diff data_manager/data_manager_snpEff_databases.py @ 1:85a23e2dd92b draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584

--- a/data_manager/data_manager_snpEff_databases.py	Thu Jan 22 09:14:50 2015 -0500
+++ b/data_manager/data_manager_snpEff_databases.py	Tue Jun 07 10:11:50 2016 -0400
@@ -1,30 +1,23 @@
 #!/usr/bin/env python
-
-import sys
+import json
+import optparse
 import os
-import re
-import tempfile
 import subprocess
-import fileinput
-import shutil
-import optparse
-import urllib2
-from ftplib import FTP
-import tarfile
+import sys
 
-from galaxy.util.json import from_json_string, to_json_string
 
 def stop_err(msg):
     sys.stderr.write(msg)
     sys.exit(1)
 
+
 def fetch_databases(data_manager_dict, target_directory, jar_path):
-    (snpEff_dir,snpEff_jar) = os.path.split(jar_path)
+    (snpEff_dir, snpEff_jar) = os.path.split(jar_path)
     if not os.path.exists(target_directory):
         os.makedirs(target_directory)
     databases_path = os.path.join( target_directory, 'databases.out' )
-    databases_output = open(databases_path,'w')
-    args = [ 'java','-jar', ]
+    databases_output = open(databases_path, 'w')
+    args = [ 'java', '-jar' ]
     args.append( snpEff_jar )
     args.append( 'databases' )
     # tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-snpEff-stderr" )
@@ -35,48 +28,48 @@
     if return_code:
         sys.exit( return_code )
     databases_output.close()
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] )
+    data_table_entries = []
     try:
-        data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
-        data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] )
-        data_table_entries = []
-        fh = open(databases_path,'r')
-        for i,line in enumerate(fh):
+        fh = open(databases_path, 'r')
+        for i, line in enumerate(fh):
             fields = line.split('\t')
             if len(fields) >= 2:
                 genome_version = fields[0].strip()
                 if genome_version.startswith("Genome") or genome_version.startswith("-"):
                     continue
-                #snpeff test genome
+                # snpeff test genome
                 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
                     continue
                 description = fields[1].strip() + ' : ' + genome_version
                 data_table_entries.append(dict(value=genome_version, name=description))
         data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries
-    except Exception, e:
-        stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
+    except Exception as e:
+        stop_err( 'Error parsing %s %s\n' % (databases_path, str( e )) )
     else:
         fh.close()
     return data_manager_dict
 
+
 def main():
-    #Parse Command Line
+    # Parse Command Line
     parser = optparse.OptionParser()
     parser.add_option( '-j', '--jar_path', dest='jar_path', action='store', type="string", default=None, help='snpEff.jar path' )
     (options, args) = parser.parse_args()
 
     filename = args[0]
 
-    params = from_json_string( open( filename ).read() )
+    params = json.loads( open( filename ).read() )
     target_directory = params[ 'output_data' ][0]['extra_files_path']
     os.mkdir( target_directory )
     data_manager_dict = {}
 
-
-    #Create Defuse Reference Data
+    # Create Defuse Reference Data
     data_manager_dict = fetch_databases( data_manager_dict, target_directory, options.jar_path)
 
-    #save info to json file
-    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+    # save info to json file
+    open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )
 
-if __name__ == "__main__": main()
-
+if __name__ == "__main__":
+    main()