diff data_manager/data_manager_snpEff_download.py @ 5:3d9dd4b9fb09 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty

--- a/data_manager/data_manager_snpEff_download.py	Tue Apr 04 18:14:37 2017 -0400
+++ b/data_manager/data_manager_snpEff_download.py	Tue Apr 18 09:40:03 2017 -0400
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-import gzip
 import json
 import optparse
 import os
@@ -13,19 +12,12 @@
     sys.exit(1)
 
 
-def fetch_databases(jar_path, genome_list=None):
+def fetch_databases(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()
+    args = ['snpEff', 'databases']
+    return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
     if return_code:
         sys.exit( return_code )
     databases_output.close()
@@ -48,28 +40,24 @@
     return snpDBs
 
 
-def getOrganismNames(jar_path, genomes, organisms):
+def getOrganismNames(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)
+        snpDBdict = fetch_databases(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):
+def getSnpeffVersion():
     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()
+    args = ['snpEff', '-h']
+    return_code = subprocess.call(args=args, shell=False, stderr=stderr_fh.fileno())
     if return_code != 255:
         sys.exit( return_code )
     stderr_fh.close()
@@ -83,27 +71,6 @@
     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
 #
@@ -112,36 +79,24 @@
 # snpEffectPredictor.bin
 # regulation_HeLa-S3.bin
 # regulation_pattern = 'regulation_(.+).bin'
-def download_database(data_manager_dict, target_directory, jar_path, config, genome_version, organism):
+def download_database(data_manager_dict, target_directory, 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()
+    args = ['snpEff', 'download', '-dataDir', data_dir, '-v', genome_version]
+    return_code = subprocess.call(args=args, shell=False)
     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'}
+    #  annotation files that are included in SnpEff by a flag
+    annotations_dict = {'nextProt.bin': '-nextprot', 'motif.bin': '-motif', 'interactions.bin': '-interaction'}
     genome_path = os.path.join(data_dir, genome_version)
-    snpeff_version = getSnpeffVersion(jar_path)
+    snpeff_version = getSnpeffVersion()
     key = snpeff_version + '_' + genome_version
     if os.path.isdir(genome_path):
         for root, dirs, files in os.walk(genome_path):
@@ -149,7 +104,6 @@
                 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:
@@ -174,10 +128,7 @@
 
 
 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()
@@ -190,8 +141,8 @@
     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 )
+    for genome_version, organism in zip(options.genome_version.split(','), getOrganismNames(options.genome_version, options.organism).split(',')):
+        download_database( data_manager_dict, target_directory, genome_version, organism )
 
     # save info to json file
     open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )