub run {
   return 0; #successful
 }
 
+
+
 sub new {
 
   my $self = {};