def homer2narrow(self, options, peak_files, output_dir=None):
'''
Convert passed Homer peak files to narrowPeak files as specified by
the IdrUtilities object.
Returns the set of filenames for generated narrowPeak files.
'''
output_dir = output_dir or options.output_dir
self.check_output_dir(output_dir)
idrutils = IdrUtilities()
output_files = []
for peak_file in peak_files:
# Get extensionless name of file
basename = os.path.splitext(os.path.basename(peak_file))[0]
# Add a randint to avoid name collision
basename = basename + '_' + str(randint(1,999))
output_file = os.path.join(output_dir, basename + '.narrowPeak')
data = idrutils.import_homer_peaks(peak_file)
idrutils.homer_to_narrow_peaks(data, output_file)
print('NarrowPeak file output to {}'.format(output_file))
output_files.append(output_file)
return output_files
def homer2narrow(self, options, peak_files, output_dir=None):
"""
Convert passed Homer peak files to narrowPeak files as specified by
the IdrUtilities object.
Returns the set of filenames for generated narrowPeak files.
"""
output_dir = output_dir or options.output_dir
self.check_output_dir(output_dir)
idrutils = IdrUtilities()
output_files = []
for peak_file in peak_files:
# Get extensionless name of file
basename = os.path.splitext(os.path.basename(peak_file))[0]
# Add a randint to avoid name collision
basename = basename + "_" + str(randint(1, 999))
output_file = os.path.join(output_dir, basename + ".narrowPeak")
data = idrutils.import_homer_peaks(peak_file)
idrutils.homer_to_narrow_peaks(data, output_file)
print("NarrowPeak file output to {}".format(output_file))
output_files.append(output_file)
return output_files
def homer2narrow(self, options, peak_files, output_dir=None):
'''
Convert passed Homer peak files to narrowPeak files as specified by
the IdrUtilities object.
Returns the set of filenames for generated narrowPeak files.
'''
self.check_output_dir(output_dir or options.output_dir)
idrutils = IdrUtilities()
output_files = []
for peak_file in peak_files:
# Get extensionless name of file
basename = os.path.splitext(os.path.basename(peak_file))[0]
output_file = os.path.join(output_dir, basename + '.narrowPeak')
data = idrutils.import_homer_peaks(peak_file)
idrutils.homer_to_narrow_peaks(data, output_file)
print('NarrowPeak file output to {}'.format(output_file))
output_files.append(output_file)
return output_files
