diff data_manager/data_manager_snpEff_download.py @ 2:6ad9205c1307

Update to SnpEff version 3.3

--- a/data_manager/data_manager_snpEff_download.py	Thu Jul 04 09:49:15 2013 -0500
+++ b/data_manager/data_manager_snpEff_download.py	Fri Oct 04 09:09:29 2013 -0500
@@ -22,7 +22,7 @@
 # Download human database 'hg19'
 java -jar snpEff.jar download -v hg19
 
-        <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
+        <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
 
 snpEffectPredictor.bin
 regulation_HeLa-S3.bin
@@ -65,6 +65,8 @@
         sys.exit( return_code )
     ## search data_dir/genome_version for files
     regulation_pattern = 'regulation_(.+).bin'
+    #  annotation files that are included in snpEff by a flag
+    annotations_dict = {'nextProt.bin' : '-nextprot','motif.bin': '-motif'}
     genome_path = os.path.join(data_dir,genome_version)
     if os.path.isdir(genome_path):
         for root, dirs, files in os.walk(genome_path):
@@ -78,8 +80,13 @@
                     m = re.match(regulation_pattern,fname)
                     if m:
                         name = m.groups()[0]
-                        data_table_entry = dict(value=genome_version, name=name)
+                        data_table_entry = dict(genome=genome_version,value=name, name=name)
                         _add_data_table_entry( data_manager_dict, 'snpeff_regulationdb', data_table_entry )
+                    elif fname in annotations_dict:
+                        value = annotations_dict[fname]
+                        name = value.lstrip('-')
+                        data_table_entry = dict(genome=genome_version,value=value, name=name)
+                        _add_data_table_entry( data_manager_dict, 'snpeff_annotations', data_table_entry )
     return data_manager_dict
 
 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):