def run(indices): starting_barcode_map = datadir + '/populations/barcode_map_pyndexact_0_ATCAGT.pkl' library = homedir + '/allele_dic_with_WT.pkl' fastqs = [] for i in range(0, len(indices)): fastqs.append(homedir + '/pynd_indices/pynd_' + str(i) + '_' + indices[i] + '.fastq') processes = [] for i in range(0, len(indices)): print("Running map_barcodes " + str(i)) process = mp.Process(target=map_barcodes.update_read_map, args=(fastqs[i], library, max_hamming_dist)) processes.append(process) process.start() for process in processes: process.join() freqs_outputs = [] for i in range(0, len(indices)): freqs_outputs.append(datadir + '/freqs_' + str(i) + '_' + indices[i] + '.pkl') for i in range(0, len(indices)): print("Running freqs " + str(i)) result = counts.calc_mutant_freqs(fastqs[i], library, freqs_outputs[i]) with open(freqs_outputs[i], 'wb') as f: pickle.dump(result, f)
def test(self, rev_comp): print("Running") #rev_comp.side_effect = lambda s: s #records = list(parse.load_fastq('../test_resources/test_allele_shortrevcomp.fastq')) records = [] records.extend([FastQRecord('a', 'a', ''), FastQRecord('a', 'a', ''), FastQRecord('a', 'a', ''), FastQRecord('b', 'b', ''), FastQRecord('b', 'b', ''), FastQRecord('c', 'c', '')]) library = ['A', 'B', 'C'] red = Red() red.data = {'a': 'A', 'aa': 'A', 'aaa': 'A', 'b': 'B', 'bb': 'B', 'c': 'C'} red.data = {lambda key, val: key: prefix + val for key, val in red.data.items()} #read_count = 0 def side_effect(self): log.debug(self.sequence) return self.sequence #read_count += 1 #return records[read_count - 1].sequence #rev_comp.side_effect = lambda self: self.sequence #rev_comp.side_effect = side_effect freqs = count.calc_mutant_freqs(records, red, library) print(freqs)