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 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)