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