def update_read_map(fastq_file_name, library_file_name, max_hamming_dist = 2, shuffle=False): red = redis.StrictRedis(host='localhost') #with open(input_map_name, 'rb') as f: input_map = pickle.load(f) with open(library_file_name, 'rb') as f: library = pickle.load(f) fastq_records = parse.load_fastq(fastq_file_name) if (shuffle): fastq_records = shuffle(list(fastq_records)) guess_alleles(fastq_records, library, red, max_hamming_dist = max_hamming_dist)
def update_read_map(fastq_file_name,
library_file_name,
max_hamming_dist=2,
shuffle=False):
red = redis.StrictRedis(host='localhost')
#with open(input_map_name, 'rb') as f: input_map = pickle.load(f)
with open(library_file_name, 'rb') as f:
library = pickle.load(f)
fastq_records = parse.load_fastq(fastq_file_name)
if (shuffle):
fastq_records = shuffle(list(fastq_records))
guess_alleles(fastq_records,
library,
red,
max_hamming_dist=max_hamming_dist)
def main(args): red = redis.StrictRedis(host='localhost') calc_mutant_freqs(parse.load_fastq(args.fastq), red, args.library) counts = calc_mutant_freqs(args.fastq_records, args.library) with open(args.output, 'wb') as f: pickle.dump(counts, f)
import parse
records = list(parse.load_fastq('../test_resources/test_allele_shortrevcomp.fastq'))
assert len(records) == 6
assert records[0].sequence == 'ATATTGAAAGTATGCGCCAGATCGGA'
assert records[0].name == 'entry1'
import parse
records = list(
parse.load_fastq('../test_resources/test_allele_shortrevcomp.fastq'))
assert len(records) == 6
assert records[0].sequence == 'ATATTGAAAGTATGCGCCAGATCGGA'
assert records[0].name == 'entry1'
