diff data_manager/data_manager_snpEff_databases.py @ 0:9ac823a8b328 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_snpEff_databases.py	Thu Jan 22 09:14:50 2015 -0500
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+import sys
+import os
+import re
+import tempfile
+import subprocess
+import fileinput
+import shutil
+import optparse
+import urllib2
+from ftplib import FTP
+import tarfile
+
+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)
+    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', ]
+    args.append( snpEff_jar )
+    args.append( 'databases' )
+    # tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-snpEff-stderr" )
+    # databases_output = open(databases_path)
+    # proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno(), stderr=tmp_stderr.fileno() )
+    proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() )
+    return_code = proc.wait()
+    if return_code:
+        sys.exit( return_code )
+    databases_output.close()
+    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):
+            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
+                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 )) )
+    else:
+        fh.close()
+    return data_manager_dict
+
+def main():
+    #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() )
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    os.mkdir( target_directory )
+    data_manager_dict = {}
+
+
+    #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 ) )
+
+if __name__ == "__main__": main()
+