diff data_manager/data_manager_snpEff_download.py @ 0:e8adfc4c0a6b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_snpEff_download.py	Wed Dec 11 08:53:32 2013 -0500
@@ -0,0 +1,114 @@
+#!/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)
+
+"""
+# Download human database 'hg19'
+java -jar snpEff.jar download -v hg19
+
+        <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
+
+snpEffectPredictor.bin
+regulation_HeLa-S3.bin
+regulation_pattern = 'regulation_(.+).bin'
+
+
+"""
+def download_database(data_manager_dict, target_directory, jar_path,config,genome_version,organism):
+    ## get data_dir from config 
+    ##---
+    ## Databases are stored here
+    ## E.g.: Information for 'hg19' is stored in data_dir/hg19/
+    ##
+    ## Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory
+    ##---
+    #data_dir = ~/snpEff/data/
+    data_dir = target_directory
+    (snpEff_dir,snpEff_jar) = os.path.split(jar_path)
+    args = [ 'java','-jar' ]
+    args.append( jar_path )
+    args.append( 'download' )
+    args.append( '-c' )
+    args.append( config )
+    args.append( '-dataDir' )
+    args.append( data_dir )
+    args.append( '-v' )
+    args.append( genome_version )
+    proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir )
+    return_code = proc.wait()
+    if return_code:
+        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):
+            for fname in files:
+                if fname.startswith('snpEffectPredictor'):
+                    # if snpEffectPredictor.bin download succeeded
+                    name = genome_version + (' : ' + organism if organism else '') 
+                    data_table_entry = dict(value=genome_version, name=name, path=data_dir)
+                    _add_data_table_entry( data_manager_dict, 'snpeff_genomedb', data_table_entry )
+                else:
+                    m = re.match(regulation_pattern,fname)
+                    if m:
+                        name = m.groups()[0]
+                        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 ):
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
+    data_manager_dict['data_tables'][data_table].append( data_table_entry )
+    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' )
+    parser.add_option( '-c', '--config', dest='config', action='store', type="string", default=None, help='snpEff.config path' )
+    parser.add_option( '-g', '--genome_version', dest='genome_version', action='store', type="string", default=None, help='genome_version' )
+    parser.add_option( '-o', '--organism', dest='organism', action='store', type="string", default=None, help='organism name' )
+    (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 SnpEff Reference Data
+    for genome_version, organism in zip(options.genome_version.split(','), options.organism.split(',')):
+        download_database( data_manager_dict, target_directory, options.jar_path, options.config, genome_version, organism )
+
+    #save info to json file
+    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+
+if __name__ == "__main__": main()
+