def compute_psi(sample_filenames,
output_dir,
event_type,
read_len,
overhang_len,
use_cluster=False,
chunk_jobs=False,
filter_events=True,
events_info_filename=None,
settings_filename=None):
"""
Compute Psi values for skipped exons. Sample filenames is a mapping from
sample label to sample.
- sample_filenames = [[sample_label1, sample_filename1],
[sample_label2, sample_filename2]]
- output_dir: output directory
- event_type: 'SE', 'RI', etc.
"""
misc_utils.make_dir(output_dir)
output_dir = os.path.join(output_dir, event_type)
output_dir = os.path.abspath(output_dir)
misc_utils.make_dir(output_dir)
print "Computing Psi for events of type %s" % (event_type)
print " - samples used: ", sample_filenames.keys()
for sample_label, sample_filename in sample_filenames.iteritems():
print "Processing sample: label=%s, filename=%s" \
%(sample_label, sample_filename)
results_output_dir = os.path.join(output_dir, sample_label)
misc_utils.make_dir(results_output_dir)
# Load the set of counts and serialize them into JSON
events = \
as_events.load_event_counts(sample_filename,
event_type,
events_info_filename=events_info_filename)
# Filter events
if filter_events:
print "Filtering events..."
events.filter_events(settings=Settings.get())
print "Running on a total of %d events." % (len(events.events))
events_filename = events.output_file(results_output_dir, sample_label)
# Run MISO on them
miso_cmd = "python %s --compute-two-iso-psi %s %s --event-type %s " \
"--read-len %d --overhang-len %d " \
%(os.path.join(miso_path, 'run_miso.py'),
events_filename,
results_output_dir,
event_type,
read_len,
overhang_len)
if use_cluster:
if chunk_jobs:
miso_cmd += ' --use-cluster --chunk-jobs %d' % (chunk_jobs)
else:
miso_cmd += ' --use-cluster'
print "Executing: %s" % (miso_cmd)
if use_cluster:
print " - Using cluster"
os.system(miso_cmd)
def compute_psi(sample_filenames, output_dir, event_type,
read_len, overhang_len,
use_cluster=False,
chunk_jobs=False,
filter_events=True,
events_info_filename=None,
settings_filename=None):
"""
Compute Psi values for skipped exons. Sample filenames is a mapping from
sample label to sample.
- sample_filenames = [[sample_label1, sample_filename1],
[sample_label2, sample_filename2]]
- output_dir: output directory
- event_type: 'SE', 'RI', etc.
"""
misc_utils.make_dir(output_dir)
output_dir = os.path.join(output_dir, event_type)
output_dir = os.path.abspath(output_dir)
misc_utils.make_dir(output_dir)
print "Computing Psi for events of type %s" %(event_type)
print " - samples used: ", sample_filenames.keys()
for sample_label, sample_filename in sample_filenames.iteritems():
print "Processing sample: label=%s, filename=%s" \
%(sample_label, sample_filename)
results_output_dir = os.path.join(output_dir, sample_label)
misc_utils.make_dir(results_output_dir)
# Load the set of counts and serialize them into JSON
events = \
as_events.load_event_counts(sample_filename,
event_type,
events_info_filename=events_info_filename)
# Filter events
if filter_events:
print "Filtering events..."
events.filter_events(settings=Settings.get())
print "Running on a total of %d events." %(len(events.events))
events_filename = events.output_file(results_output_dir,
sample_label)
# Run MISO on them
miso_cmd = "python %s --compute-two-iso-psi %s %s --event-type %s " \
"--read-len %d --overhang-len %d " \
%(os.path.join(miso_path, 'run_miso.py'),
events_filename,
results_output_dir,
event_type,
read_len,
overhang_len)
if use_cluster:
if chunk_jobs:
miso_cmd += ' --use-cluster --chunk-jobs %d' %(chunk_jobs)
else:
miso_cmd += ' --use-cluster'
print "Executing: %s" %(miso_cmd)
if use_cluster:
print " - Using cluster"
os.system(miso_cmd)