def run_miso_on_samples(settings_filename, output_dir,
use_cluster=True,
delay=120):
"""
Run MISO on a set of samples.
"""
misowrap_obj = MISOWrap(settings_filename, output_dir,
logger_label="run")
bam_files = misowrap_obj.bam_files
read_len = misowrap_obj.read_len
overhang_len = misowrap_obj.overhang_len
events_dir = misowrap_obj.miso_events_dir
single_end = True
if misowrap_obj.insert_lens_dir is not None:
insert_lens_dir = misowrap_obj.insert_lens_dir
misowrap_obj.logger.info("Running in paired-end mode...")
misowrap_obj.logger.info(" - Insert length directory: %s" \
%(insert_lens_dir))
single_end = False
else:
misowrap_obj.logger.info("Running in single-end mode...")
run_events_analysis = misowrap_obj.run_events_cmd
event_types_dirs = \
miso_utils.get_event_types_dirs(misowrap_obj.settings_info)
miso_settings_filename = misowrap_obj.miso_settings_filename
for bam_input in bam_files:
bam_filename, sample_label = bam_input
bam_filename = utils.pathify(bam_filename)
misowrap_obj.logger.info("Processing: %s" %(bam_filename))
for event_type_dir in event_types_dirs:
event_type = os.path.basename(event_type_dir)
print " - Using event dir: %s" %(event_type_dir)
miso_cmd = "%s" %(run_events_analysis)
bam_basename = os.path.basename(bam_filename)
# Output directory for sample
sample_output_dir = os.path.join(output_dir,
sample_label,
event_type)
# Pass sample to MISO along with event
miso_cmd += " --compute-genes-psi %s %s" %(event_type_dir,
bam_filename)
if not single_end:
insert_len_filename = \
os.path.join(insert_lens_dir,
"%s.insert_len" %(bam_basename))
misowrap_obj.logger.info("Reading paired-end parameters " \
"from file...")
misowrap_obj.logger.info(" - PE file: %s" \
%(insert_len_filename))
pe_params = miso_utils.read_pe_params(insert_len_filename)
# Paired-end parameters
miso_cmd += " --paired-end %.2f %.2f" %(pe_params["mean"],
pe_params["sdev"])
# Read length
miso_cmd += " --read-len %d" %(read_len)
# Overhang length
miso_cmd += " --overhang-len %d" %(overhang_len)
# Prefilter?
if misowrap_obj.prefilter_miso:
miso_cmd += " --prefilter"
# Output directory
miso_cmd += " --output-dir %s" %(sample_output_dir)
# Use cluster
if misowrap_obj.use_cluster:
miso_cmd += " --use-cluster"
miso_cmd += " --chunk-jobs %d" %(misowrap_obj.chunk_jobs)
# Settings
miso_cmd += " --settings %s" %(miso_settings_filename)
misowrap_obj.logger.info("Executing: %s" %(miso_cmd))
job_name = "%s_%s" %(sample_label, event_type)
if use_cluster:
misowrap_obj.my_cluster.launch_job(miso_cmd,
job_name)
time.sleep(delay)
else:
os.system(miso_cmd)
def run(
settings,
logs_outdir,
use_cluster=True,
base_delay=10,
# Batch delay (20 mins by default)
batch_delay=60 * 20,
delay_every_n_jobs=30,
dry_run=False,
event_types=None,
):
"""
Run MISO on a set of samples.
"""
settings_filename = utils.pathify(settings)
if event_types is not None:
print "Only running MISO on event types: ", event_types
misowrap_obj = mw.MISOWrap(settings_filename, logs_outdir, logger_label="run")
output_dir = misowrap_obj.miso_outdir
bam_files = misowrap_obj.bam_files
read_len = misowrap_obj.read_len
overhang_len = misowrap_obj.overhang_len
events_dir = misowrap_obj.miso_events_dir
single_end = True
if misowrap_obj.insert_lens_dir is not None:
insert_lens_dir = misowrap_obj.insert_lens_dir
misowrap_obj.logger.info("Running in paired-end mode...")
misowrap_obj.logger.info(" - Insert length directory: %s" % (insert_lens_dir))
single_end = False
else:
misowrap_obj.logger.info("Running in single-end mode...")
run_events_analysis = misowrap_obj.run_events_cmd
event_types_dirs = miso_utils.get_event_types_dirs(misowrap_obj.settings_info)
miso_settings_filename = misowrap_obj.miso_settings_filename
n = 0
for bam_input in bam_files:
bam_filename, sample_label = bam_input
bam_filename = utils.pathify(bam_filename)
misowrap_obj.logger.info("Processing: %s" % (bam_filename))
for event_type_dir in event_types_dirs:
event_type = os.path.basename(event_type_dir)
if event_types is not None:
if event_type not in event_types:
print "Skipping event type: %s" % (event_type)
continue
print " - Using event dir: %s" % (event_type_dir)
miso_cmd = "%s" % (run_events_analysis)
bam_basename = os.path.basename(bam_filename)
# Output directory for sample
sample_output_dir = os.path.join(output_dir, sample_label, event_type)
# Pass sample to MISO along with event
miso_cmd += " --run %s %s" % (event_type_dir, bam_filename)
if not single_end:
insert_len_filename = os.path.join(insert_lens_dir, "%s.insert_len" % (bam_basename))
misowrap_obj.logger.info("Reading paired-end parameters " "from file...")
misowrap_obj.logger.info(" - PE file: %s" % (insert_len_filename))
pe_params = miso_utils.read_pe_params(insert_len_filename)
# Paired-end parameters
miso_cmd += " --paired-end %.2f %.2f" % (pe_params["mean"], pe_params["sdev"])
# Read length
miso_cmd += " --read-len %d" % (read_len)
# Overhang length
miso_cmd += " --overhang-len %d" % (overhang_len)
# Prefilter?
if misowrap_obj.prefilter_miso:
miso_cmd += " --prefilter"
# Output directory
miso_cmd += " --output-dir %s" % (sample_output_dir)
# Use cluster
if misowrap_obj.use_cluster:
miso_cmd += " --use-cluster"
miso_cmd += " --chunk-jobs %d" % (misowrap_obj.chunk_jobs)
# Settings
miso_cmd += " --settings %s" % (miso_settings_filename)
misowrap_obj.logger.info("Executing: %s" % (miso_cmd))
job_name = "%s_%s" % (sample_label, event_type)
if use_cluster:
if not dry_run:
misowrap_obj.my_cluster.launch_job(miso_cmd, job_name, ppn=1)
if n == delay_every_n_jobs:
# Larger delay everytime we've submitted n jobs
misowrap_obj.logger.info("Submitted %d jobs, now waiting %.2f mins." % (n, batch_delay / 60.0))
time.sleep(batch_delay)
n = 0
time.sleep(base_delay)
else:
if not dry_run:
os.system(miso_cmd)
n += 1
def run(settings, logs_outdir,
use_cluster=True,
base_delay=10,
# Batch delay (20 mins by default)
batch_delay=60*20,
delay_every_n_jobs=30,
dry_run=False,
event_types=None):
"""
Run MISO on a set of samples.
"""
settings_filename = utils.pathify(settings)
if event_types is not None:
print "Only running MISO on event types: ", event_types
misowrap_obj = mw.MISOWrap(settings_filename,
logs_outdir,
logger_label="run")
output_dir = misowrap_obj.miso_outdir
bam_files = misowrap_obj.bam_files
read_len = misowrap_obj.read_len
overhang_len = misowrap_obj.overhang_len
events_dir = misowrap_obj.miso_events_dir
single_end = True
if misowrap_obj.insert_lens_dir is not None:
insert_lens_dir = misowrap_obj.insert_lens_dir
misowrap_obj.logger.info("Running in paired-end mode...")
misowrap_obj.logger.info(" - Insert length directory: %s" \
%(insert_lens_dir))
single_end = False
else:
misowrap_obj.logger.info("Running in single-end mode...")
run_events_analysis = misowrap_obj.run_events_cmd
event_types_dirs = \
miso_utils.get_event_types_dirs(misowrap_obj.settings_info)
miso_settings_filename = misowrap_obj.miso_settings_filename
n = 0
for bam_input in bam_files:
bam_filename, sample_label = bam_input
bam_filename = utils.pathify(bam_filename)
misowrap_obj.logger.info("Processing: %s" %(bam_filename))
for event_type_dir in event_types_dirs:
event_type = os.path.basename(event_type_dir)
if event_types is not None:
if event_type not in event_types:
print "Skipping event type: %s" %(event_type)
continue
print " - Using event dir: %s" %(event_type_dir)
miso_cmd = "%s" %(run_events_analysis)
bam_basename = os.path.basename(bam_filename)
# Output directory for sample
sample_output_dir = os.path.join(output_dir,
sample_label,
event_type)
# Pass sample to MISO along with event
miso_cmd += " --run %s %s" %(event_type_dir,
bam_filename)
if not single_end:
insert_len_filename = \
os.path.join(insert_lens_dir,
"%s.insert_len" %(bam_basename))
misowrap_obj.logger.info("Reading paired-end parameters " \
"from file...")
misowrap_obj.logger.info(" - PE file: %s" \
%(insert_len_filename))
pe_params = miso_utils.read_pe_params(insert_len_filename)
# Paired-end parameters
miso_cmd += " --paired-end %.2f %.2f" %(pe_params["mean"],
pe_params["sdev"])
# Read length
miso_cmd += " --read-len %d" %(read_len)
# Overhang length
miso_cmd += " --overhang-len %d" %(overhang_len)
# Prefilter?
if misowrap_obj.prefilter_miso:
miso_cmd += " --prefilter"
# Output directory
miso_cmd += " --output-dir %s" %(sample_output_dir)
# Use cluster
if misowrap_obj.use_cluster:
miso_cmd += " --use-cluster"
miso_cmd += " --chunk-jobs %d" %(misowrap_obj.chunk_jobs)
# Settings
miso_cmd += " --settings %s" %(miso_settings_filename)
misowrap_obj.logger.info("Executing: %s" %(miso_cmd))
job_name = "%s_%s" %(sample_label, event_type)
if use_cluster:
if not dry_run:
misowrap_obj.my_cluster.launch_job(miso_cmd,
job_name,
ppn=1)
if n == delay_every_n_jobs:
# Larger delay everytime we've submitted n jobs
misowrap_obj.logger.info("Submitted %d jobs, now waiting %.2f mins." \
%(n, batch_delay / 60.))
time.sleep(batch_delay)
n = 0
time.sleep(base_delay)
else:
if not dry_run:
os.system(miso_cmd)
n += 1