Added species-specific regexps for gene description filtering.

misc-scripts/xref_mapping/XrefMapper/mus_musculus.pm

@@ -6,10 +6,43 @@ use vars '@ISA';
 
 @ISA = qw{ XrefMapper::BasicMapper };
 
-sub get_set_lists{
+sub get_set_lists {
 
   return [["ExonerateGappedBest1", ["mus_musculus","*"]]];
 
 }
 
+sub gene_description_filter_regexps {
+
+  return ('\(?[0-9A-Z]{10}RIK PROTEIN\)?[ \.]',
+	  'RIKEN CDNA [0-9A-Z]{10}[ \.;]',
+	  '.*RIKEN FULL-LENGTH ENRICHED LIBRARY.*PRODUCT:',
+	  '.*RIKEN FULL-LENGTH ENRICHED LIBRARY.*',
+	  '\(*HYPOTHETICAL\s+.*',
+	  '^UNKNOWN\s+.*',
+	  'CDNA SEQUENCE\s?,? [A-Z]+\d+[ \.;]',
+	  'CLONE MGC:\d+[ \.;]',
+	  ' MGC:\s*\d+[ \.;]',
+	  'HYPOTHETICAL PROTEIN,',
+	  'HYPOTHETICAL PROTEIN \S+[\.;]',
+	  'DNA SEGMENT, CHR.*',
+	  'PROTEIN \S+ HOMOLOG\.?',
+	  '^SIMILAR TO GENE.*',
+	  'SIMILAR TO PUTATIVE[ \.]',
+	  '^SIMILAR TO HYPOTHETICAL.*',
+	  'SIMILAR TO (KIAA|LOC|RIKEN).*',
+	  'SIMILAR TO GENBANK ACCESSION NUMBER\s+\S+',
+	  'SIMILAR TO\s+$',
+          'EXPRESSED SEQUENCE [A-Z]+\d+[ \.;]',
+          'EST [A-Z]+\d+[ \.;]',
+          '^\s*\(FRAGMENT\)\.?\s*$',
+	  '^\s*\(?GENE\)?\.?;?\s*$',
+          '\s*\(?GENE\)?\.?;?',
+          '\s*\(?PRECURSOR\)?\.?;?',
+          '^\s*\(\s*\)\s*$',
+	  '^\s*\(\d*\)\s*[ \.]$',
+          '^\s+\(?\s*$');
+
+}
+
 1;