def run_prepare(*data):
"""
Run seqcluster prepare to merge all samples in one file
"""
out_dir = os.path.join(dd.get_work_dir(data[0][0]), "seqcluster", "prepare")
out_dir = os.path.abspath(safe_makedir(out_dir))
prepare_dir = os.path.join(out_dir, "prepare")
tools = dd.get_expression_caller(data[0][0])
if len(tools) == 0:
logger.info("You didn't specify any other expression caller tool."
"You can add to the YAML file:"
"expression_caller:[trna, seqcluster, mirdeep2]")
fn = []
for sample in data:
name = sample[0]["rgnames"]['sample']
fn.append("%s\t%s" % (sample[0]['collapse'], name))
args = namedtuple('args', 'debug print_debug minc minl maxl out')
args = args(False, False, 2, 17, 40, out_dir)
ma_out = op.join(out_dir, "seqs.ma")
seq_out = op.join(out_dir, "seqs.fastq")
min_shared = max(int(len(fn) / 10.0), 1)
if not file_exists(ma_out):
seq_l, sample_l = prepare._read_fastq_files(fn, args)
with file_transaction(ma_out) as ma_tx:
with open(ma_tx, 'w') as ma_handle:
with open(seq_out, 'w') as seq_handle:
prepare._create_matrix_uniq_seq(sample_l, seq_l, ma_handle, seq_handle, min_shared)
for sample in data:
sample[0]["seqcluster_prepare_ma"] = ma_out
sample[0]["seqcluster_prepare_fastq"] = seq_out
return data
def run_prepare(*data):
"""
Run seqcluster prepare to merge all samples in one file
"""
out_dir = os.path.join(dd.get_work_dir(data[0][0]), "seqcluster", "prepare")
out_dir = os.path.abspath(safe_makedir(out_dir))
prepare_dir = os.path.join(out_dir, "prepare")
tools = dd.get_expression_caller(data[0][0])
if len(tools) == 0:
logger.info("You didn't specify any other expression caller tool."
"You can add to the YAML file:"
"expression_caller:[trna, seqcluster, mirdeep2]")
fn = []
for sample in data:
name = sample[0]["rgnames"]['sample']
fn.append("%s\t%s" % (sample[0]['collapse'], name))
args = namedtuple('args', 'debug print_debug minc minl maxl out')
args = args(False, False, 2, 17, 40, out_dir)
ma_out = op.join(out_dir, "seqs.ma")
seq_out = op.join(out_dir, "seqs.fastq")
min_shared = max(int(len(fn) / 10.0), 1)
if not file_exists(ma_out):
seq_l, sample_l = prepare._read_fastq_files(fn, args)
with file_transaction(ma_out) as ma_tx:
with open(ma_tx, 'w') as ma_handle:
with open(seq_out, 'w') as seq_handle:
logger.info("Prepare seqs.fastq with -minl 17 -maxl 40 -minc 2 --min_shared 0.1")
prepare._create_matrix_uniq_seq(sample_l, seq_l, ma_handle, seq_handle, min_shared)
for sample in data:
sample[0]["seqcluster_prepare_ma"] = ma_out
sample[0]["seqcluster_prepare_fastq"] = seq_out
return data
def run_prepare(*data):
"""
Run seqcluster prepare to merge all samples in one file
"""
out_dir = os.path.join(dd.get_work_dir(data[0][0]), "seqcluster",
"prepare")
out_dir = os.path.abspath(safe_makedir(out_dir))
prepare_dir = os.path.join(out_dir, "prepare")
fn = []
for sample in data:
name = sample[0]["rgnames"]['sample']
fn.append("%s\t%s" % (sample[0]['collapse'], name))
args = namedtuple('args', 'debug print_debug minc minl maxl out')
args = args(False, False, 2, 17, 40, out_dir)
ma_out = op.join(out_dir, "seqs.ma")
seq_out = op.join(out_dir, "seqs.fastq")
min_shared = max(int(len(fn) / 10.0), 1)
if not file_exists(ma_out):
seq_l, sample_l = prepare._read_fastq_files(fn, args)
with file_transaction(ma_out) as ma_tx:
with open(ma_tx, 'w') as ma_handle:
with open(seq_out, 'w') as seq_handle:
prepare._create_matrix_uniq_seq(sample_l, seq_l, ma_handle,
seq_handle, min_shared)
return data
def run_prepare(data):
"""
Run seqcluster prepare to merge all samples in one file
"""
out_dir = os.path.join(dd.get_work_dir(data[0]), "seqcluster", "prepare")
out_dir = os.path.abspath(safe_makedir(out_dir))
config_file = os.path.join(out_dir, "prepare.conf")
prepare_dir = os.path.join(out_dir, "prepare")
fn = []
for sample in data:
name = sample["rgnames"]['sample']
fn.append("%s\t%s" % (sample['collapse'], name))
args = namedtuple('args', 'debug print_debug minc minl maxl out')
args = args(False, False, 1, 17, 40, out_dir)
seq_l, sample_l = prepare._read_fastq_files(fn, args)
ma_out = op.join(out_dir, "seqs.ma")
seq_out = op.join(out_dir, "seqs.fastq")
min_shared = max(int(len(fn) / 10.0), 1)
if not file_exists(ma_out):
with file_transaction(ma_out) as ma_tx:
with open(ma_tx, 'w') as ma_handle:
with open(seq_out, 'w') as seq_handle:
prepare._create_matrix_uniq_seq(sample_l, seq_l, ma_handle, seq_handle, min_shared)
return [data]
def test_preparedata(self):
out_dir = "test/test_out_prepare"
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
os.mkdir(out_dir)
arg = namedtuple('args', 'minl maxl minc out')
args = arg(15, 40, 1, out_dir)
seq_l, list_s = _read_fastq_files(open("data/examples/collapse/config"), args)
ma_out = open(os.path.join(out_dir, "seqs.ma"), 'w')
seq_out = open(os.path.join(out_dir, "seqs.fa"), 'w')
_create_matrix_uniq_seq(list_s, seq_l, ma_out, seq_out, 1)
self.assertTrue(os.path.exists(os.path.join(out_dir, "seqs.ma")))
self.assertTrue(os.path.exists(os.path.join(out_dir, "seqs.fa")))
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
def test_preparedata(self):
mod_dir = os.path.dirname(inspect.getfile(seqcluster)).replace("seqcluster/","")
os.chdir(os.path.join(mod_dir, "data/test_collapse"))
if os.path.exists("seqs.ma"):
os.remove("seqs.ma")
if os.path.exists("seqs.fa"):
os.remove("seqs.fa")
arg = namedtuple('args', 'minl maxl minc')
args = arg(15, 40, 1)
seq_l, list_s = _read_fastq_files(open("config"), args)
ma_out = open("seqs.ma", 'w')
seq_out = open("seqs.fa", 'w')
_create_matrix_uniq_seq(list_s, seq_l, ma_out, seq_out, 1)
self.assertTrue(os.path.exists("seqs.ma"))
self.assertTrue(os.path.exists("seqs.fa"))
def test_preparedata(self):
out_dir = "test/test_out_prepare"
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
os.mkdir(out_dir)
arg = namedtuple('args', 'minl maxl minc out')
args = arg(15, 40, 1, out_dir)
seq_l, list_s = _read_fastq_files(
open("data/examples/collapse/config"), args)
ma_out = open(os.path.join(out_dir, "seqs.ma"), 'w')
seq_out = open(os.path.join(out_dir, "seqs.fa"), 'w')
_create_matrix_uniq_seq(list_s, seq_l, ma_out, seq_out, 1)
self.assertTrue(os.path.exists(os.path.join(out_dir, "seqs.ma")))
self.assertTrue(os.path.exists(os.path.join(out_dir, "seqs.fa")))
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
def test_preparedata(self):
mod_dir = os.path.dirname(inspect.getfile(seqcluster)).replace("seqcluster/","")
os.chdir(os.path.join(mod_dir, "data/examples/collapse"))
out_dir = "test_out_prepare"
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
os.mkdir(out_dir)
arg = namedtuple('args', 'minl maxl minc out')
args = arg(15, 40, 1, out_dir)
seq_l, list_s = _read_fastq_files(open("config"), args)
ma_out = open(os.path.join(out_dir, "seqs.ma"), 'w')
seq_out = open(os.path.join(out_dir, "seqs.fa"), 'w')
_create_matrix_uniq_seq(list_s, seq_l, ma_out, seq_out, 1)
os.chdir(out_dir)
self.assertTrue(os.path.exists("seqs.ma"))
self.assertTrue(os.path.exists("seqs.fa"))
def test_preparedata(self):
mod_dir = os.path.dirname(inspect.getfile(seqcluster)).replace(
"seqcluster/", "")
os.chdir(os.path.join(mod_dir, "data/examples/collapse"))
out_dir = "test_out_prepare"
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
os.mkdir(out_dir)
arg = namedtuple('args', 'minl maxl minc out')
args = arg(15, 40, 1, out_dir)
seq_l, list_s = _read_fastq_files(open("config"), args)
ma_out = open(os.path.join(out_dir, "seqs.ma"), 'w')
seq_out = open(os.path.join(out_dir, "seqs.fa"), 'w')
_create_matrix_uniq_seq(list_s, seq_l, ma_out, seq_out, 1)
os.chdir(out_dir)
self.assertTrue(os.path.exists("seqs.ma"))
self.assertTrue(os.path.exists("seqs.fa"))
files = sys.argv[2]
out_dir = "./"
fn = []
args = namedtuple('args', 'debug print_debug minc minl maxl out')
args = args(False, False, 2, 17, 40, out_dir)
ma_out = op.join(out_dir, "seqs.ma")
seq_out = op.join(out_dir, "seqs.fastq")
min_shared = max(int(len(fn) / 10.0), 1)
arr_ids = ids.split(',')
arr_files = files.split(',')
for id_, file_ in zip( arr_ids, arr_files ):
fn.append("%s\t%s"%(file_,id_))
if not file_exists(ma_out):
seq_l, sample_l = prepare._read_fastq_files(fn, args)
with file_transaction(ma_out) as ma_tx:
with open(ma_tx, 'w') as ma_handle:
with open(seq_out, 'w') as seq_handle:
prepare._create_matrix_uniq_seq(sample_l, seq_l, ma_handle, seq_handle, min_shared)