def parse(args,kmap = {}):
import os.path as OP
import getopt
from trident import chromosome_chopper as chopper
if len(args) < 2:
print("trident processes require at least two filenames")
return None
header_map = {}
rsc_memory_limit = default_memory_limit
app_profile = None
project_name = None
chunk_size = default_chunk_size
host = None
if 'assembly' in kmap:
header_map['assembly'] = " ".join(kmap['assembly'])
print("Labeling Assembly: {0}".format(header_map['assembly']))
if 'species' in kmap:
header_map['species'] = kmap['species']
if len(header_map['species']) > 2:
print("WARNING: Species contains more than three words.")
print("Labeling Species: {0}".format(header_map['species']))
if 'memory_limit' in kmap:
rsc_memory_limit = int(kmap['memory_limit'][0])
print("Using memory limit of {0} bytes".format(rsc_memory_limit))
if 'app' in kmap:
app_profile = kmap['app'][0]
if 'project_name' in kmap:
project_name = kmap['project_name'][0]
if 'chunk_size' in kmap:
chunk_size = int(kmap['chunk_size'][0])
if 'host' in kmap:
host = kmap['host'][0]
mirna = args[0]
dna = args[1]
print("Running trident with miRNA %s and DNA %s" % (mirna, dna))
if len(args) > 2:
print ("with flags %s" % " ".join(args[2:]))
if not OP.isdir(temp_directory):
OP.os.mkdir(temp_directory)
num_files = 1
if OP.isfile(dna):
if "-sc" in args:
for i in range(0,len(args)):
if args[i] == "-sc":
if i+1 < len(args):
if int(args[i+1]) < 140:
chunk_size /= 3
num_files = chopper.chopper(dna,segment_fmt % OP.basename(dna),chunk_size,overwrite = False,header_map = header_map)
# sanity check chopper. No need to chop the sequence into one segment file
if num_files == 1:
chopped_file = (segment_fmt + "-1") % OP.basename(dna)
if OP.isfile(chopped_file):
OP.os.unlink(chopped_file)
else:
print("Created %d dna files" % num_files)
retval = []
strargs = " ".join(args)
have_output = ("-out" in args[2:])
if num_files == 1:
# in case the dna did not need to be segmented
proc = TridentInstance(mirna,dna,strargs)
proc.rsc_memory_limit = rsc_memory_limit
proc.executable_name = "trident.centos6.1"
if project_name:
proc.project_name = project_name
if app_profile:
proc.application_profile = app_profile
if not have_output:
proc.args += " -out %s.out" % dna
if host:
proc.host = host
retval.append(proc.get_dag_node())
else:
for i in list(range(1,num_files+1)):
#iterate through segments and setup work units
# for the sake of running on a grid, an output file is required.
segment_name = (segment_fmt + "-%s") % (OP.basename(dna),i)
proc = TridentInstance(mirna,segment_name,strargs)
proc.rsc_memory_limit = rsc_memory_limit
proc.executable_name = "trident.centos6.1"
if host:
proc.host = host
if app_profile:
proc.application_profile = app_profile
if project_name:
proc.project_name = project_name
if not have_output:
proc.args += " -out {0}.out".format(segment_name)
proc.args = proc.args.replace(".out",".out-{0}".format(i))
retval.append(proc.get_dag_node())
return retval
def parse(args,kmap = {}):
import os.path as OP
from trident import chromosome_chopper as chopper
if len(args) < 2:
print("trident processes require at least two filenames")
return None
header_map = {}
if 'assembly' in kmap:
header_map['assembly'] = " ".join(kmap['assembly'])
print("Labeling Assembly: {0}".format(header_map['assembly']))
if 'species' in kmap:
header_map['species'] = kmap['species']
if len(header_map['species']) > 2:
print("WARNING: Species contains more than three words.")
print("Labeling Species: {0}".format(header_map['species']))
mirna = args[0]
dna = args[1]
print("Running trident with miRNA %s and DNA %s" % (mirna, dna))
if len(args) > 2:
print ("with flags %s" % " ".join(args[2:]))
if not OP.isdir(".GRID"):
OP.os.mkdir(".GRID")
num_files = 1
if OP.isfile(dna):
chunk_size = default_chunk_size
if "-sc" in args:
for i in range(0,len(args)):
if args[i] == "-sc":
if i+1 < len(args):
if int(args[i+1]) < 140:
chunk_size /= 3
num_files = chopper.chopper(dna,segment_fmt % OP.basename(dna),chunk_size,overwrite = False,header_map = header_map)
# sanity check chopper. No need to chop the sequence into one segment file
if num_files == 1:
chopped_file = (segment_fmt + "-1") % OP.basename(dna)
if OP.isfile(chopped_file):
OP.os.unlink(chopped_file)
else:
print("Created %d dna files" % num_files)
retval = []
strargs = " ".join(args[2:])
have_output = ("-out" in args[2:])
if num_files == 1:
# in case the dna did not need to be segmented
proc = TridentInstance(mirna,dna,strargs)
if not have_output:
proc.args += " -out %s.out" % dna
retval.append(proc.get_dag_node())
else:
for i in list(range(1,num_files+1)):
#iterate through segments and setup work units
# for the sake of running on a grid, an output file is required.
segment_name = (segment_fmt + "-%s") % (OP.basename(dna),i)
proc = TridentInstance(mirna,segment_name,strargs)
if not have_output:
proc.args += " -out %s.out" % segment_name
retval.append(proc.get_dag_node())
return retval
