def process(self): ret_list = [] sample_ids = [] if type(self.input_files) != list: self.input_files = [self.input_files] for filename in self.input_files: for row in Fofn.get_rows(filename): ret_list.append(row[0]) ret_list.append(row[1]) sample_ids.extend(2 * [row[2]]) self.output_files = ret_list self.meta["job"]["sample_id"] = sample_ids
def process(self): ret_list = [] sample_ids = [] if type(self.input_files) != list: self.input_files = [self.input_files] for filename in self.input_files: for row in Fofn.get_rows(filename): ret_list.append(row[0]) ret_list.append(row[1]) sample_ids.extend(2 * [row[2]]) self.output_files = ret_list self.meta['job']['sample_id'] = sample_ids
def process(self): fofns = [] if not hasattr(self.input_dirs, '__iter__'): self.input_dirs = [self.input_dirs] for i, idir in enumerate(self.input_dirs): sample_sheet = '' if self.input_files: sample_sheet = self.input_files[i] else: sample_sheet = os.path.join(idir, self.ss_name) ifofn = 'fofn_%03d.csv' % i fofns.append( Fofn.create(sample_sheet, idir, self.output_dir, ifofn)) mfofn = os.path.join(self.output_dir, self.output_files) with open(mfofn, 'w') as ofh: for fofn in fofns: with open(fofn) as ifh: ofh.write(''.join(ifh.readlines())) os.remove(fofn) self.output_files = [mfofn]
def process(self): fofns = [] if not hasattr(self.input_dirs, '__iter__'): self.input_dirs = [self.input_dirs] for i, idir in enumerate(self.input_dirs): sample_sheet = '' if self.input_files: sample_sheet = self.input_files[i] else: sample_sheet = os.path.join(idir, self.ss_name) ifofn = 'fofn_%03d.csv' % i fofns.append(Fofn.create( sample_sheet, idir, self.output_dir, ifofn) ) mfofn = os.path.join(self.output_dir, self.output_files) with open(mfofn, 'w') as ofh: for fofn in fofns: with open(fofn) as ifh: ofh.write( ''.join(ifh.readlines()) ) os.remove(fofn) self.output_files = [mfofn]