def run_mp_and_delete(manager):
"""main method to run igblast through multiprocessing protocol,
takes in a list of dictionaires each with a seperate set of arguments"""
# blast options
blast_options = manager["blast_options"]
# bools
_zip_bool = manager["zip_bool"]
# file name outputs, these will all be temp files to be parsed later
_file = manager["split_file"]
_blast_out = _file + ".blast_out"
if not _zip_bool:
_json_out = _file + ".json"
else:
_json_out = _file + ".json.gz"
# set the filename in the instance:
blast_options["-query"] = _file
blast_options["-out"] = _blast_out
# temporary path
_temporary_path = manager["temporary_path"]
# output options
_output_options = manager["output_options"]
# set up the command line
_cline = [manager["executable"]] # we know its in this directory since we copied it here to make this executable
for argument in blast_options:
arg = blast_options[argument]
if arg.startswith("C"):
arg = '"' + arg + '"'
current_argument = [argument, arg]
_cline += current_argument
print "Running BLAST on processor {0} for split file {1}".format(manager["proc_number"], _file)
print " ".join(_cline)
sub = sp.Popen(_cline, stdout=sp.PIPE, stderr=sp.PIPE)
stdout, stderr = sub.communicate()
# if we have output, lets print it
if stdout:
print stdout
if stderr:
raise Exception("ERROR FROM BLAST {0}".format(stderr))
_output_type = manager["output_type"]
print "Parsing BLAST output to {0} on Processor {1}".format(_output_type, manager["proc_number"])
if _output_type == "blast_out":
os.remove(_file)
print "Removing {0}".format(_file)
else:
print _blast_out, _file, _temporary_path
op = output_parser.igblast_output(
_blast_out, _file, _temporary_path, _output_options, species="human", gui=True, zip_bool=_zip_bool
)
op.parse_blast_file_to_type(_json_out, _output_type)
print "Done parsing {0} type\nRemoving {1} and {2}".format(_output_type, _file, _blast_out)
os.remove(_file)
os.remove(_blast_out)
def run_mp_and_delete(manager):
'''main method to run igblast through multiprocessing protocol,
takes in a list of dictionaires each with a seperate set of arguments'''
# bools
_zip_bool = manager['zip_bool']
_json_bool = manager['json_bool']
_concat_bool = manager['concat_bool']
_output_options = manager['output_options']
if _json_bool:
_output_type = "json"
else:
_output_type = "csv"
# file name outputs, these will all be temp files to be parsed later
_file = manager['split_file']
_blast_out = _file.split('.')[0] + ".blast_out"
_output_file = _file.split('.')[0] + "." + _output_type
# temporary path
_temporary_path = manager['tmp_path']
# check on internal data
_internal_data = manager['internal_data']
_current_directory = os.getcwd()
_species = manager['species']
if not os.path.exists(os.path.join(_current_directory, os.path.basename(_internal_data))):
print "Copying internal data to current directory"
copytree(_internal_data, os.getcwd())
# set up the command line
_blast_options = manager['blast_options']
# add executable
_cline = [manager['executable']]
# add all blast options
for argument in _blast_options:
arg = _blast_options[argument]
current_argument = [argument, arg]
_cline += current_argument
# change them to strings
_cline = [str(i) for i in _cline]
# add query and output to command line
_cline += ["-query", _file]
_cline += ["-out", _blast_out]
# run command line
print "Running BLAST on processor {0} for split file {1}".format(manager['proc_number'], _file)
sub = sp.Popen(_cline, stdout=sp.PIPE, stderr=sp.PIPE)
# If we have stderr and stdout, lets print it
stderr, stdout = sub.communicate()
if stderr or stdout:
print stderr, stdout
# Now parse the output
print "Parsing BLAST output to {0} on Processor {1}".format(_output_type, manager['proc_number'])
op = output_parser.igblast_output(_blast_out, _file,
_temporary_path, _output_options, species=_species, gui=False, zip_bool=_zip_bool, germ_properties=manager['germ_properties'])
op.parse_blast_file_to_type(_output_file, _output_type)
print "Done parsing {0} type".format(_output_type)
if _concat_bool:
print "Removing {0} and {1}".format(_file, _blast_out)
os.remove(_file)
os.remove(_blast_out)
