def main():
args = sanitize_help(get_parser()).parse_args()
ksize = args.ksize
filenames = args.input_filenames
nodegraph = Nodegraph(ksize, 1, 1)
partitionmap_file = args.graphbase + '.pmap.merged'
check_input_files(partitionmap_file, args.force)
for _ in filenames:
check_input_files(_, args.force)
check_space(filenames, args.force)
print('loading partition map from:', partitionmap_file, file=sys.stderr)
nodegraph.load_partitionmap(partitionmap_file)
for infile in filenames:
print('outputting partitions for', infile, file=sys.stderr)
outfile = os.path.basename(infile) + '.part'
part_count = nodegraph.output_partitions(infile, outfile)
print('output %d partitions for %s' % (part_count, infile),
file=sys.stderr)
print('partitions are in', outfile, file=sys.stderr)
def test_read_cleaning_abundance_distribution(Countingtype):
infile = utils.get_test_data('valid-read-testing.fq')
x = Countingtype(15, *params_1m)
y = Nodegraph(15, 1, 1, primes=PRIMES_1m)
x.consume_seqfile(infile)
dist = x.abundance_distribution(infile, y)
assert dist[1] == 35 # k-mers with non-ACGTN => ignored.
assert dist[2] == 69
def test_abund_dist_A(AnyTabletype):
A_filename = utils.get_test_data('all-A.fa')
kh = AnyTabletype(4)
tracking = Nodegraph(4, 1, 1, primes=PRIMES_1m)
kh.consume_seqfile(A_filename)
dist = kh.abundance_distribution(A_filename, tracking)
print(dist[:10])
assert sum(dist) == 1
assert dist[0] == 0
def main():
info('filter-stoptags.py', ['graph'])
args = sanitize_help(get_parser()).parse_args()
stoptags = args.stoptags_file
infiles = args.input_filenames
for _ in infiles:
check_input_files(_, args.force)
check_space(infiles, args.force)
print('loading stop tags, with K', args.ksize, file=sys.stderr)
nodegraph = Nodegraph(args.ksize, 1, 1)
nodegraph.load_stop_tags(stoptags)
def process_fn(record):
name = record['name']
seq = record['sequence']
if 'N' in seq:
return None, None
trim_seq, trim_at = nodegraph.trim_on_stoptags(seq)
if trim_at >= args.ksize:
return name, trim_seq
return None, None
# the filtering loop
for infile in infiles:
print('filtering', infile, file=sys.stderr)
outfile = os.path.basename(infile) + '.stopfilt'
outfp = open(outfile, 'w')
tsp = ThreadedSequenceProcessor(process_fn)
tsp.start(verbose_loader(infile), outfp)
print('output in', outfile, file=sys.stderr)
def test_get_labels_save_load():
lb_pre = GraphLabels.NodeGraphLabels(20, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
lb_pre.consume_seqfile_and_tag_with_labels(filename)
# save labels to a file
savepath = utils.get_temp_filename('saved.labels')
lb_pre.save_labels_and_tags(savepath)
# trash the old GraphLabels
del lb_pre
# create new, load labels & tags
graph = Nodegraph(20, 1e7, 4)
lb = GraphLabels.load(savepath, graph)
labels = list(lb.labels())
expected = [0, 1, 2, 3]
for e_label in expected:
assert e_label in labels
for a_label in labels:
assert a_label in expected
def test_bad_primes():
try:
Nodegraph(6, 1, 1, primes=["a", "b", "c"])
assert 0, "this should fail"
except TypeError as e:
print(str(e))
