X-Git-Url: https://git.donarmstrong.com/?p=function2gene.git;a=blobdiff_plain;f=bin%2Fparse_genecard_results;h=fbd98851a4a8d27f88cb7e9eee567b4ebda35643;hp=a6718c5434030239316d5e425ff666d7699188f5;hb=029f32c46252899b050634e52c46a0e15505bc47;hpb=dd8ec1d4cecf282940831171ef0f796570d781fd

diff --git a/bin/parse_genecard_results b/bin/parse_genecard_results
index a6718c5..fbd9885 100755
--- a/bin/parse_genecard_results
+++ b/bin/parse_genecard_results
@@ -70,6 +70,9 @@ BEGIN{
 use IO::File;
 use IO::Dir;
 
+use HTML::TreeBuilder;
+use HTML::ElementTable;
+
 my %options = (debug    => 0,
 	       help     => 0,
 	       man      => 0,
@@ -115,6 +118,8 @@ my $dir = new IO::Dir $options{dir} or die "Unable to open dir $options{dir}: $!
 
 print join(",", map {qq("$_");} qw(Name RefSeq Location Alias Function Description Keyword DBName Filename)),qq(\n);
 
+my ($keyword) = $options{keyword} || $options{dir} =~ m#(?:^|/)([^\/]+)_results_genecard#;
+
 while ($_ = $dir->read) {
      my $file_name = $_;
      next if $file_name =~ /^\./;
@@ -128,50 +133,59 @@ while ($_ = $dir->read) {
      my @results;
 
      # Find gene name
-     ($results[NAME]) = $result =~ m&(?:Lean|Gene)Card\s+for\s+(?:(?:disorder\s+locus|uncategorized|
-				     hugo\s*reserved\s*symbol|cluster|
-				     potentially\s*expressed\s*sequence)|(?:predicted\s+|pseudo|rna\s+|)gene)
-				     \s*(?:with\s*support\s*|)<FONT\s+COLOR=\"[^\"]+\">\s*<FONT\s+SIZE=\+2>\s*([^\s]+)\s*&xis;
+     ($results[NAME]) = $result =~ m{(?:Lean|Gene)Card\s+for\s+[^<]+<FONT[^>]+>\s*([^<]+)}xis;
 
      $results[NAME] ||= 'NO NAME';
      # Find REF SEQ number
-     ($results[REFSEQ]) = $result =~ m|http://www.ncbi.nlm.nih.gov/entrez/query.fcgi\?
-			       cmd=Search\&db=nucleotide\&doptcmdl=GenBank\&term=([^\"]+)\"|xis;
+     ($results[REFSEQ]) = $result =~ m{http://www.ncbi.nlm.nih.gov/entrez/query.fcgi\?
+				       (?:cmd=Search\&db=nucleotide|db=nucleotide\&cmd=search)
+				       \&doptcmdl=GenBank\&term=([^\"]+)\"}xis;
 
      $results[REFSEQ] ||= 'NO REFSEQ';
 
      # Find Gene Location
-     ($results[LOCATION]) = $result =~ m&<I>LocusLink\s+cytogenetic\s+band:</I><b>\s+
-					 <a\s+href="[^\"]+"\s+target\s+=\s+"aaa">\s*([^\<]+?)\s*</a>&xis;
+     ($results[LOCATION]) = $result =~ m{cytogenetic\s+band:</I><b>\s+
+					 <a\s+href="[^\"]+"\s+target\s*=\s*"aaa"[^>]*>\s*([^\<]+?)\s*</a>}xis;
 
      $results[LOCATION] ||= 'NO LOCATION';
 
      # Find gene aliases
-     my ($alias_table) = $result =~ m|<b>Aliases and Descriptions</b>(.+?)</TR>|is;
-     $alias_table ||='';
-
-     my @gene_aliases = $alias_table =~ m|<li>\s*([^\(]{0,20}?)\s*\(<FONT|gis;
+     my ($alias_table) = $result =~ m{(<table[^>]+><tr><th[^>]+>Aliases.+?</table>)}is;
+     $alias_table ||= '';
+     my @gene_aliases = map {s/\s*$//; $_;} $alias_table =~ m{<td(?: nowrap)?>\s*([^<]+)<}gis;
 
      $results[ALIAS] = join('; ', @gene_aliases);
      $results[ALIAS] ||= 'NO ALIASES';
 
      # Find gene function(s)
 
-     # Swiss prot functions
-     my @functions = $result =~ m&<li><b>Function:</b>\s+(.+?)(?:<li>)|(?:</ul>)&gis;
-
+     my @functions;
      # GO Functions
-     push @functions, (map {s#\s*</a>\s*# #g; $_;} $result =~ m&(GO:\d+\s*</a>.+?)(?:<dd>|<p>)&gis);
+     push @functions, (map {s/\n//g; $_;}
+		       map {s#\s*</a>(?:</td><td>\s*)?\s*# #g; $_;}
+		       $result =~ m{(GO:\d+\s*</a>(?:</td><td>\s*)?.+?)(?:</font>|</td>|<dd>|<p>)}gis
+		      );
      $results[FUNCTION] = join('; ', map {(defined $_)?($_):()} @functions);
      $results[FUNCTION] ||= 'NO FUNCTION';
 
      # Figure out the keyword used
-     ($results[KEYWORD]) = $file_name =~ /search=([^&]+)/;
+     ($results[KEYWORD]) = $file_name =~ /search=?([^&]+)$/;
+
+     $results[KEYWORD] ||= $keyword || 'NO KEYWORD';
 
-     $results[KEYWORD] ||= 'NO KEYWORD';
+     # Swiss prot functions
+     my @description = (map {s/<[^>]+>/ /g;
+			   s/\s+/ /g;
+			   $_;
+		      }
+		      $result =~ m{<(?:dd|li)><b>Function(?::</b>|</b>:)\s+
+				   (.+?)<(?:/dd|li)>}xgis
+		     );
 
      # Figure out what the description is
-     $results[DESCRIPTION] = '';
+     $results[DESCRIPTION] = join('; ',
+				  map {(defined $_)?($_):()}
+				  @description);
 
      # Database searched
      $results[DBNAME] = 'genecard';