def align_and_pickle_mappings():
print 'loading ref_hash pickle...'
pickle_filename = 'ref_hash_{}_{}.pkl'.format(c.DATASET, c.KEY_SIZE)
ref_hash = load_hash_pickle(pickle_filename)
print 'loading ref...'
ref_file = c.REF_FILE
ref = utils.read_reference('{}/{}/{}'.format(c.DATA_PATH, c.DATASET, ref_file))
print 'loading reads...'
reads_file = c.READS_FILE
reads = utils.read_reads('{}/{}/{}'.format(c.DATA_PATH, c.DATASET, reads_file))
print 'loaded reads'
print 'aligning {}...'.format(c.DATASET)
start = time.time()
alignments = [align_paired_read(pr, ref, ref_hash) for pr in reads]
alignments = [x for x in alignments if x]
print 'alignment complete, elapsed: {}'.format(time.time() - start)
directory = '{}/{}/{}'.format(c.DATA_PATH, c.DATASET, 'alignments/')
if not os.path.exists(directory):
print 'creating folder {}'.format(directory)
os.makedirs(directory)
start = time.time()
alignments_pickle_path = 'alignments_{}_{}.pkl'.format(c.DATASET, c.KEY_SIZE)
pickle.dump(alignments, open(alignments_pickle_path, 'wb'))
print '{} alignment pickled in {}'.format(reads_file, time.time() - start)
def align_and_pickle_mappings_split(split_no, ref, ref_hash):
print 'loading reads file {}...'.format(split_no)
reads = utils.read_reads('{}/{}/reads_split/part_{}.txt'.format(c.DATA_PATH, c.DATASET, split_no))
print 'loaded reads file {}'.format(split_no)
print 'aligning {} part {}'.format(c.DATASET, split_no)
start = time.time()
alignments = [align_paired_read(pr, ref, ref_hash) for pr in reads]
alignments = [x for x in alignments if x]
print 'alignment complete, elapsed: {}'.format(time.time() - start)
directory = '{}/{}/{}'.format(c.DATA_PATH, c.DATASET, 'alignments/')
if not os.path.exists(directory):
print 'creating folder {}'.format(directory)
os.makedirs(directory)
start = time.time()
alignments_pickle_path = '{}/alignments_{}_{}_part_{}.pkl'.format(directory, c.DATASET, c.KEY_SIZE, split_no)
pickle.dump(alignments, open(alignments_pickle_path, 'wb'))
print '{} part {} alignment pickled in {}'.format(c.DATASET, split_no, time.time() - start)
