data_manager_snpeff: data_manager/data_manager_snpEff

comparison data_manager/data_manager_snpEff_download.py @ 0:111fc9457ec6 draft

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

author	iuc
date	Tue, 07 Jun 2016 10:13:35 -0400
parents
children	821c34cdacb6

comparison

equal deleted inserted replaced

--1:000000000000
+:111fc9457ec6
+#!/usr/bin/env python
+import gzip
+import json
+import optparse
+import os
+import re
+import subprocess
+import sys
+def stop_err(msg):
+sys.stderr.write(msg)
+sys.exit(1)
+def fetch_databases(jar_path, genome_list=None):
+snpDBs = dict()
+(snpEff_dir, snpEff_jar) = os.path.split(jar_path)
+databases_path = '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:
+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_list and genome_version not in genome_list:
+continue
+if genome_version.startswith("Genome") or genome_version.startswith("-"):
+continue
+description = fields[1].strip()
+snpDBs[genome_version] = description
+except Exception as e:
+stop_err( 'Error parsing %s %s\n' % (databases_path, str( e )) )
+else:
+fh.close()
+return snpDBs
+def getOrganismNames(jar_path, genomes, organisms):
+genome_list = genomes.split(',')
+organism_list = organisms.split(',') if organisms else []
+if len(genome_list) != len(organism_list):
+descriptions = []
+snpDBdict = fetch_databases(jar_path, genome_list=genome_list)
+for genome in snpDBdict:
+descriptions.append(snpDBdict[genome] if genome in snpDBdict else genome)
+return ','.join(descriptions)
+return organisms
+def getSnpeffVersion(jar_path):
+snpeff_version = 'SnpEff ?.?'
+(snpEff_dir, snpEff_jar) = os.path.split(jar_path)
+stderr_path = 'snpeff.err'
+stderr_fh = open(stderr_path, 'w')
+args = [ 'java', '-jar' ]
+args.append( snpEff_jar )
+args.append( '-h' )
+proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stderr=stderr_fh.fileno() )
+return_code = proc.wait()
+if return_code != 255:
+sys.exit( return_code )
+stderr_fh.close()
+fh = open(stderr_path, 'r')
+for line in fh:
+m = re.match('^[Ss]npEff version (SnpEff)\s*(\d+\.\d+).*$', line)
+if m:
+snpeff_version = m.groups()[0] + m.groups()[1]
+break
+fh.close()
+return snpeff_version
+# Starting with SnpEff 4.1 the .bin files contain the SnpEff version:
+# Example - the first 3 line of GRCh37.75/snpEffectPredictor.bin (uncompressed):
+#
+# SnpEff  4.1
+# CHROMOSOME      2       1       0       179197  GL000219.1      false
+# CHROMOSOME      3       1       0       81347269        HSCHR17_1       false
+def getSnpeffVersionFromFile(path):
+snpeff_version = None
+try:
+fh = gzip.open(path, 'rb')
+buf = fh.read(100)
+lines = buf.splitlines()
+m = re.match('^(SnpEff)\s+(\d+\.\d+).*$', lines[0].strip())
+if m:
+snpeff_version = m.groups()[0] + m.groups()[1]
+fh.close()
+except Exception as e:
+stop_err( 'Error parsing SnpEff version from: %s %s\n' % (path, str( e )) )
+return snpeff_version
+# 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)
+snpeff_version = getSnpeffVersion(jar_path)
+key = snpeff_version + '_' + 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 '')
+# version = getSnpeffVersionFromFile(os.path.join(root,fname))
+data_table_entry = dict(key=key, version=snpeff_version, value=genome_version, name=name, path=data_dir)
+_add_data_table_entry( data_manager_dict, 'snpeffv_genomedb', data_table_entry )
+else:
+m = re.match(regulation_pattern, fname)
+if m:
+name = m.groups()[0]
+data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=name, name=name)
+_add_data_table_entry( data_manager_dict, 'snpeffv_regulationdb', data_table_entry )
+elif fname in annotations_dict:
+value = annotations_dict[fname]
+name = value.lstrip('-')
+data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=value, name=name)
+_add_data_table_entry( data_manager_dict, 'snpeffv_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 = json.loads( 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(','), getOrganismNames(options.jar_path, options.genome_version, 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( json.dumps( data_manager_dict ) )
+if __name__ == "__main__":
+main()

Mercurial > repos > iuc > data_manager_snpeff

comparison data_manager/data_manager_snpEff_download.py @ 0:111fc9457ec6 draft