def main():
args = sanitize_help(get_parser()).parse_args()
output_file = args.graphbase + '.pmap.merged'
pmap_files = glob.glob(args.graphbase + '.subset.*.pmap')
print('loading %d pmap files (first one: %s)' %
(len(pmap_files), pmap_files[0]), file=sys.stderr)
ksize = args.ksize
nodegraph = khmer.Nodegraph(ksize, 1, 1)
for _ in pmap_files:
check_input_files(_, args.force)
check_space(pmap_files, args.force)
for pmap_file in pmap_files:
print('merging', pmap_file, file=sys.stderr)
nodegraph.merge_subset_from_disk(pmap_file)
print('saving merged to', output_file, file=sys.stderr)
nodegraph.save_partitionmap(output_file)
if args.remove_subsets:
print('removing pmap files', file=sys.stderr)
for pmap_file in pmap_files:
os.unlink(pmap_file)
def main():
info('filter-abund.py', ['counting'])
args = sanitize_help(get_parser()).parse_args()
check_input_files(args.input_graph, args.force)
infiles = args.input_filename
if ('-' in infiles or '/dev/stdin' in infiles) and not \
args.single_output_file:
print("Accepting input from stdin; output filename must "
"be provided with -o.", file=sys.stderr)
sys.exit(1)
for filename in infiles:
check_input_files(filename, args.force)
check_space(infiles, args.force)
print('loading countgraph:', args.input_graph,
file=sys.stderr)
countgraph = khmer.load_countgraph(args.input_graph)
ksize = countgraph.ksize()
print("K:", ksize, file=sys.stderr)
# the filtering function.
def process_fn(record):
name = record.name
seq = record.sequence
seqN = seq.replace('N', 'A')
if args.variable_coverage: # only trim when sequence has high enough C
med, _, _ = countgraph.get_median_count(seqN)
if med < args.normalize_to:
return name, seq
_, trim_at = countgraph.trim_on_abundance(seqN, args.cutoff)
if trim_at >= ksize:
# be sure to not to change the 'N's in the trimmed sequence -
# so, return 'seq' and not 'seqN'.
return name, seq[:trim_at]
return None, None
if args.single_output_file:
outfile = args.single_output_file.name
outfp = get_file_writer(args.single_output_file, args.gzip, args.bzip)
# the filtering loop
for infile in infiles:
print('filtering', infile, file=sys.stderr)
if not args.single_output_file:
outfile = os.path.basename(infile) + '.abundfilt'
outfp = open(outfile, 'wb')
outfp = get_file_writer(outfp, args.gzip, args.bzip)
tsp = ThreadedSequenceProcessor(process_fn, n_workers=args.threads)
tsp.start(verbose_loader(infile), outfp)
print('output in', outfile, file=sys.stderr)
def main():
info('annotate-partitions.py', ['graph'])
args = get_parser().parse_args()
ksize = args.ksize
filenames = args.input_filenames
htable = khmer.new_hashbits(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 >>sys.stderr, 'loading partition map from:', partitionmap_file
htable.load_partitionmap(partitionmap_file)
for infile in filenames:
print >>sys.stderr, 'outputting partitions for', infile
outfile = os.path.basename(infile) + '.part'
part_count = htable.output_partitions(infile, outfile)
print >>sys.stderr, 'output %d partitions for %s' % (
part_count, infile)
print >>sys.stderr, 'partitions are in', outfile
def main():
info("annotate-partitions.py", ["graph"])
args = get_parser().parse_args()
ksize = args.ksize
filenames = args.input_filenames
htable = khmer.Hashbits(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)
htable.load_partitionmap(partitionmap_file)
for infile in filenames:
print("outputting partitions for", infile, file=sys.stderr)
outfile = os.path.basename(infile) + ".part"
part_count = htable.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 main():
args = sanitize_help(get_parser()).parse_args()
htfile = args.countgraph
input_filename = args.input
output = args.output
infiles = [htfile, input_filename]
for infile in infiles:
check_input_files(infile, args.force)
check_space(infiles, args.force)
print('loading k-mer countgraph from', htfile, file=sys.stderr)
countgraph = load_countgraph(htfile)
ksize = countgraph.ksize()
print('writing to', output.name, file=sys.stderr)
output = csv.writer(output)
# write headers:
output.writerow(['name', 'median', 'average', 'stddev', 'seqlen'])
for record in screed.open(input_filename):
seq = record.sequence.upper()
if 'N' in seq:
seq = seq.replace('N', 'A')
if ksize <= len(seq):
medn, ave, stdev = countgraph.get_median_count(seq)
ave, stdev = [round(x, 9) for x in (ave, stdev)]
output.writerow([record.name, medn, ave, stdev, len(seq)])
def main():
info('annotate-partitions.py', ['graph'])
args = get_parser().parse_args()
ksize = args.ksize
filenames = args.input_filenames
nodegraph = khmer.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 main():
info('merge-partitions.py', ['graph'])
args = get_parser().parse_args()
output_file = args.graphbase + '.pmap.merged'
pmap_files = glob.glob(args.graphbase + '.subset.*.pmap')
print('loading %d pmap files (first one: %s)' %
(len(pmap_files), pmap_files[0]), file=sys.stderr)
ksize = args.ksize
htable = khmer.new_hashbits(ksize, 1, 1)
for _ in pmap_files:
check_input_files(_, args.force)
check_space(pmap_files, args.force)
for pmap_file in pmap_files:
print('merging', pmap_file, file=sys.stderr)
htable.merge_subset_from_disk(pmap_file)
print('saving merged to', output_file, file=sys.stderr)
htable.save_partitionmap(output_file)
if args.remove_subsets:
print('removing pmap files', file=sys.stderr)
for pmap_file in pmap_files:
os.unlink(pmap_file)
def main():
info('count-median.py', ['diginorm'])
args = get_parser().parse_args()
htfile = args.ctfile
input_filename = args.input
output_filename = args.output
infiles = [htfile, input_filename]
for infile in infiles:
check_file_status(infile, args.force)
check_space(infiles, args.force)
print >>sys.stderr, 'loading k-mer counting table from', htfile
htable = khmer.load_counting_hash(htfile)
ksize = htable.ksize()
print >>sys.stderr, 'writing to', output_filename
output = open(output_filename, 'w')
for record in screed.open(input_filename):
seq = record.sequence.upper()
if 'N' in seq:
seq = seq.replace('N', 'G')
if ksize <= len(seq):
medn, ave, stdev = htable.get_median_count(seq)
print >> output, record.name, medn, ave, stdev, len(seq)
def main():
info("count-median.py", ["diginorm"])
args = sanitize_help(get_parser()).parse_args()
htfile = args.countgraph
input_filename = args.input
output = args.output
infiles = [htfile, input_filename]
for infile in infiles:
check_input_files(infile, args.force)
check_space(infiles, args.force)
print("loading k-mer countgraph from", htfile, file=sys.stderr)
countgraph = load_countgraph(htfile)
ksize = countgraph.ksize()
print("writing to", output.name, file=sys.stderr)
output = csv.writer(output)
# write headers:
output.writerow(["name", "median", "average", "stddev", "seqlen"])
for record in screed.open(input_filename):
seq = record.sequence.upper()
if "N" in seq:
seq = seq.replace("N", "A")
if ksize <= len(seq):
medn, ave, stdev = countgraph.get_median_count(seq)
ave, stdev = [round(x, 9) for x in (ave, stdev)]
output.writerow([record.name, medn, ave, stdev, len(seq)])
def main(args):
info('build-graph.py', ['graph', 'SeqAn'])
report_on_config(args, hashtype='nodegraph')
base = args.output_filename
filenames = args.input_filenames
for fname in args.input_filenames:
check_input_files(fname, args.force)
# if optimization args are given, do optimization
args = functions.do_sanity_checking(args, 0.01)
check_space(args.input_filenames, args.force)
check_space_for_hashtable(args, 'nodegraph', args.force)
print('Saving k-mer presence table to %s' % base, file=sys.stderr)
print('Loading kmers from sequences in %s' %
repr(filenames), file=sys.stderr)
if args.no_build_tagset:
print('We WILL NOT build the tagset.', file=sys.stderr)
else:
print('We WILL build the tagset (for partitioning/traversal).',
file=sys.stderr)
print('making nodegraph', file=sys.stderr)
htable = khmer_args.create_nodegraph(args)
functions.build_graph(filenames, htable, args.threads,
not args.no_build_tagset)
print('Total number of unique k-mers: {0}'.format(htable.n_unique_kmers()),
file=sys.stderr)
print('saving k-mer presence table in', base + '.pt', file=sys.stderr)
htable.save(base + '.pt')
if not args.no_build_tagset:
print('saving tagset in', base + '.tagset', file=sys.stderr)
htable.save_tagset(base + '.tagset')
info_fp = open(base + '.info', 'w')
info_fp.write('%d unique k-mers' % htable.n_unique_kmers())
fp_rate = \
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.15)
# 0.18 is ACTUAL MAX. Do not change.
print('false positive rate estimated to be %1.3f' % fp_rate,
file=sys.stderr)
print('\nfalse positive rate estimated to be %1.3f' % fp_rate,
file=info_fp)
print('wrote to', base + '.info and', base + '.pt', file=sys.stderr)
if not args.no_build_tagset:
print('and ' + base + '.tagset', file=sys.stderr)
sys.exit(0)
def main():
args = sanitize_help(get_parser()).parse_args()
configure_logging(args.quiet)
check_input_files(args.datafile, args.force)
check_space([args.datafile], args.force)
if args.savegraph:
tablesize = calculate_graphsize(args, "countgraph")
check_space_for_graph(args.savegraph, tablesize, args.force)
report_on_config(args)
log_info("making countgraph")
graph = khmer_args.create_countgraph(args)
# first, load reads into graph
rparser = khmer.ReadParser(args.datafile)
threads = []
log_info("consuming input, round 1 -- {datafile}", datafile=args.datafile)
for _ in range(args.threads):
cur_thread = threading.Thread(target=graph.consume_fasta_with_reads_parser, args=(rparser,))
threads.append(cur_thread)
cur_thread.start()
for _ in threads:
_.join()
log_info("Total number of unique k-mers: {nk}", nk=graph.n_unique_kmers())
fp_rate = khmer.calc_expected_collisions(graph, args.force)
log_info("fp rate estimated to be {fpr:1.3f}", fpr=fp_rate)
# the filtering loop
log_info("filtering {datafile}", datafile=args.datafile)
if args.outfile is None:
outfile = os.path.basename(args.datafile) + ".abundfilt"
else:
outfile = args.outfile
outfp = open(outfile, "wb")
outfp = get_file_writer(outfp, args.gzip, args.bzip)
paired_iter = broken_paired_reader(ReadParser(args.datafile), min_length=graph.ksize(), force_single=True)
for n, is_pair, read1, read2 in paired_iter:
assert not is_pair
assert read2 is None
trimmed_record, _ = trim_record(graph, read1, args.cutoff, args.variable_coverage, args.normalize_to)
if trimmed_record:
print((trimmed_record,))
write_record(trimmed_record, outfp)
log_info("output in {outfile}", outfile=outfile)
if args.savegraph:
log_info("Saving k-mer countgraph filename {graph}", graph=args.savegraph)
graph.save(args.savegraph)
def main():
info('interleave-reads.py')
args = get_parser().parse_args()
for _ in args.infiles:
check_file_status(_, args.force)
check_space(args.infiles, args.force)
s1_file = args.infiles[0]
if len(args.infiles) == 2:
s2_file = args.infiles[1]
else:
s2_file = s1_file.replace('_R1_', '_R2_')
print >> sys.stderr, ("given only one file; "
"guessing that R2 file is %s" % s2_file)
fail = False
if not os.path.exists(s1_file):
print >> sys.stderr, "Error! R1 file %s does not exist" % s1_file
fail = True
if not os.path.exists(s2_file):
print >> sys.stderr, "Error! R2 file %s does not exist" % s2_file
fail = True
if fail and not args.force:
sys.exit(1)
print >> sys.stderr, "Interleaving:\n\t%s\n\t%s" % (s1_file, s2_file)
counter = 0
for read1, read2 in itertools.izip(screed.open(s1_file),
screed.open(s2_file)):
if counter % 100000 == 0:
print >> sys.stderr, '...', counter, 'pairs'
counter += 1
name1 = read1.name
if not name1.endswith('/1'):
name1 += '/1'
name2 = read2.name
if not name2.endswith('/2'):
name2 += '/2'
assert name1[:-2] == name2[:-2], \
"This doesn't look like paired data! %s %s" % (name1, name2)
read1.name = name1
read2.name = name2
write_record(read1, args.output)
write_record(read2, args.output)
print >> sys.stderr, 'final: interleaved %d pairs' % counter
print >> sys.stderr, 'output written to', args.output
def main():
info('optimal_args_nodegraph.py', ['graph', 'SeqAn'])
args = get_parser().parse_args()
report_on_config(args, graphtype='nodegraph')
filenames = args.input_filenames
base = filenames[0]
for _ in args.input_filenames:
check_input_files(_, False)
check_space(args.input_filenames, False)
print('Counting kmers from sequences in %s' % repr(filenames),
file=sys.stderr)
htable = khmer.new_nodegraph(args.ksize, args.max_tablesize, args.n_tables)
target_method = htable.consume_fasta_with_reads_parser
for _, filename in enumerate(filenames):
rparser = khmer.ReadParser(filename)
threads = []
print('consuming input', filename, file=sys.stderr)
for num in xrange(args.threads):
cur_thread = threading.Thread(
target=target_method, args=(rparser,))
threads.append(cur_thread)
cur_thread.start()
for thread in threads:
thread.join()
unique_kmers = htable.n_unique_kmers()
print('Total number of unique k-mers: {0}'.format(unique_kmers),
file=sys.stderr)
info_optimal = open(base + '.optimal_args', 'w')
fp_rate = khmer.calc_expected_collisions(htable)
print('fp rate estimated to be %1.3f' % fp_rate, file=sys.stderr)
if fp_rate > 0.15: # 0.18 is ACTUAL MAX. Do not change.
print("**", file=sys.stderr)
print("** ERROR: the graph structure is too small for this data set."
"Increase table size/# tables.", file=sys.stderr)
print("**", file=sys.stderr)
if not False:
sys.exit(1)
to_print = graphsize_args_report(unique_kmers, fp_rate)
print(to_print, file=info_optimal)
print('optimal arguments were written to', base + '.optimal_args',
file=sys.stderr)
def main():
info('make-initial-stoptags.py', ['graph'])
args = get_parser().parse_args()
graphbase = args.graphbase
# @RamRS: This might need some more work
infiles = [graphbase + '.pt', graphbase + '.tagset']
if args.stoptags:
infiles.append(args.stoptags)
for _ in infiles:
check_input_files(_, args.force)
check_space(infiles, args.force)
print >>sys.stderr, 'loading htable %s.pt' % graphbase
htable = khmer.load_hashbits(graphbase + '.pt')
# do we want to load stop tags, and do they exist?
if args.stoptags:
print >>sys.stderr, 'loading stoptags from', args.stoptags
htable.load_stop_tags(args.stoptags)
print >>sys.stderr, 'loading tagset %s.tagset...' % graphbase
htable.load_tagset(graphbase + '.tagset')
ksize = htable.ksize()
counting = khmer.new_counting_hash(ksize, args.min_tablesize,
args.n_tables)
# divide up into SUBSET_SIZE fragments
divvy = htable.divide_tags_into_subsets(args.subset_size)
# pick off the first one
if len(divvy) == 1:
start, end = 0, 0
else:
start, end = divvy[:2]
# partition!
print >>sys.stderr, 'doing pre-partitioning from', start, 'to', end
subset = htable.do_subset_partition(start, end)
# now, repartition...
print >>sys.stderr, 'repartitioning to find HCKs.'
htable.repartition_largest_partition(subset, counting,
EXCURSION_DISTANCE,
EXCURSION_KMER_THRESHOLD,
EXCURSION_KMER_COUNT_THRESHOLD)
print >>sys.stderr, 'saving stop tags'
htable.save_stop_tags(graphbase + '.stoptags')
print >> sys.stderr, 'wrote to:', graphbase + '.stoptags'
def main(args):
info('build-graph.py', ['graph', 'SeqAn'])
report_on_config(args, hashtype='hashbits')
base = args.output_filename
filenames = args.input_filenames
for fname in args.input_filenames:
check_input_files(fname, args.force)
check_space(args.input_filenames, args.force)
check_space_for_hashtable(
(float(args.n_tables * args.min_tablesize) / 8.), args.force)
print >>sys.stderr, 'Saving k-mer presence table to %s' % base
print >>sys.stderr, 'Loading kmers from sequences in %s' % repr(filenames)
if args.no_build_tagset:
print >>sys.stderr, 'We WILL NOT build the tagset.'
else:
print >>sys.stderr, 'We WILL build the tagset', \
' (for partitioning/traversal).'
print >>sys.stderr, 'making k-mer presence table'
htable = khmer.new_hashbits(args.ksize, args.min_tablesize, args.n_tables)
functions.build_graph(filenames, htable, args.threads,
not args.no_build_tagset)
print >> sys.stderr, 'Total number of unique k-mers: {0}'.format(
htable.n_unique_kmers())
print >>sys.stderr, 'saving k-mer presence table in', base + '.pt'
htable.save(base + '.pt')
if not args.no_build_tagset:
print >>sys.stderr, 'saving tagset in', base + '.tagset'
htable.save_tagset(base + '.tagset')
info_fp = open(base + '.info', 'w')
info_fp.write('%d unique k-mers' % htable.n_unique_kmers())
fp_rate = \
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.15)
# 0.18 is ACTUAL MAX. Do not change.
print >>sys.stderr, 'false positive rate estimated to be %1.3f' % fp_rate
print >>info_fp, '\nfalse positive rate estimated to be %1.3f' % fp_rate
print >> sys.stderr, 'wrote to', base + '.info and', base + '.pt'
if not args.no_build_tagset:
print >> sys.stderr, 'and ' + base + '.tagset'
sys.exit(0)
def main():
info('filter-abund.py', ['counting'])
args = get_parser().parse_args()
check_input_files(args.input_table, args.force)
infiles = args.input_filename
for filename in infiles:
check_input_files(filename, args.force)
check_space(infiles, args.force)
print('loading counting table:', args.input_table,
file=sys.stderr)
htable = khmer.load_counting_hash(args.input_table)
ksize = htable.ksize()
print("K:", ksize, file=sys.stderr)
# the filtering function.
def process_fn(record):
name = record.name
seq = record.sequence
seqN = seq.replace('N', 'A')
if args.variable_coverage: # only trim when sequence has high enough C
med, _, _ = htable.get_median_count(seqN)
if med < args.normalize_to:
return name, seq
_, trim_at = htable.trim_on_abundance(seqN, args.cutoff)
if trim_at >= ksize:
# be sure to not to change the 'N's in the trimmed sequence -
# so, return 'seq' and not 'seqN'.
return name, seq[:trim_at]
return None, None
# the filtering loop
for infile in infiles:
print('filtering', infile, file=sys.stderr)
if args.single_output_filename != '':
outfile = args.single_output_filename
outfp = open(outfile, 'a')
else:
outfile = os.path.basename(infile) + '.abundfilt'
outfp = open(outfile, 'w')
tsp = ThreadedSequenceProcessor(process_fn, n_workers=args.threads)
tsp.start(verbose_loader(infile), outfp)
print('output in', outfile, file=sys.stderr)
def main():
info('filter-abund.py', ['counting'])
args = get_parser().parse_args()
counting_ht = args.input_table
infiles = args.input_filename
for _ in infiles:
check_file_status(_, args.force)
check_space(infiles, args.force)
print >>sys.stderr, 'loading hashtable'
htable = khmer.load_counting_hash(counting_ht)
ksize = htable.ksize()
print >>sys.stderr, "K:", ksize
# the filtering function.
def process_fn(record):
name = record['name']
seq = record['sequence']
if 'N' in seq:
return None, None
if args.variable_coverage: # only trim when sequence has high enough C
med, _, _ = htable.get_median_count(seq)
if med < args.normalize_to:
return name, seq
trim_seq, trim_at = htable.trim_on_abundance(seq, args.cutoff)
if trim_at >= ksize:
return name, trim_seq
return None, None
# the filtering loop
for infile in infiles:
print >>sys.stderr, 'filtering', infile
if args.single_output_filename != '':
outfile = args.single_output_filename
outfp = open(outfile, 'a')
else:
outfile = os.path.basename(infile) + '.abundfilt'
outfp = open(outfile, 'w')
tsp = ThreadedSequenceProcessor(process_fn, n_workers=args.threads)
tsp.start(verbose_loader(infile), outfp)
print >>sys.stderr, 'output in', outfile
def main():
info('interleave-reads.py')
args = sanitize_help(get_parser()).parse_args()
check_input_files(args.left, args.force)
check_input_files(args.right, args.force)
check_space([args.left, args.right], args.force)
s1_file = args.left
s2_file = args.right
fail = False
print("Interleaving:\n\t%s\n\t%s" % (s1_file, s2_file), file=sys.stderr)
outfp = get_file_writer(args.output, args.gzip, args.bzip)
counter = 0
screed_iter_1 = screed.open(s1_file)
screed_iter_2 = screed.open(s2_file)
for read1, read2 in zip_longest(screed_iter_1, screed_iter_2):
if read1 is None or read2 is None:
print(("ERROR: Input files contain different number"
" of records."), file=sys.stderr)
sys.exit(1)
if counter % 100000 == 0:
print('...', counter, 'pairs', file=sys.stderr)
counter += 1
name1 = read1.name
name2 = read2.name
if not args.no_reformat:
if not check_is_left(name1):
name1 += '/1'
if not check_is_right(name2):
name2 += '/2'
read1.name = name1
read2.name = name2
if not check_is_pair(read1, read2):
print("ERROR: This doesn't look like paired data! "
"%s %s" % (read1.name, read2.name), file=sys.stderr)
sys.exit(1)
write_record_pair(read1, read2, outfp)
print('final: interleaved %d pairs' % counter, file=sys.stderr)
print('output written to', describe_file_handle(outfp), file=sys.stderr)
def main():
args = sanitize_help(get_parser()).parse_args()
configure_logging(args.quiet)
infiles = args.input_filename
if ('-' in infiles or '/dev/stdin' in infiles) and not \
args.single_output_file:
log_error("Accepting input from stdin; output filename must "
"be provided with -o.")
sys.exit(1)
for filename in infiles:
check_input_files(filename, args.force)
check_space(infiles, args.force)
log_info('loading countgraph: {graph}', graph=args.input_graph)
countgraph = khmer.load_countgraph(args.input_graph)
ksize = countgraph.ksize()
log_info("K: {ksize}", ksize=ksize)
if args.single_output_file:
outfile = args.single_output_file.name
outfp = get_file_writer(args.single_output_file, args.gzip, args.bzip)
# the filtering loop
for infile in infiles:
log_info('filtering {infile}', infile=infile)
if not args.single_output_file:
outfile = os.path.basename(infile) + '.abundfilt'
outfp = open(outfile, 'wb')
outfp = get_file_writer(outfp, args.gzip, args.bzip)
paired_iter = broken_paired_reader(ReadParser(infile),
min_length=ksize,
force_single=True)
for n, is_pair, read1, read2 in paired_iter:
assert not is_pair
assert read2 is None
trimmed_record, _ = trim_record(countgraph, read1, args.cutoff,
args.variable_coverage,
args.normalize_to)
if trimmed_record:
write_record(trimmed_record, outfp)
log_info('output in {outfile}', outfile=outfile)
def main(args):
info("build-graph.py", ["graph", "SeqAn"])
report_on_config(args, hashtype="hashbits")
base = args.output_filename
filenames = args.input_filenames
for fname in args.input_filenames:
check_input_files(fname, args.force)
check_space(args.input_filenames, args.force)
check_space_for_hashtable((float(args.n_tables * args.min_tablesize) / 8.0), args.force)
print("Saving k-mer presence table to %s" % base, file=sys.stderr)
print("Loading kmers from sequences in %s" % repr(filenames), file=sys.stderr)
if args.no_build_tagset:
print("We WILL NOT build the tagset.", file=sys.stderr)
else:
print("We WILL build the tagset (for partitioning/traversal).", file=sys.stderr)
print("making k-mer presence table", file=sys.stderr)
htable = khmer.new_hashbits(args.ksize, args.min_tablesize, args.n_tables)
functions.build_graph(filenames, htable, args.threads, not args.no_build_tagset)
print("Total number of unique k-mers: {0}".format(htable.n_unique_kmers()), file=sys.stderr)
print("saving k-mer presence table in", base + ".pt", file=sys.stderr)
htable.save(base + ".pt")
if not args.no_build_tagset:
print("saving tagset in", base + ".tagset", file=sys.stderr)
htable.save_tagset(base + ".tagset")
info_fp = open(base + ".info", "w")
info_fp.write("%d unique k-mers" % htable.n_unique_kmers())
fp_rate = khmer.calc_expected_collisions(htable, args.force, max_false_pos=0.15)
# 0.18 is ACTUAL MAX. Do not change.
print("false positive rate estimated to be %1.3f" % fp_rate, file=sys.stderr)
print("\nfalse positive rate estimated to be %1.3f" % fp_rate, file=info_fp)
print("wrote to", base + ".info and", base + ".pt", file=sys.stderr)
if not args.no_build_tagset:
print("and " + base + ".tagset", file=sys.stderr)
sys.exit(0)
def main():
info('split-paired-reads.py')
args = get_parser().parse_args()
infile = args.infile
check_file_status(infile, args.force)
filenames = [infile]
check_space(filenames, args.force)
if args.output_directory:
if not os.path.exists(args.output_directory):
os.makedirs(args.output_directory)
out1 = args.output_directory + '/' + os.path.basename(infile) + '.1'
out2 = args.output_directory + '/' + os.path.basename(infile) + '.2'
else:
out1 = os.path.basename(infile) + '.1'
out2 = os.path.basename(infile) + '.2'
# OVERRIDE defaults with -1, -2
if args.output_first:
out1 = args.output_first
if args.output_second:
out2 = args.output_second
fp_out1 = open(out1, 'w')
fp_out2 = open(out2, 'w')
counter1 = 0
counter2 = 0
index = None
for index, record in enumerate(screed.open(infile)):
if index % 100000 == 0 and index:
print >> sys.stderr, '...', index
name = record.name
if name.endswith('/1'):
write_record(record, fp_out1)
counter1 += 1
elif name.endswith('/2'):
write_record(record, fp_out2)
counter2 += 1
print >> sys.stderr, "DONE; split %d sequences (%d left, %d right)" % \
(index + 1, counter1, counter2)
print >> sys.stderr, "/1 reads in %s" % out1
print >> sys.stderr, "/2 reads in %s" % out2
def main():
info('extract-paired-reads.py')
args = get_parser().parse_args()
check_input_files(args.infile, args.force)
infiles = [args.infile]
check_space(infiles, args.force)
outfile = os.path.basename(args.infile)
if len(sys.argv) > 2:
outfile = sys.argv[2]
single_fp = open(outfile + '.se', 'w')
paired_fp = open(outfile + '.pe', 'w')
print >>sys.stderr, 'reading file "%s"' % args.infile
print >>sys.stderr, 'outputting interleaved pairs to "%s.pe"' % outfile
print >>sys.stderr, 'outputting orphans to "%s.se"' % outfile
n_pe = 0
n_se = 0
screed_iter = screed.open(args.infile, parse_description=False)
for index, is_pair, read1, read2 in broken_paired_reader(screed_iter):
if index % 100000 == 0 and index > 0:
print >>sys.stderr, '...', index
if is_pair:
write_record_pair(read1, read2, paired_fp)
n_pe += 1
else:
write_record(read1, single_fp)
n_se += 1
single_fp.close()
paired_fp.close()
if n_pe == 0:
raise Exception("no paired reads!? check file formats...")
print >>sys.stderr, 'DONE; read %d sequences,' \
' %d pairs and %d singletons' % \
(n_pe * 2 + n_se, n_pe, n_se)
print >> sys.stderr, 'wrote to: ' + outfile \
+ '.se' + ' and ' + outfile + '.pe'
def main():
info('count-median.py', ['diginorm'])
args = get_parser().parse_args()
htfile = args.ctfile
input_filename = args.input
output_filename = args.output
infiles = [htfile, input_filename]
for infile in infiles:
check_input_files(infile, args.force)
check_space(infiles, args.force)
print('loading k-mer counting table from', htfile, file=sys.stderr)
htable = khmer.load_counting_hash(htfile)
ksize = htable.ksize()
print('writing to', output_filename, file=sys.stderr)
output = open(output_filename, 'w')
if args.csv:
output = csv.writer(output)
# write headers:
output.writerow(['name', 'median', 'average', 'stddev', 'seqlen'])
parse_description = True # @legacy behavior: split seq headers
if args.csv:
parse_description = False # only enable if we're doing csv out
for record in screed.open(input_filename,
parse_description=parse_description):
seq = record.sequence.upper()
if 'N' in seq:
seq = seq.replace('N', 'A')
if ksize <= len(seq):
medn, ave, stdev = htable.get_median_count(seq)
ave, stdev = [round(x, 9) for x in (ave, stdev)]
if args.csv:
output.writerow([record.name, medn, ave, stdev, len(seq)])
else:
print(record.name, medn, ave, stdev, len(seq), file=output)
def main():
info('count-overlap.py', ['counting'])
args = get_parser().parse_args()
report_on_config(args, hashtype='hashbits')
for infile in [args.ptfile, args.fafile]:
check_input_files(infile, args.force)
check_space([args.ptfile, args.fafile], args.force)
print('loading k-mer presence table from', args.ptfile, file=sys.stderr)
ht1 = khmer.load_hashbits(args.ptfile)
kmer_size = ht1.ksize()
output = open(args.report_filename, 'w')
f_curve_obj = open(args.report_filename + '.curve', 'w')
if args.csv:
f_curve_obj_csv = csv.writer(f_curve_obj)
# write headers:
f_curve_obj_csv.writerow(['input_seq', 'overlap_kmer'])
ht2 = khmer.new_hashbits(kmer_size, args.min_tablesize, args.n_tables)
(n_unique, n_overlap, list_curve) = ht2.count_overlap(args.fafile, ht1)
printout1 = """\
dataset1(pt file): %s
dataset2: %s
# of unique k-mers in dataset2: %d
# of overlap unique k-mers: %d
""" % (args.ptfile, args.fafile, n_unique, n_overlap)
output.write(printout1)
for i in range(100):
if args.csv:
f_curve_obj_csv.writerow([list_curve[100 + i], list_curve[i]])
else:
print(list_curve[100 + i], list_curve[i], file=f_curve_obj)
print('wrote to: ' + args.report_filename, file=sys.stderr)
def main():
info('filter-stoptags.py', ['graph'])
args = 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 >>sys.stderr, 'loading stop tags, with K', args.ksize
htable = khmer.new_hashbits(args.ksize, 1, 1)
htable.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 = htable.trim_on_stoptags(seq)
if trim_at >= args.ksize:
return name, trim_seq
return None, None
# the filtering loop
for infile in infiles:
print >>sys.stderr, 'filtering', infile
outfile = os.path.basename(infile) + '.stopfilt'
outfp = open(outfile, 'w')
tsp = ThreadedSequenceProcessor(process_fn)
tsp.start(verbose_loader(infile), outfp)
print >>sys.stderr, 'output in', outfile
def main():
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 main():
info('merge-stoptags.py')
args = get_parser().parse_args()
stdbase = args.stdbase
# @RamRS: This might need some more work
infiles = []
for _ in glob.glob(stdbase + "*/*.stoptags") :
if os.path.exists(_):
check_input_files(_, False)
infiles.append(_)
check_space(infiles, False)
ht = khmer.new_hashbits(args.ksize, 1, 1)
for _ in infiles:
print >>sys.stderr, 'loading stoptags %s' % _
ht.load_stop_tags(_, 0)
print >>sys.stderr, 'writing file merge.stoptags'
ht.save_stop_tags('merge.stoptags')
print >>sys.stderr, 'done!'
def main():
info('count-overlap.py', ['counting'])
args = get_parser().parse_args()
report_on_config(args, hashtype='hashbits')
for infile in [args.ptfile, args.fafile]:
check_file_status(infile, args.force)
check_space([args.ptfile, args.fafile], args.force)
print >>sys.stderr, 'loading k-mer presence table from', args.ptfile
ht1 = khmer.load_hashbits(args.ptfile)
kmer_size = ht1.ksize()
output = open(args.report_filename, 'w')
f_curve_obj = open(args.report_filename + '.curve', 'w')
ht2 = khmer.new_hashbits(kmer_size, args.min_tablesize, args.n_tables)
(n_unique, n_overlap, list_curve) = ht2.count_overlap(args.fafile, ht1)
printout1 = """\
dataset1(pt file): %s
dataset2: %s
# of unique k-mers in dataset2: %d
# of overlap unique k-mers: %d
""" % (args.ptfile, args.fafile, n_unique, n_overlap)
output.write(printout1)
for i in range(100):
to_print = str(list_curve[100 + i]) + ' ' + str(list_curve[i]) + '\n'
f_curve_obj.write(to_print)
print >> sys.stderr, 'wrote to: ' + args.report_filename
def main():
info('interleave-reads.py')
args = get_parser().parse_args()
for _ in args.infiles:
check_input_files(_, args.force)
check_space(args.infiles, args.force)
s1_file = args.infiles[0]
if len(args.infiles) == 2:
s2_file = args.infiles[1]
else:
s2_file = s1_file.replace('_R1_', '_R2_')
if s1_file == s2_file:
print >>sys.stderr, ("ERROR: given only one filename, that "
"doesn't contain _R1_. Exiting.")
sys.exit(1)
print >> sys.stderr, ("given only one file; "
"guessing that R2 file is %s" % s2_file)
fail = False
if not os.path.exists(s1_file):
print >> sys.stderr, "Error! R1 file %s does not exist" % s1_file
fail = True
if not os.path.exists(s2_file):
print >> sys.stderr, "Error! R2 file %s does not exist" % s2_file
fail = True
if fail and not args.force:
sys.exit(1)
print >> sys.stderr, "Interleaving:\n\t%s\n\t%s" % (s1_file, s2_file)
counter = 0
screed_iter_1 = screed.open(s1_file, parse_description=False)
screed_iter_2 = screed.open(s2_file, parse_description=False)
for read1, read2 in itertools.izip_longest(screed_iter_1, screed_iter_2):
if read1 is None or read2 is None:
print >>sys.stderr, ("ERROR: Input files contain different number"
" of records.")
sys.exit(1)
if counter % 100000 == 0:
print >> sys.stderr, '...', counter, 'pairs'
counter += 1
name1 = read1.name
if not check_is_left(name1):
name1 += '/1'
name2 = read2.name
if not check_is_right(name2):
name2 += '/2'
read1.name = name1
read2.name = name2
if not check_is_pair(read1, read2):
print >>sys.stderr, "ERROR: This doesn't look like paired data! " \
"%s %s" % (read1.name, read2.name)
sys.exit(1)
write_record_pair(read1, read2, args.output)
print >> sys.stderr, 'final: interleaved %d pairs' % counter
print >> sys.stderr, 'output written to', args.output.name
def main(): # pylint: disable=too-many-branches,too-many-statements
info('normalize-by-median.py', ['diginorm'])
args = get_parser().parse_args()
report_on_config(args)
report_fp = args.report
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, args.force)
if args.savetable:
check_space_for_hashtable(args.n_tables * args.min_tablesize,
args.force)
# list to save error files along with throwing exceptions
if args.force:
corrupt_files = []
if args.loadtable:
print 'loading k-mer counting table from', args.loadtable
htable = khmer.load_counting_hash(args.loadtable)
else:
print 'making k-mer counting table'
htable = khmer.new_counting_hash(args.ksize, args.min_tablesize,
args.n_tables)
total = 0
discarded = 0
input_filename = None
for index, input_filename in enumerate(args.input_filenames):
if args.single_output_filename != '':
output_name = args.single_output_filename
outfp = open(args.single_output_filename, 'a')
else:
output_name = os.path.basename(input_filename) + '.keep'
outfp = open(output_name, 'w')
total_acc = 0
discarded_acc = 0
try:
total_acc, discarded_acc = normalize_by_median(
input_filename, outfp, htable, args, report_fp)
except IOError as err:
handle_error(err, output_name, input_filename, args.fail_save,
htable)
if not args.force:
print >> sys.stderr, '** Exiting!'
sys.exit(1)
else:
print >> sys.stderr, '*** Skipping error file, moving on...'
corrupt_files.append(input_filename)
else:
if total_acc == 0 and discarded_acc == 0:
print 'SKIPPED empty file', input_filename
else:
total += total_acc
discarded += discarded_acc
print 'DONE with {inp}; kept {kept} of {total} or {perc:2}%'\
.format(inp=input_filename, kept=total - discarded,
total=total, perc=int(100. - discarded /
float(total) * 100.))
print 'output in', output_name
if (args.dump_frequency > 0 and index > 0
and index % args.dump_frequency == 0):
print 'Backup: Saving k-mer counting file through', input_filename
if args.savetable:
hashname = args.savetable
print '...saving to', hashname
else:
hashname = 'backup.ct'
print 'Nothing given for savetable, saving to', hashname
htable.save(hashname)
if args.report_total_kmers:
print >> sys.stderr, 'Total number of unique k-mers: {0}'.format(
htable.n_unique_kmers())
if args.savetable:
print 'Saving k-mer counting table through', input_filename
print '...saving to', args.savetable
htable.save(args.savetable)
fp_rate = khmer.calc_expected_collisions(htable)
print 'fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate)
if args.force and len(corrupt_files) > 0:
print >> sys.stderr, "** WARNING: Finished with errors!"
print >> sys.stderr, "** IOErrors occurred in the following files:"
print >> sys.stderr, "\t", " ".join(corrupt_files)
if fp_rate > MAX_FALSE_POSITIVE_RATE:
print >> sys.stderr, "**"
print >> sys.stderr, ("** ERROR: the k-mer counting table is too small"
" for this data set. Increase tablesize/# "
"tables.")
print >> sys.stderr, "**"
print >> sys.stderr, "** Do not use these results!!"
if not args.force:
sys.exit(1)
def main(): # pylint: disable=too-many-locals,too-many-statements
args = sanitize_help(get_parser()).parse_args()
report_on_config(args, graphtype='nodegraph')
for infile in args.input_filenames:
check_input_files(infile, args.force)
check_space(args.input_filenames, args.force)
print('Saving k-mer nodegraph to %s' %
args.graphbase, file=sys.stderr)
print('Loading kmers from sequences in %s' %
repr(args.input_filenames), file=sys.stderr)
print('--', file=sys.stderr)
print('SUBSET SIZE', args.subset_size, file=sys.stderr)
print('N THREADS', args.threads, file=sys.stderr)
print('--', file=sys.stderr)
# load-graph.py
print('making nodegraph', file=sys.stderr)
nodegraph = khmer_args.create_nodegraph(args)
for _, filename in enumerate(args.input_filenames):
print('consuming input', filename, file=sys.stderr)
nodegraph.consume_fasta_and_tag(filename)
# 0.18 is ACTUAL MAX. Do not change.
fp_rate = \
khmer.calc_expected_collisions(
nodegraph, args.force, max_false_pos=.15)
print('fp rate estimated to be %1.3f' % fp_rate, file=sys.stderr)
# partition-graph
# do we want to exhaustively traverse the graph?
stop_big_traversals = args.no_big_traverse
if stop_big_traversals:
print('** This script brakes for lumps: ',
'stop_big_traversals is true.', file=sys.stderr)
else:
print('** Traverse all the things:',
' stop_big_traversals is false.', file=sys.stderr)
#
# now, partition!
#
# divide the tags up into subsets
divvy = nodegraph.divide_tags_into_subsets(int(args.subset_size))
divvy = list(divvy)
n_subsets = len(divvy)
divvy.append(0)
# build a queue of tasks:
worker_q = queue.Queue()
# break up the subsets into a list of worker tasks
for _ in range(0, n_subsets):
start = divvy[_]
end = divvy[_ + 1]
worker_q.put((nodegraph, _, start, end))
print('enqueued %d subset tasks' % n_subsets, file=sys.stderr)
open('%s.info' % args.graphbase, 'w').write('%d subsets total\n'
% (n_subsets))
if n_subsets < args.threads:
args.threads = n_subsets
# start threads!
print('starting %d threads' % args.threads, file=sys.stderr)
print('---', file=sys.stderr)
threads = []
for _ in range(args.threads):
cur_thread = threading.Thread(target=worker,
args=(worker_q, args.graphbase,
stop_big_traversals))
threads.append(cur_thread)
cur_thread.start()
print('done starting threads', file=sys.stderr)
# wait for threads
for _ in threads:
_.join()
print('---', file=sys.stderr)
print('done making subsets! see %s.subset.*.pmap' %
(args.graphbase,), file=sys.stderr)
# merge-partitions
pmap_files = glob.glob(args.graphbase + '.subset.*.pmap')
print('loading %d pmap files (first one: %s)' %
(len(pmap_files), pmap_files[0]), file=sys.stderr)
nodegraph = khmer.Nodegraph(args.ksize, 1, 1)
for pmap_file in pmap_files:
print('merging', pmap_file, file=sys.stderr)
nodegraph.merge_subset_from_disk(pmap_file)
if args.remove_subsets:
print('removing pmap files', file=sys.stderr)
for pmap_file in pmap_files:
os.unlink(pmap_file)
# annotate-partitions
for infile in args.input_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 main():
info('split-paired-reads.py')
args = sanitize_help(get_parser()).parse_args()
infile = args.infile
filenames = [infile]
check_input_files(infile, args.force)
check_space(filenames, args.force)
basename = os.path.basename(infile)
# decide where to put output files - specific directory? or just default?
if infile in ('/dev/stdin', '-'):
if not (args.output_first and args.output_second):
print(
"Accepting input from stdin; "
"output filenames must be provided.",
file=sys.stderr)
sys.exit(1)
elif args.output_directory:
if not os.path.exists(args.output_directory):
os.makedirs(args.output_directory)
out1 = os.path.join(args.output_directory, basename + '.1')
out2 = os.path.join(args.output_directory, basename + '.2')
else:
out1 = basename + '.1'
out2 = basename + '.2'
# OVERRIDE output file locations with -1, -2
if args.output_first:
fp_out1 = get_file_writer(args.output_first, args.gzip, args.bzip)
out1 = fp_out1.name
else:
# Use default filename created above
fp_out1 = get_file_writer(open(out1, 'wb'), args.gzip, args.bzip)
if args.output_second:
fp_out2 = get_file_writer(args.output_second, args.gzip, args.bzip)
out2 = fp_out2.name
else:
# Use default filename created above
fp_out2 = get_file_writer(open(out2, 'wb'), args.gzip, args.bzip)
# put orphaned reads here, if -0!
if args.output_orphaned:
fp_out0 = get_file_writer(args.output_orphaned, args.gzip, args.bzip)
out0 = describe_file_handle(args.output_orphaned)
counter1 = 0
counter2 = 0
counter3 = 0
index = None
screed_iter = screed.open(infile)
# walk through all the reads in broken-paired mode.
paired_iter = broken_paired_reader(screed_iter,
require_paired=not args.output_orphaned)
try:
for index, is_pair, record1, record2 in paired_iter:
if index % 10000 == 0:
print('...', index, file=sys.stderr)
if is_pair:
write_record(record1, fp_out1)
counter1 += 1
write_record(record2, fp_out2)
counter2 += 1
elif args.output_orphaned:
write_record(record1, fp_out0)
counter3 += 1
except UnpairedReadsError as e:
print("Unpaired reads found starting at {name}; exiting".format(
name=e.r1.name),
file=sys.stderr)
sys.exit(1)
print("DONE; split %d sequences (%d left, %d right, %d orphans)" %
(counter1 + counter2, counter1, counter2, counter3),
file=sys.stderr)
print("/1 reads in %s" % out1, file=sys.stderr)
print("/2 reads in %s" % out2, file=sys.stderr)
if args.output_orphaned:
print("orphans in %s" % out0, file=sys.stderr)
def main():
args = sanitize_help(get_parser()).parse_args()
if not args.quiet:
info('filter-abund-single.py', ['counting', 'SeqAn'])
configure_logging(args.quiet)
check_input_files(args.datafile, args.force)
check_space([args.datafile], args.force)
if args.savegraph:
tablesize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(args.savegraph, tablesize, args.force)
report_on_config(args)
log_info('making countgraph')
graph = khmer_args.create_countgraph(args)
# first, load reads into graph
rparser = khmer.ReadParser(args.datafile)
threads = []
log_info('consuming input, round 1 -- {datafile}', datafile=args.datafile)
for _ in range(args.threads):
cur_thread = \
threading.Thread(
target=graph.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(cur_thread)
cur_thread.start()
for _ in threads:
_.join()
log_info('Total number of unique k-mers: {nk}', nk=graph.n_unique_kmers())
fp_rate = khmer.calc_expected_collisions(graph, args.force)
log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
# the filtering loop
log_info('filtering {datafile}', datafile=args.datafile)
if args.outfile is None:
outfile = os.path.basename(args.datafile) + '.abundfilt'
else:
outfile = args.outfile
outfp = open(outfile, 'wb')
outfp = get_file_writer(outfp, args.gzip, args.bzip)
screed_iter = screed.open(args.datafile)
paired_iter = broken_paired_reader(screed_iter, min_length=graph.ksize(),
force_single=True)
for n, is_pair, read1, read2 in paired_iter:
assert not is_pair
assert read2 is None
trimmed_record, _ = trim_record(graph, read1, args.cutoff,
args.variable_coverage,
args.normalize_to)
if trimmed_record:
print((trimmed_record,))
write_record(trimmed_record, outfp)
log_info('output in {outfile}', outfile=outfile)
if args.savegraph:
log_info('Saving k-mer countgraph filename {graph}',
graph=args.savegraph)
graph.save(args.savegraph)
def main(): # pylint: disable=too-many-branches,too-many-statements
info('saturate-by-median.py', ['diginorm'])
args = get_parser().parse_args()
report_on_config(args)
report_fp = args.report
report_frequency = args.report_frequency
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, False)
if args.savetable:
check_space_for_hashtable(args.n_tables * args.min_tablesize, False)
# list to save error files along with throwing exceptions
if args.force:
corrupt_files = []
if args.loadtable:
print 'loading k-mer counting table from', args.loadtable
htable = khmer.load_counting_hash(args.loadtable)
else:
print 'making k-mer counting table'
htable = khmer.new_counting_hash(args.ksize, args.min_tablesize,
args.n_tables)
total = 0
discarded = 0
for index, input_filename in enumerate(args.input_filenames):
total_acc = 0
discarded_acc = 0
try:
total_acc, discarded_acc = normalize_by_median(
input_filename, htable, args, report_fp, report_frequency)
except IOError as err:
handle_error(err, input_filename)
if not args.force:
print >> sys.stderr, '** Exiting!'
sys.exit(1)
else:
print >> sys.stderr, '*** Skipping error file, moving on...'
corrupt_files.append(input_filename)
else:
if total_acc == 0 and discarded_acc == 0:
print 'SKIPPED empty file', input_filename
else:
total += total_acc
discarded += discarded_acc
print 'DONE with {inp}; kept {kept} of {total} or {perc:2}%'\
.format(inp=input_filename,
kept=total - discarded, total=total,
perc=int(100. - discarded / float(total) * 100.))
if args.savetable:
print 'Saving k-mer counting table through', input_filename
print '...saving to', args.savetable
htable.save(args.savetable)
fp_rate = khmer.calc_expected_collisions(htable)
print 'fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate)
if args.force and len(corrupt_files) > 0:
print >> sys.stderr, "** WARNING: Finished with errors!"
print >> sys.stderr, "** IOErrors occurred in the following files:"
print >> sys.stderr, "\t", " ".join(corrupt_files)
if fp_rate > MAX_FALSE_POSITIVE_RATE:
print >> sys.stderr, "**"
print >> sys.stderr, ("** ERROR: the k-mer counting table is too small"
" for this data set. Increase tablesize/# "
"tables.")
print >> sys.stderr, "**"
print >> sys.stderr, "** Do not use these results!!"
sys.exit(1)
def main():
args = sanitize_help(get_parser()).parse_args()
if not args.quiet:
info('filter-abund-single.py', ['counting', 'SeqAn'])
configure_logging(args.quiet)
check_input_files(args.datafile, args.force)
check_space([args.datafile], args.force)
if args.savegraph:
tablesize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(args.savegraph, tablesize, args.force)
report_on_config(args)
log_info('making countgraph')
graph = khmer_args.create_countgraph(args)
# first, load reads into graph
rparser = khmer.ReadParser(args.datafile)
threads = []
log_info('consuming input, round 1 -- {datafile}', datafile=args.datafile)
for _ in range(args.threads):
cur_thread = \
threading.Thread(
target=graph.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(cur_thread)
cur_thread.start()
for _ in threads:
_.join()
log_info('Total number of unique k-mers: {nk}', nk=graph.n_unique_kmers())
fp_rate = khmer.calc_expected_collisions(graph, args.force)
log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
# now, trim.
# the filtering function.
def process_fn(record):
name = record.name
seq = record.sequence
seqN = seq.replace('N', 'A')
_, trim_at = graph.trim_on_abundance(seqN, args.cutoff)
if trim_at >= args.ksize:
# be sure to not to change the 'N's in the trimmed sequence -
# so, return 'seq' and not 'seqN'.
return name, seq[:trim_at]
return None, None
# the filtering loop
log_info('filtering {datafile}', datafile=args.datafile)
if args.outfile is None:
outfile = os.path.basename(args.datafile) + '.abundfilt'
else:
outfile = args.outfile
outfp = open(outfile, 'wb')
outfp = get_file_writer(outfp, args.gzip, args.bzip)
tsp = ThreadedSequenceProcessor(process_fn, verbose=not args.quiet)
tsp.start(verbose_loader(args.datafile), outfp)
log_info('output in {outfile}', outfile=outfile)
if args.savegraph:
log_info('Saving k-mer countgraph filename {graph}',
graph=args.savegraph)
graph.save(args.savegraph)
def main():
info('collect-reads.py', ['counting'])
args = get_parser().parse_args()
report_on_config(args)
base = args.output_countingtable_filename
filenames = args.input_sequence_filename
for name in args.input_sequence_filename:
check_input_files(name, False)
check_space(args.input_sequence_filename, False)
check_space_for_hashtable(args.n_tables * args.min_tablesize, False)
print 'Saving k-mer counting table to %s' % base
print 'Loading sequences from %s' % repr(filenames)
if args.output:
print 'Outputting sequences to', args.output
print 'making k-mer counting table'
htable = khmer.new_counting_hash(args.ksize, args.min_tablesize)
htable.set_use_bigcount(args.bigcount)
total_coverage = 0.
n = 0
for index, filename in enumerate(filenames):
for record in screed.open(filename):
seq = record.sequence.upper()
if 'N' in seq:
seq = seq.replace('N', 'G')
try:
med, _, _ = htable.get_median_count(seq)
except ValueError:
continue
total_coverage += med
n += 1
if total_coverage / float(n) > args.coverage:
print 'reached target average coverage:', \
total_coverage / float(n)
break
htable.consume(seq)
if args.output:
args.output.write(output_single(record))
if n % 100000 == 0:
print '...', index, filename, n, total_coverage / float(n)
if total_coverage / float(n) > args.coverage:
break
print 'Collected %d reads' % (n, )
if args.report_total_kmers:
print >> sys.stderr, 'Total number of k-mers: {0}'.format(
htable.n_occupied())
print 'saving', base
htable.save(base)
info_fp = open(base + '.info', 'w')
info_fp.write('through end: %s\n' % filenames[-1])
# Change 0.2 only if you really grok it. HINT: You don't.
fp_rate = khmer.calc_expected_collisions(htable,
args.force,
max_false_pos=.2)
print 'fp rate estimated to be %1.3f' % fp_rate
print >> info_fp, 'fp rate estimated to be %1.3f' % fp_rate
print 'DONE.'
def main(): # pylint: disable=too-many-locals,too-many-branches
info('abundance-dist-single.py', ['counting', 'SeqAn'])
args = get_parser().parse_args()
report_on_config(args)
check_file_status(args.input_sequence_filename, args.force)
check_space([args.input_sequence_filename], args.force)
if args.savetable:
check_space_for_hashtable(args.n_tables * args.min_tablesize,
args.force)
if (not args.squash_output and
os.path.exists(args.output_histogram_filename)):
print >> sys.stderr, 'ERROR: %s exists; not squashing.' % \
args.output_histogram_filename
sys.exit(1)
else:
hist_fp = open(args.output_histogram_filename, 'w')
print >>sys.stderr, 'making k-mer counting table'
counting_hash = khmer.new_counting_hash(args.ksize, args.min_tablesize,
args.n_tables)
counting_hash.set_use_bigcount(args.bigcount)
print >> sys.stderr, 'building k-mer tracking table'
tracking = khmer.new_hashbits(counting_hash.ksize(), args.min_tablesize,
args.n_tables)
print >>sys.stderr, 'kmer_size:', counting_hash.ksize()
print >>sys.stderr, 'k-mer counting table sizes:', \
counting_hash.hashsizes()
print >>sys.stderr, 'outputting to', args.output_histogram_filename
# start loading
rparser = khmer.ReadParser(args.input_sequence_filename)
threads = []
print >>sys.stderr, 'consuming input, round 1 --', \
args.input_sequence_filename
for _ in xrange(args.threads):
thread = \
threading.Thread(
target=counting_hash.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(thread)
thread.start()
for thread in threads:
thread.join()
if args.report_total_kmers:
print >> sys.stderr, 'Total number of unique k-mers: {0}'.format(
counting_hash.n_unique_kmers())
abundance_lists = []
def __do_abundance_dist__(read_parser):
abundances = counting_hash.abundance_distribution_with_reads_parser(
read_parser, tracking)
abundance_lists.append(abundances)
print >>sys.stderr, 'preparing hist from %s...' % \
args.input_sequence_filename
rparser = khmer.ReadParser(args.input_sequence_filename)
threads = []
print >>sys.stderr, 'consuming input, round 2 --', \
args.input_sequence_filename
for _ in xrange(args.threads):
thread = \
threading.Thread(
target=__do_abundance_dist__,
args=(rparser, )
)
threads.append(thread)
thread.start()
for thread in threads:
thread.join()
assert len(abundance_lists) == args.threads, len(abundance_lists)
abundance = {}
for abundance_list in abundance_lists:
for i, count in enumerate(abundance_list):
abundance[i] = abundance.get(i, 0) + count
total = sum(abundance.values())
if 0 == total:
print >> sys.stderr, \
"ERROR: abundance distribution is uniformly zero; " \
"nothing to report."
print >> sys.stderr, "\tPlease verify that the input files are valid."
sys.exit(1)
sofar = 0
for _, i in sorted(abundance.items()):
if i == 0 and not args.output_zero:
continue
sofar += i
frac = sofar / float(total)
print >> hist_fp, _, i, sofar, round(frac, 3)
if sofar == total:
break
if args.savetable:
print >>sys.stderr, 'Saving k-mer counting table ', args.savetable
print >>sys.stderr, '...saving to', args.savetable
counting_hash.save(args.savetable)
print >> sys.stderr, 'wrote to: ' + args.output_histogram_filename
def main():
parser = get_parser()
parser.epilog = parser.epilog.replace(
":doc:`partitioning-big-data`",
"http://khmer.readthedocs.io/en/stable/user/"
"partitioning-big-data.html")
args = sanitize_help(parser).parse_args()
graphbase = args.graphbase
# @RamRS: This might need some more work
infiles = [graphbase, graphbase + '.tagset']
if os.path.exists(graphbase + '.stoptags'):
infiles.append(graphbase + '.stoptags')
for _ in infiles:
check_input_files(_, args.force)
check_space(infiles, args.force)
print('loading k-mer nodegraph %s' % graphbase, file=sys.stderr)
graph = khmer.load_nodegraph(graphbase)
print('loading tagset %s.tagset...' % graphbase, file=sys.stderr)
graph.load_tagset(graphbase + '.tagset')
initial_stoptags = False # @CTB regularize with make-initial
if os.path.exists(graphbase + '.stoptags'):
print('loading stoptags %s.stoptags' % graphbase, file=sys.stderr)
graph.load_stop_tags(graphbase + '.stoptags')
initial_stoptags = True
pmap_files = glob.glob(args.graphbase + '.subset.*.pmap')
print('loading %d pmap files (first one: %s)' %
(len(pmap_files), pmap_files[0]),
file=sys.stderr)
print('---', file=sys.stderr)
print('output stoptags will be in',
graphbase + '.stoptags',
file=sys.stderr)
if initial_stoptags:
print('(these output stoptags will include the already-loaded set)',
file=sys.stderr)
print('---', file=sys.stderr)
# create countgraph
ksize = graph.ksize()
counting = khmer_args.create_countgraph(args, ksize=ksize)
# load & merge
for index, subset_file in enumerate(pmap_files):
print('<-', subset_file, file=sys.stderr)
subset = graph.load_subset_partitionmap(subset_file)
print('** repartitioning subset... %s' % subset_file, file=sys.stderr)
graph.repartition_largest_partition(subset, counting,
EXCURSION_DISTANCE,
EXCURSION_KMER_THRESHOLD,
EXCURSION_KMER_COUNT_THRESHOLD)
print('** merging subset... %s' % subset_file, file=sys.stderr)
graph.merge_subset(subset)
print('** repartitioning, round 2... %s' % subset_file,
file=sys.stderr)
size = graph.repartition_largest_partition(
None, counting, EXCURSION_DISTANCE, EXCURSION_KMER_THRESHOLD,
EXCURSION_KMER_COUNT_THRESHOLD)
print('** repartitioned size:', size, file=sys.stderr)
print('saving stoptags binary', file=sys.stderr)
graph.save_stop_tags(graphbase + '.stoptags')
os.rename(subset_file, subset_file + '.processed')
print('(%d of %d)\n' % (index, len(pmap_files)), file=sys.stderr)
print('done!', file=sys.stderr)
def main():
args = sanitize_help(get_parser()).parse_args()
distfilename = args.prefix + '.dist'
for infile in args.part_filenames:
check_input_files(infile, args.force)
check_space(args.part_filenames, args.force)
print('---', file=sys.stderr)
print('reading partitioned files:',
repr(args.part_filenames),
file=sys.stderr)
if args.output_groups:
print('outputting to files named "%s.groupN.fa"' % args.prefix,
file=sys.stderr)
print('min reads to keep a partition:',
args.min_part_size,
file=sys.stderr)
print('max size of a group file:', args.max_size, file=sys.stderr)
else:
print('NOT outputting groups! Beware!', file=sys.stderr)
if args.output_unassigned:
print('outputting unassigned reads to "%s.unassigned.fa"' %
args.prefix,
file=sys.stderr)
print('partition size distribution will go to %s' % distfilename,
file=sys.stderr)
print('---', file=sys.stderr)
#
suffix = None
is_fastq = None
with PartitionedReader(args.part_filenames, True, True) as reader:
for read, _ in reader:
if is_fastq is None:
is_fastq = hasattr(read, 'quality')
else:
assert hasattr(read, 'quality') == is_fastq,\
"Input files must have consistent format."
if is_fastq:
suffix = "fq"
else:
suffix = "fa"
# remember folks, generators exhaust themseleves
extractor = PartitionExtractor(args.part_filenames, args.min_part_size,
args.max_size)
if args.output_unassigned:
ofile = open('%s.unassigned.%s' % (args.prefix, suffix), 'wb')
unassigned_fp = get_file_writer(ofile, args.gzip, args.bzip)
extractor.process_unassigned(unassigned_fp)
unassigned_fp.close()
else:
extractor.process_unassigned()
extractor.output_histogram(distfilename)
if not args.output_groups:
sys.exit(0)
extractor.develop_groups()
print('%d groups' % extractor.group_n, file=sys.stderr)
if extractor.group_n == 0:
print('nothing to output; exiting!', file=sys.stderr)
return
# open a bunch of output files for the different groups
group_fps = {}
for index in range(extractor.group_n):
fname = '%s.group%04d.%s' % (args.prefix, index, suffix)
group_fp = get_file_writer(open(fname, 'wb'), args.gzip, args.bzip)
group_fps[index] = group_fp
# write 'em all out!
# refresh the generator
read_generator = PartitionExtractor.ReadGroupGenerator(extractor)
with PartitionedReader(args.part_filenames) as reader:
for read, group_n in read_generator(reader):
outfp = group_fps[group_n]
write_record(read, outfp)
print('---', file=sys.stderr)
print('Of %d total seqs,' % read_generator.total_seqs, file=sys.stderr)
print('extracted %d partitioned seqs into group files,' %
read_generator.part_seqs,
file=sys.stderr)
print('discarded %d sequences from small partitions (see -m),' %
read_generator.toosmall_parts,
file=sys.stderr)
print('and found %d unpartitioned sequences (see -U).' %
extractor.n_unassigned,
file=sys.stderr)
print('', file=sys.stderr)
print('Created %d group files named %s.groupXXXX.%s' %
(len(group_fps), args.prefix, suffix),
file=sys.stderr)
def main():
info('sweep-reads-buffered.py', ['sweep'])
parser = get_parser()
args = parser.parse_args()
if args.min_tablesize < MIN_HSIZE:
args.min_tablesize = MIN_HSIZE
if args.ksize < MIN_KSIZE:
args.ksize = MIN_KSIZE
report_on_config(args, hashtype='hashbits')
K = args.ksize
HT_SIZE = args.min_tablesize
N_HT = args.n_tables
traversal_range = args.traversal_range
input_fastp = args.input_fastp
if not args.outdir:
outdir = os.path.dirname(input_fastp)
else:
outdir = args.outdir
max_buffers = args.max_buffers
output_pref = args.output_prefix
buf_size = args.buffer_size
max_reads = args.max_reads
check_input_files(args.input_fastp, args.force)
check_valid_file_exists(args.input_files)
all_input_files = [input_fastp]
all_input_files.extend(args.input_files)
# Check disk space availability
check_space(all_input_files, args.force)
# figure out input file type (FA/FQ) -- based on first file
ix = iter(screed.open(args.input_files[0]))
record = ix.next()
del ix
extension = 'fa'
if hasattr(record, 'quality'): # fastq!
extension = 'fq'
output_buffer = ReadBufferManager(max_buffers, max_reads, buf_size,
output_pref, outdir, extension)
# consume the partitioned fasta with which to label the graph
ht = khmer.LabelHash(K, HT_SIZE, N_HT)
try:
print >> sys.stderr, 'consuming input sequences...'
if args.label_by_pid:
print >> sys.stderr, '...labeling by partition id (pid)'
ht.consume_partitioned_fasta_and_tag_with_labels(input_fastp)
elif args.label_by_seq:
print >> sys.stderr, '...labeling by sequence'
for n, record in enumerate(screed.open(input_fastp)):
if n % 50000 == 0:
print >>sys.stderr, \
'...consumed {n} sequences...'.format(n=n)
ht.consume_sequence_and_tag_with_labels(record.sequence, n)
else:
print >>sys.stderr, \
'...labeling to create groups of size {s}'.format(
s=args.group_size)
label = -1
g = 0
try:
outfp = open(
'{pref}_base_{g}.{ext}'.format(pref=output_pref,
g=g,
ext=extension), 'wb')
for n, record in enumerate(screed.open(input_fastp)):
if n % args.group_size == 0:
label += 1
if label > g:
g = label
outfp = open(
'{pref}_base_{g}.{ext}'.format(
pref=output_pref, g=g, ext=extension),
'wb')
if n % 50000 == 0:
print >>sys.stderr, \
'...consumed {n} sequences...'.format(n=n)
ht.consume_sequence_and_tag_with_labels(
record.sequence, label)
write_record(record, outfp)
except IOError as e:
print >> sys.stderr, '!! ERROR !!', e
print >> sys.stderr, '...error splitting input. exiting...'
except IOError as e:
print >> sys.stderr, '!! ERROR: !!', e
print >> sys.stderr, '...error consuming \
{i}. exiting...'.format(i=input_fastp)
print >> sys.stderr, 'done consuming input sequence. \
added {t} tags and {l} \
labels...'.format(t=ht.n_tags(), l=ht.n_labels())
label_dict = defaultdict(int)
label_number_dist = []
n_orphaned = 0
n_labeled = 0
n_mlabeled = 0
total_t = time.clock()
start_t = time.clock()
for read_file in args.input_files:
print >> sys.stderr, '** sweeping {read_file} for labels...'.format(
read_file=read_file)
file_t = 0.0
try:
read_fp = screed.open(read_file)
except IOError as error:
print >> sys.stderr, '!! ERROR: !!', error
print >> sys.stderr, '*** Could not open {fn}, skipping...'.format(
fn=read_file)
else:
for _, record in enumerate(read_fp):
if _ % 50000 == 0:
end_t = time.clock()
batch_t = end_t - start_t
file_t += batch_t
print >>sys.stderr, '\tswept {n} reads [{nc} labeled, \
{no} orphaned] \
** {sec}s ({sect}s total)' \
.format(n=_, nc=n_labeled,
no=n_orphaned,
sec=batch_t, sect=file_t)
start_t = time.clock()
seq = record.sequence
name = record.name
try:
labels = ht.sweep_label_neighborhood(seq, traversal_range)
except ValueError as e:
pass
else:
if hasattr(record, 'quality'):
seq_str = fmt_fastq(name, seq, record.quality, labels)
else:
seq_str = fmt_fasta(name, seq, labels)
label_number_dist.append(len(labels))
if labels:
n_labeled += 1
if len(labels) > 1:
output_buffer.queue(seq_str, 'multi')
n_mlabeled += 1
label_dict['multi'] += 1
else:
output_buffer.queue(seq_str, labels[0])
label_dict[labels[0]] += 1
else:
n_orphaned += 1
output_buffer.queue(seq_str, 'orphaned')
label_dict['orphaned'] += 1
print >> sys.stderr, '** End of file {fn}...'.format(fn=read_file)
output_buffer.flush_all()
read_fp.close()
# gotta output anything left in the buffers at the end!
print >> sys.stderr, '** End of run...'
output_buffer.flush_all()
total_t = time.clock() - total_t
if output_buffer.num_write_errors > 0 or output_buffer.num_file_errors > 0:
print >> sys.stderr, '! WARNING: Sweep finished with errors !'
print >> sys.stderr, '** {writee} reads not written'.format(
writee=output_buffer.num_write_errors)
print >> sys.stderr, '** {filee} errors opening files'.format(
filee=output_buffer.num_file_errors)
print >> sys.stderr, 'swept {n_reads} for labels...'.format(
n_reads=n_labeled + n_orphaned)
print >> sys.stderr, '...with {nc} labeled and {no} orphaned'.format(
nc=n_labeled, no=n_orphaned)
print >> sys.stderr, '...and {nmc} multilabeled'.format(nmc=n_mlabeled)
print >> sys.stderr, '** outputting label number distribution...'
fn = os.path.join(outdir, '{pref}.dist.txt'.format(pref=output_pref))
with open(fn, 'wb') as outfp:
for nc in label_number_dist:
outfp.write('{nc}\n'.format(nc=nc))
fn = os.path.join(outdir, '{pref}.counts.csv'.format(pref=output_pref))
print >> sys.stderr, '** outputting label read counts...'
with open(fn, 'wb') as outfp:
for k in label_dict:
outfp.write('{l},{c}\n'.format(l=k, c=label_dict[k]))
def main():
info('partition-graph.py', ['graph'])
args = get_parser().parse_args()
basename = args.basename
filenames = [basename + '.pt', basename + '.tagset']
for _ in filenames:
check_input_files(_, args.force)
check_space(filenames, args.force)
print >> sys.stderr, '--'
print >> sys.stderr, 'SUBSET SIZE', args.subset_size
print >> sys.stderr, 'N THREADS', args.threads
if args.stoptags:
print >> sys.stderr, 'stoptag file:', args.stoptags
print >> sys.stderr, '--'
print >> sys.stderr, 'loading ht %s.pt' % basename
htable = khmer.load_hashbits(basename + '.pt')
htable.load_tagset(basename + '.tagset')
# do we want to load stop tags, and do they exist?
if args.stoptags:
print >> sys.stderr, 'loading stoptags from', args.stoptags
htable.load_stop_tags(args.stoptags)
# do we want to exhaustively traverse the graph?
stop_big_traversals = args.no_big_traverse
if stop_big_traversals:
print >>sys.stderr, '** This script brakes for lumps:', \
' stop_big_traversals is true.'
else:
print >>sys.stderr, '** Traverse all the things:', \
' stop_big_traversals is false.'
#
# now, partition!
#
# divide the tags up into subsets
divvy = htable.divide_tags_into_subsets(int(args.subset_size))
n_subsets = len(divvy)
divvy.append(0)
# build a queue of tasks:
worker_q = Queue.Queue()
# break up the subsets into a list of worker tasks
for _ in range(0, n_subsets):
start = divvy[_]
end = divvy[_ + 1]
worker_q.put((htable, _, start, end))
print >> sys.stderr, 'enqueued %d subset tasks' % n_subsets
open('%s.info' % basename, 'w').write('%d subsets total\n' % (n_subsets))
n_threads = args.threads
if n_subsets < n_threads:
n_threads = n_subsets
# start threads!
print >> sys.stderr, 'starting %d threads' % n_threads
print >> sys.stderr, '---'
threads = []
for _ in range(n_threads):
cur_thrd = threading.Thread(target=worker,
args=(worker_q, basename,
stop_big_traversals))
threads.append(cur_thrd)
cur_thrd.start()
print >> sys.stderr, 'done starting threads'
# wait for threads
for _ in threads:
_.join()
print >> sys.stderr, '---'
print >>sys.stderr, 'done making subsets! see %s.subset.*.pmap' % \
(basename,)
def main(): # pylint: disable=too-many-locals,too-many-branches
info('extract-partitions.py', ['graph'])
args = get_parser().parse_args()
distfilename = args.prefix + '.dist'
n_unassigned = 0
for infile in args.part_filenames:
check_file_status(infile, args.force)
check_space(args.part_filenames, args.force)
print >> sys.stderr, '---'
print >> sys.stderr, 'reading partitioned files:', repr(
args.part_filenames)
if args.output_groups:
print >>sys.stderr, 'outputting to files named "%s.groupN.fa"' % \
args.prefix
print >>sys.stderr, 'min reads to keep a partition:', \
args.min_part_size
print >> sys.stderr, 'max size of a group file:', args.max_size
else:
print >> sys.stderr, 'NOT outputting groups! Beware!'
if args.output_unassigned:
print >>sys.stderr, \
'outputting unassigned reads to "%s.unassigned.fa"' % \
args.prefix
print >>sys.stderr, 'partition size distribution will go to %s' \
% distfilename
print >> sys.stderr, '---'
#
suffix = 'fa'
is_fastq = False
for index, read, pid in read_partition_file(args.part_filenames[0]):
if hasattr(read, 'quality'):
suffix = 'fq'
is_fastq = True
break
for filename in args.part_filenames:
for index, read, pid in read_partition_file(filename):
if is_fastq:
assert hasattr(read, 'quality'), \
"all input files must be FASTQ if the first one is"
else:
assert not hasattr(read, 'quality'), \
"all input files must be FASTA if the first one is"
break
if args.output_unassigned:
unassigned_fp = open('%s.unassigned.%s' % (args.prefix, suffix), 'w')
count = {}
for filename in args.part_filenames:
for index, read, pid in read_partition_file(filename):
if index % 100000 == 0:
print >> sys.stderr, '...', index
count[pid] = count.get(pid, 0) + 1
if pid == 0:
n_unassigned += 1
if args.output_unassigned:
write_record(read, unassigned_fp)
if args.output_unassigned:
unassigned_fp.close()
if 0 in count: # eliminate unpartitioned sequences
del count[0]
# develop histogram of partition sizes
dist = {}
for pid, size in count.items():
dist[size] = dist.get(size, 0) + 1
# output histogram
distfp = open(distfilename, 'w')
total = 0
wtotal = 0
for counter, index in sorted(dist.items()):
total += index
wtotal += counter * index
distfp.write('%d %d %d %d\n' % (counter, index, total, wtotal))
distfp.close()
if not args.output_groups:
sys.exit(0)
# sort groups by size
divvy = sorted(count.items(), key=lambda y: y[1])
divvy = [y for y in divvy if y[1] > args.min_part_size]
# divvy up into different groups, based on having max_size sequences
# in each group.
total = 0
group = set()
group_n = 0
group_d = {}
for partition_id, n_reads in divvy:
group.add(partition_id)
total += n_reads
if total > args.max_size:
for partition_id in group:
group_d[partition_id] = group_n
# print 'group_d', partition_id, group_n
group_n += 1
group = set()
total = 0
if group:
for partition_id in group:
group_d[partition_id] = group_n
# print 'group_d', partition_id, group_n
group_n += 1
print >> sys.stderr, '%d groups' % group_n
if group_n == 0:
print >> sys.stderr, 'nothing to output; exiting!'
return
# open a bunch of output files for the different groups
group_fps = {}
for _ in range(group_n):
group_fp = open('%s.group%04d.%s' % (args.prefix, _, suffix), 'w')
group_fps[_] = group_fp
# write 'em all out!
total_seqs = 0
part_seqs = 0
toosmall_parts = 0
for filename in args.part_filenames:
for index, read, partition_id in read_partition_file(filename):
total_seqs += 1
if index % 100000 == 0:
print >> sys.stderr, '...x2', index
if partition_id == 0:
continue
try:
group_n = group_d[partition_id]
except KeyError:
assert count[partition_id] <= args.min_part_size
toosmall_parts += 1
continue
outfp = group_fps[group_n]
write_record(read, outfp)
part_seqs += 1
print >> sys.stderr, '---'
print >> sys.stderr, 'Of %d total seqs,' % total_seqs
print >>sys.stderr, 'extracted %d partitioned seqs into group files,' % \
part_seqs
print >>sys.stderr, \
'discarded %d sequences from small partitions (see -m),' % \
toosmall_parts
print >>sys.stderr, 'and found %d unpartitioned sequences (see -U).' % \
n_unassigned
print >> sys.stderr, ''
print >>sys.stderr, 'Created %d group files named %s.groupXXXX.%s' % \
(len(group_fps),
args.prefix,
suffix)
def main(): # pylint: disable=too-many-branches,too-many-statements
parser = sanitize_help(get_parser())
args = parser.parse_args()
if not args.quiet:
info('normalize-by-median.py', ['diginorm'])
configure_logging(args.quiet)
report_on_config(args)
report_fp = args.report
force_single = args.force_single
# check for similar filenames
# if we're using a single output file only check for identical filenames
# otherwise, check for identical BASE names as well.
filenames = []
basenames = []
for pathfilename in args.input_filenames:
filenames.append(pathfilename)
if args.single_output_file:
continue # nothing more to worry about
basename = os.path.basename(pathfilename)
if basename in basenames:
log_error('ERROR: Duplicate filename--Cannot handle this!')
log_error('** Exiting!')
sys.exit(1)
basenames.append(basename)
# check that files exist and there is sufficient output disk space.
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, args.force)
if args.savegraph:
graphsize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(args.savegraph, graphsize, args.force)
# load or create counting table.
if args.loadgraph:
log_info('loading k-mer countgraph from {graph}', graph=args.loadgraph)
countgraph = khmer.load_countgraph(args.loadgraph)
else:
log_info('making countgraph')
countgraph = khmer_args.create_countgraph(args)
# create an object to handle diginorm of all files
norm = Normalizer(args.cutoff, countgraph)
with_diagnostics = WithDiagnostics(norm, report_fp, args.report_frequency)
# make a list of all filenames and if they're paired or not;
# if we don't know if they're paired, default to allowing but not
# forcing pairing.
files = []
for element in filenames:
files.append([element, args.paired])
if args.unpaired_reads:
files.append([args.unpaired_reads, False])
corrupt_files = []
outfp = None
output_name = None
if args.single_output_file:
outfp = get_file_writer(args.single_output_file, args.gzip, args.bzip)
else:
if '-' in filenames or '/dev/stdin' in filenames:
print(
"Accepting input from stdin; output filename must "
"be provided with '-o'.",
file=sys.stderr)
sys.exit(1)
#
# main loop: iterate over all files given, do diginorm.
#
for filename, require_paired in files:
if not args.single_output_file:
output_name = os.path.basename(filename) + '.keep'
outfp = open(output_name, 'wb')
outfp = get_file_writer(outfp, args.gzip, args.bzip)
# failsafe context manager in case an input file breaks
with catch_io_errors(filename, outfp, args.single_output_file,
args.force, corrupt_files):
screed_iter = screed.open(filename)
reader = broken_paired_reader(screed_iter,
min_length=args.ksize,
force_single=force_single,
require_paired=require_paired)
# actually do diginorm
for record in with_diagnostics(reader, filename):
if record is not None:
write_record(record, outfp)
log_info('output in {name}', name=describe_file_handle(outfp))
if not args.single_output_file:
outfp.close()
# finished - print out some diagnostics.
log_info('Total number of unique k-mers: {umers}',
umers=countgraph.n_unique_kmers())
if args.savegraph:
log_info('...saving to {name}', name=args.savegraph)
countgraph.save(args.savegraph)
fp_rate = \
khmer.calc_expected_collisions(countgraph, False, max_false_pos=.8)
# for max_false_pos see Zhang et al., http://arxiv.org/abs/1309.2975
log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
if args.force and len(corrupt_files) > 0:
log_error("** WARNING: Finished with errors!")
log_error("** I/O Errors occurred in the following files:")
log_error("\t" + " ".join(corrupt_files))
def main():
info('split-paired-reads.py')
args = get_parser().parse_args()
infile = args.infile
filenames = [infile]
check_input_files(infile, args.force)
check_space(filenames, args.force)
# decide where to put output files - specific directory? or just default?
if infile == '/dev/stdin' or infile == '-':
if not (args.output_first and args.output_second):
print >> sys.stderr, ("Accepting input from stdin; "
"output filenames must be provided.")
sys.exit(1)
elif args.output_directory:
if not os.path.exists(args.output_directory):
os.makedirs(args.output_directory)
out1 = args.output_directory + '/' + os.path.basename(infile) + '.1'
out2 = args.output_directory + '/' + os.path.basename(infile) + '.2'
else:
out1 = os.path.basename(infile) + '.1'
out2 = os.path.basename(infile) + '.2'
# OVERRIDE output file locations with -1, -2
if args.output_first:
fp_out1 = args.output_first
out1 = fp_out1.name
else:
# Use default filename created above
fp_out1 = open(out1, 'w')
if args.output_second:
fp_out2 = args.output_second
out2 = fp_out2.name
else:
# Use default filename created above
fp_out2 = open(out2, 'w')
counter1 = 0
counter2 = 0
index = None
screed_iter = screed.open(infile, parse_description=False)
# walk through all the reads in broken-paired mode.
paired_iter = broken_paired_reader(screed_iter)
for index, is_pair, record1, record2 in paired_iter:
if index % 10000 == 0:
print('...', index, file=sys.stderr)
# are we requiring pairs?
if args.force_paired and not is_pair:
print('ERROR, %s is not part of a pair' % record1.name,
file=sys.stderr)
sys.exit(1)
if is_pair:
write_record(record1, fp_out1)
counter1 += 1
write_record(record2, fp_out2)
counter2 += 1
else:
name = record1.name
if check_is_left(name):
write_record(record1, fp_out1)
counter1 += 1
elif check_is_right(name):
write_record(record1, fp_out2)
counter2 += 1
else:
print("Unrecognized format for read pair information: %s" %
name,
file=sys.stderr)
print("Exiting.", file=sys.stderr)
sys.exit(1)
print("DONE; split %d sequences (%d left, %d right)" %
(counter1 + counter2, counter1, counter2),
file=sys.stderr)
print("/1 reads in %s" % out1, file=sys.stderr)
print("/2 reads in %s" % out2, file=sys.stderr)
def main(): # pylint: disable=too-many-branches,too-many-statements
info('saturate-by-median.py', ['diginorm'])
parser = sanitize_help(get_parser())
args = parser.parse_args()
report_on_config(args)
report_fp = args.report
report_frequency = args.report_frequency
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, False)
if args.savegraph:
check_space_for_graph(args, 'countgraph', False)
# list to save error files along with throwing exceptions
if args.force:
corrupt_files = []
if args.loadgraph:
print('loading k-mer countgraph from', args.loadgraph)
htable = khmer.load_countgraph(args.loadgraph)
else:
print('making countgraph')
htable = create_countgraph(args)
total = 0
discarded = 0
for index, input_filename in enumerate(args.input_filenames):
total_acc = 0
discarded_acc = 0
try:
total_acc, discarded_acc = normalize_by_median(input_filename,
htable, args,
report_fp,
report_frequency)
except IOError as err:
handle_error(err, input_filename)
if not args.force:
print("NOTE: This can be overridden using the --force"
" argument", file=sys.stderr)
print('** Exiting!', file=sys.stderr)
sys.exit(1)
else:
print('*** Skipping error file, moving on...', file=sys.stderr)
corrupt_files.append(input_filename)
else:
if total_acc == 0 and discarded_acc == 0:
print('SKIPPED empty file', input_filename)
else:
total += total_acc
discarded += discarded_acc
print('DONE with {inp}; kept {kept} of {total} or {perc:2}%'\
.format(inp=input_filename,
kept=total - discarded, total=total,
perc=int(100. - discarded / float(total) * 100.)))
if args.savegraph:
print('Saving k-mer countgraph through', input_filename)
print('...saving to', args.savegraph)
htable.save(args.savegraph)
# re: threshold, see Zhang et al.,
# http://arxiv.org/abs/1309.2975
fp_rate = khmer.calc_expected_collisions(htable, args.force, max_false_pos=.8)
print('fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate))
if args.force and len(corrupt_files) > 0:
print("** WARNING: Finished with errors!", file=sys.stderr)
print("** I/O Errors occurred in the following files:", file=sys.stderr)
print("\t", " ".join(corrupt_files), file=sys.stderr)
def main():
info('find-knots.py', ['graph'])
args = get_parser().parse_args()
graphbase = args.graphbase
# @RamRS: This might need some more work
infiles = [graphbase + '.pt', graphbase + '.tagset']
if os.path.exists(graphbase + '.stoptags'):
infiles.append(graphbase + '.stoptags')
for _ in infiles:
check_input_files(_, False)
check_space(infiles)
print >> sys.stderr, 'loading k-mer presence table %s.pt' % graphbase
htable = khmer.load_hashbits(graphbase + '.pt')
print >> sys.stderr, 'loading tagset %s.tagset...' % graphbase
htable.load_tagset(graphbase + '.tagset')
initial_stoptags = False # @CTB regularize with make-initial
if os.path.exists(graphbase + '.stoptags'):
print >> sys.stderr, 'loading stoptags %s.stoptags' % graphbase
htable.load_stop_tags(graphbase + '.stoptags')
initial_stoptags = True
pmap_files = glob.glob(args.graphbase + '.subset.*.pmap')
print >>sys.stderr, 'loading %d pmap files (first one: %s)' % \
(len(pmap_files), pmap_files[0])
print >> sys.stderr, '---'
print >> sys.stderr, 'output stoptags will be in', graphbase + '.stoptags'
if initial_stoptags:
print >>sys.stderr, \
'(these output stoptags will include the already-loaded set)'
print >> sys.stderr, '---'
# create counting hash
ksize = htable.ksize()
counting = khmer.new_counting_hash(ksize, args.min_tablesize,
args.n_tables)
# load & merge
for index, subset_file in enumerate(pmap_files):
print >> sys.stderr, '<-', subset_file
subset = htable.load_subset_partitionmap(subset_file)
print >> sys.stderr, '** repartitioning subset... %s' % subset_file
htable.repartition_largest_partition(subset, counting,
EXCURSION_DISTANCE,
EXCURSION_KMER_THRESHOLD,
EXCURSION_KMER_COUNT_THRESHOLD)
print >> sys.stderr, '** merging subset... %s' % subset_file
htable.merge_subset(subset)
print >> sys.stderr, '** repartitioning, round 2... %s' % subset_file
size = htable.repartition_largest_partition(
None, counting, EXCURSION_DISTANCE, EXCURSION_KMER_THRESHOLD,
EXCURSION_KMER_COUNT_THRESHOLD)
print >> sys.stderr, '** repartitioned size:', size
print >> sys.stderr, 'saving stoptags binary'
htable.save_stop_tags(graphbase + '.stoptags')
os.rename(subset_file, subset_file + '.processed')
print >> sys.stderr, '(%d of %d)\n' % (index, len(pmap_files))
print >> sys.stderr, 'done!'
def main():
info('load-graph.py', ['graph', 'SeqAn'])
args = get_parser().parse_args()
report_on_config(args, hashtype='hashbits')
base = args.output_filename
filenames = args.input_filenames
for _ in args.input_filenames:
check_input_files(_, args.force)
check_space(args.input_filenames, args.force)
check_space_for_hashtable(
(float(args.n_tables * args.min_tablesize) / 8.), args.force)
print >>sys.stderr, 'Saving k-mer presence table to %s' % base
print >>sys.stderr, 'Loading kmers from sequences in %s' % repr(filenames)
if args.no_build_tagset:
print >>sys.stderr, 'We WILL NOT build the tagset.'
else:
print >>sys.stderr, 'We WILL build the tagset', \
' (for partitioning/traversal).'
print >>sys.stderr, 'making k-mer presence table'
htable = khmer.new_hashbits(args.ksize, args.min_tablesize, args.n_tables)
if args.no_build_tagset:
target_method = htable.consume_fasta_with_reads_parser
else:
target_method = htable.consume_fasta_and_tag_with_reads_parser
for _, filename in enumerate(filenames):
rparser = khmer.ReadParser(filename)
threads = []
print >>sys.stderr, 'consuming input', filename
for num in xrange(args.threads):
cur_thread = threading.Thread(
target=target_method, args=(rparser,))
threads.append(cur_thread)
cur_thread.start()
for thread in threads:
thread.join()
if args.report_total_kmers:
print >> sys.stderr, 'Total number of unique k-mers: {0}'.format(
htable.n_unique_kmers())
print >>sys.stderr, 'saving k-mer presence table in', base + '.pt'
htable.save(base + '.pt')
if not args.no_build_tagset:
print >>sys.stderr, 'saving tagset in', base + '.tagset'
htable.save_tagset(base + '.tagset')
info_fp = open(base + '.info', 'w')
info_fp.write('%d unique k-mers' % htable.n_unique_kmers())
fp_rate = \
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.15)
# 0.18 is ACTUAL MAX. Do not change.
print >>sys.stderr, 'fp rate estimated to be %1.3f' % fp_rate
if args.write_fp_rate:
print >> info_fp, \
'\nfalse positive rate estimated to be %1.3f' % fp_rate
print >> sys.stderr, 'wrote to', base + '.info and', base + '.pt'
if not args.no_build_tagset:
print >> sys.stderr, 'and ' + base + '.tagset'
def main():
info('load-into-counting.py', ['counting', 'SeqAn'])
args = get_parser().parse_args()
report_on_config(args)
base = args.output_countingtable_filename
filenames = args.input_sequence_filename
for name in args.input_sequence_filename:
check_input_files(name, args.force)
check_space(args.input_sequence_filename, args.force)
check_space_for_hashtable(args.n_tables * args.min_tablesize, args.force)
check_file_writable(base)
check_file_writable(base + ".info")
print >> sys.stderr, 'Saving k-mer counting table to %s' % base
print >> sys.stderr, 'Loading kmers from sequences in %s' % repr(filenames)
# clobber the '.info' file now, as we always open in append mode below
if os.path.exists(base + '.info'):
os.remove(base + '.info')
print >> sys.stderr, 'making k-mer counting table'
htable = khmer.new_counting_hash(args.ksize, args.min_tablesize,
args.n_tables)
htable.set_use_bigcount(args.bigcount)
filename = None
total_num_reads = 0
for index, filename in enumerate(filenames):
rparser = khmer.ReadParser(filename)
threads = []
print >> sys.stderr, 'consuming input', filename
for _ in xrange(args.threads):
cur_thrd = \
threading.Thread(
target=htable.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(cur_thrd)
cur_thrd.start()
for thread in threads:
thread.join()
if index > 0 and index % 10 == 0:
check_space_for_hashtable(args.n_tables * args.min_tablesize,
args.force)
print >> sys.stderr, 'mid-save', base
htable.save(base)
with open(base + '.info', 'a') as info_fh:
print >> info_fh, 'through', filename
total_num_reads += rparser.num_reads
n_kmers = htable.n_unique_kmers()
if args.report_total_kmers:
print >> sys.stderr, 'Total number of unique k-mers:', n_kmers
with open(base + '.info', 'a') as info_fp:
print >> info_fp, 'Total number of unique k-mers:', n_kmers
print >> sys.stderr, 'saving', base
htable.save(base)
# Change max_false_pos=0.2 only if you really grok it. HINT: You don't
fp_rate = \
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.2)
with open(base + '.info', 'a') as info_fp:
print >> info_fp, 'fp rate estimated to be %1.3f\n' % fp_rate
if args.summary_info:
mr_fmt = args.summary_info.lower()
mr_file = base + '.info.' + mr_fmt
print >> sys.stderr, "Writing summmary info to", mr_file
with open(mr_file, 'w') as mr_fh:
if mr_fmt == 'json':
mr_data = {
"ht_name": os.path.basename(base),
"fpr": fp_rate,
"num_kmers": n_kmers,
"files": filenames,
"mrinfo_version": "0.2.0",
"num_reads": total_num_reads,
}
json.dump(mr_data, mr_fh)
mr_fh.write('\n')
elif mr_fmt == 'tsv':
mr_fh.write("ht_name\tfpr\tnum_kmers\tnum_reads\tfiles\n")
vals = [
os.path.basename(base),
"{:1.3f}".format(fp_rate),
str(n_kmers),
str(total_num_reads),
";".join(filenames),
]
mr_fh.write("\t".join(vals) + "\n")
print >> sys.stderr, 'fp rate estimated to be %1.3f' % fp_rate
print >> sys.stderr, 'DONE.'
print >> sys.stderr, 'wrote to:', base + '.info'
def main():
info('trim-low-abund.py', ['streaming'])
parser = sanitize_help(get_parser())
args = parser.parse_args()
###
if len(set(args.input_filenames)) != len(args.input_filenames):
print("Error: Cannot input the same filename multiple times.",
file=sys.stderr)
sys.exit(1)
if args.trim_at_coverage != DEFAULT_TRIM_AT_COVERAGE and \
not args.variable_coverage:
print("Error: --trim-at-coverage/-Z given, but",
"--variable-coverage/-V not specified.",
file=sys.stderr)
sys.exit(1)
if args.diginorm_coverage != DEFAULT_DIGINORM_COVERAGE and \
not args.diginorm:
print("Error: --diginorm-coverage given, but",
"--diginorm not specified.",
file=sys.stderr)
sys.exit(1)
if args.diginorm and args.single_pass:
print("Error: --diginorm and --single-pass are incompatible!\n"
"You probably want to use normalize-by-median.py instead.",
file=sys.stderr)
sys.exit(1)
###
report_on_config(args)
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, args.force)
if args.savegraph:
graphsize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(args.savegraph, graphsize, args.force)
if ('-' in args.input_filenames or '/dev/stdin' in args.input_filenames) \
and not args.output:
print("Accepting input from stdin; output filename must "
"be provided with -o.", file=sys.stderr)
sys.exit(1)
if args.loadgraph:
print('loading countgraph from', args.loadgraph, file=sys.stderr)
ct = khmer.load_countgraph(args.loadgraph)
else:
print('making countgraph', file=sys.stderr)
ct = khmer_args.create_countgraph(args)
K = ct.ksize()
tempdir = tempfile.mkdtemp('khmer', 'tmp', args.tempdir)
print('created temporary directory %s; '
'use -T to change location' % tempdir, file=sys.stderr)
trimmer = Trimmer(ct, not args.variable_coverage, args.cutoff,
args.trim_at_coverage)
if args.diginorm:
trimmer.set_diginorm(args.diginorm_coverage)
# ### FIRST PASS ###
save_pass2_total = 0
written_bp = 0
written_reads = 0
# only create the file writer once if outfp is specified; otherwise,
# create it for each file.
if args.output:
trimfp = get_file_writer(args.output, args.gzip, args.bzip)
pass2list = []
for filename in args.input_filenames:
# figure out temporary filename for 2nd pass
pass2filename = os.path.basename(filename) + '.pass2'
pass2filename = os.path.join(tempdir, pass2filename)
pass2fp = open(pass2filename, 'w')
# construct output filenames
if args.output is None:
# note: this will be saved in trimfp.
outfp = open(os.path.basename(filename) + '.abundtrim', 'wb')
# get file handle w/gzip, bzip
trimfp = get_file_writer(outfp, args.gzip, args.bzip)
# record all this info
pass2list.append((filename, pass2filename, trimfp))
# input file stuff: get a broken_paired reader.
screed_iter = screed.open(filename)
paired_iter = broken_paired_reader(screed_iter, min_length=K,
force_single=args.ignore_pairs)
# main loop through the file.
n_start = trimmer.n_reads
save_start = trimmer.n_saved
watermark = REPORT_EVERY_N_READS
for read in trimmer.pass1(paired_iter, pass2fp):
if (trimmer.n_reads - n_start) > watermark:
print('...', filename, trimmer.n_saved,
trimmer.n_reads, trimmer.n_bp,
written_reads, written_bp, file=sys.stderr)
watermark += REPORT_EVERY_N_READS
# write out the trimmed/etc sequences that AREN'T going to be
# revisited in a 2nd pass.
write_record(read, trimfp)
written_bp += len(read)
written_reads += 1
pass2fp.close()
print('%s: kept aside %d of %d from first pass, in %s' %
(filename,
trimmer.n_saved - save_start, trimmer.n_reads - n_start,
filename),
file=sys.stderr)
# first pass goes across all the data, so record relevant stats...
n_reads = trimmer.n_reads
n_bp = trimmer.n_bp
n_skipped = trimmer.n_skipped
bp_skipped = trimmer.bp_skipped
save_pass2_total = trimmer.n_saved
# ### SECOND PASS. ###
# nothing should have been skipped yet!
assert trimmer.n_skipped == 0
assert trimmer.bp_skipped == 0
if args.single_pass:
pass2list = []
# go back through all the files again.
for _, pass2filename, trimfp in pass2list:
print('second pass: looking at sequences kept aside in %s' %
pass2filename,
file=sys.stderr)
# note that for this second pass, we don't care about paired
# reads - they will be output in the same order they're read in,
# so pairs will stay together if not orphaned. This is in contrast
# to the first loop. Hence, force_single=True below.
screed_iter = screed.open(pass2filename, parse_description=False)
paired_iter = broken_paired_reader(screed_iter, min_length=K,
force_single=True)
watermark = REPORT_EVERY_N_READS
for read in trimmer.pass2(paired_iter):
if (trimmer.n_reads - n_start) > watermark:
print('... x 2', trimmer.n_reads - n_start,
pass2filename, trimmer.n_saved,
trimmer.n_reads, trimmer.n_bp,
written_reads, written_bp, file=sys.stderr)
watermark += REPORT_EVERY_N_READS
write_record(read, trimfp)
written_reads += 1
written_bp += len(read)
print('removing %s' % pass2filename, file=sys.stderr)
os.unlink(pass2filename)
# if we created our own trimfps, close 'em.
if not args.output:
trimfp.close()
print('removing temp directory & contents (%s)' % tempdir, file=sys.stderr)
shutil.rmtree(tempdir)
trimmed_reads = trimmer.trimmed_reads
n_passes = 1.0 + (float(save_pass2_total) / n_reads)
percent_reads_trimmed = float(trimmed_reads + (n_reads - written_reads)) /\
n_reads * 100.0
print('read %d reads, %d bp' % (n_reads, n_bp,), file=sys.stderr)
print('wrote %d reads, %d bp' % (written_reads, written_bp,),
file=sys.stderr)
print('looked at %d reads twice (%.2f passes)' % (save_pass2_total,
n_passes),
file=sys.stderr)
print('removed %d reads and trimmed %d reads (%.2f%%)' %
(n_reads - written_reads, trimmed_reads, percent_reads_trimmed),
file=sys.stderr)
print('trimmed or removed %.2f%% of bases (%d total)' %
((1 - (written_bp / float(n_bp))) * 100.0, n_bp - written_bp),
file=sys.stderr)
if args.variable_coverage:
percent_reads_hicov = 100.0 * float(n_reads - n_skipped) / n_reads
print('%d reads were high coverage (%.2f%%);' % (n_reads - n_skipped,
percent_reads_hicov),
file=sys.stderr)
print('skipped %d reads/%d bases because of low coverage' %
(n_skipped, bp_skipped),
file=sys.stderr)
fp_rate = \
khmer.calc_expected_collisions(ct, args.force, max_false_pos=.8)
# for max_false_pos see Zhang et al., http://arxiv.org/abs/1309.2975
print('fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate),
file=sys.stderr)
print('output in *.abundtrim', file=sys.stderr)
if args.savegraph:
print("Saving k-mer countgraph to",
args.savegraph, file=sys.stderr)
ct.save(args.savegraph)
def main(): # pylint: disable=too-many-branches,too-many-statements
info('normalize-by-median.py', ['diginorm'])
args = get_parser().parse_args()
report_on_config(args)
report_fp = args.report
# check for similar filenames
filenames = []
for pathfilename in args.input_filenames:
filename = pathfilename.split('/')[-1]
if (filename in filenames):
print >> sys.stderr, "WARNING: At least two input files are named \
%s . (The script normalize-by-median.py can not handle this, only one .keep \
file for one of the input files will be generated.)" % filename
else:
filenames.append(filename)
# check for others
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, args.force)
if args.savetable:
check_space_for_hashtable(args.n_tables * args.min_tablesize,
args.force)
# list to save error files along with throwing exceptions
corrupt_files = []
if args.loadtable:
print 'loading k-mer counting table from', args.loadtable
htable = khmer.load_counting_hash(args.loadtable)
else:
print >> sys.stderr, 'making k-mer counting table'
htable = khmer.new_counting_hash(args.ksize, args.min_tablesize,
args.n_tables)
input_filename = None
for index, input_filename in enumerate(args.input_filenames):
total_acc, discarded_acc, corrupt_files = \
normalize_by_median_and_check(
input_filename, htable, args.single_output_file,
args.fail_save, args.paired, args.cutoff, args.force,
corrupt_files, report_fp)
if (args.dump_frequency > 0 and index > 0
and index % args.dump_frequency == 0):
print 'Backup: Saving k-mer counting file through', input_filename
if args.savetable:
hashname = args.savetable
print '...saving to', hashname
else:
hashname = 'backup.ct'
print 'Nothing given for savetable, saving to', hashname
htable.save(hashname)
if args.paired and args.unpaired_reads:
args.paired = False
output_name = args.unpaired_reads
if not args.single_output_file:
output_name = os.path.basename(args.unpaired_reads) + '.keep'
outfp = open(output_name, 'w')
total_acc, discarded_acc, corrupt_files = \
normalize_by_median_and_check(
args.unpaired_reads, htable, args.single_output_file,
args.fail_save, args.paired, args.cutoff, args.force,
corrupt_files, report_fp)
if args.report_total_kmers:
print >> sys.stderr, 'Total number of unique k-mers: {0}'.format(
htable.n_unique_kmers())
if args.savetable:
print 'Saving k-mer counting table through', input_filename
print '...saving to', args.savetable
htable.save(args.savetable)
fp_rate = \
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.8)
# for max_false_pos see Zhang et al., http://arxiv.org/abs/1309.2975
print >> sys.stderr, \
'fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate)
if args.force and len(corrupt_files) > 0:
print >> sys.stderr, "** WARNING: Finished with errors!"
print >> sys.stderr, "** IOErrors occurred in the following files:"
print >> sys.stderr, "\t", " ".join(corrupt_files)
def main():
info('sample-reads-randomly.py')
args = get_parser().parse_args()
for _ in args.filenames:
check_input_files(_, args.force)
check_space(args.filenames, args.force)
# seed the random number generator?
if args.random_seed:
random.seed(args.random_seed)
# bound n_samples
num_samples = max(args.num_samples, 1)
#
# Figure out what the output filename is going to be
#
output_file = args.output_file
if output_file:
if num_samples > 1:
sys.stderr.write(
"Error: cannot specify -o with more than one sample.")
if not args.force:
sys.exit(1)
output_filename = output_file.name
else:
filename = args.filenames[0]
output_filename = os.path.basename(filename) + '.subset'
if num_samples == 1:
print >>sys.stderr, 'Subsampling %d reads using reservoir sampling.' %\
args.num_reads
print >>sys.stderr, 'Subsampled reads will be placed in %s' % \
output_filename
print >> sys.stderr, ''
else: # > 1
print >>sys.stderr, 'Subsampling %d reads, %d times,' \
% (args.num_reads, num_samples), ' using reservoir sampling.'
print >>sys.stderr, 'Subsampled reads will be placed in %s.N' \
% output_filename
print >> sys.stderr, ''
reads = []
for n in range(num_samples):
reads.append([])
# read through all the sequences and load/resample the reservoir
for filename in args.filenames:
print >> sys.stderr, 'opening', filename, 'for reading'
screed_iter = screed.open(filename, parse_description=False)
for count, (_, ispair, rcrd1, rcrd2) in enumerate(
broken_paired_reader(screed_iter,
force_single=args.force_single)):
if count % 10000 == 0:
print >> sys.stderr, '...', count, 'reads scanned'
if count >= args.max_reads:
print >>sys.stderr, 'reached upper limit of %d reads' % \
args.max_reads, '(see -M); exiting'
break
# collect first N reads
if count < args.num_reads:
for n in range(num_samples):
reads[n].append((rcrd1, rcrd2))
else:
assert len(reads[n]) <= count
# use reservoir sampling to replace reads at random
# see http://en.wikipedia.org/wiki/Reservoir_sampling
for n in range(num_samples):
guess = random.randint(1, count)
if guess <= args.num_reads:
reads[n][guess - 1] = (rcrd1, rcrd2)
# output all the subsampled reads:
if len(reads) == 1:
print >>sys.stderr, 'Writing %d sequences to %s' % \
(len(reads[0]), output_filename)
if not output_file:
output_file = open(output_filename, 'w')
for records in reads[0]:
write_record(records[0], output_file)
if records[1] is not None:
write_record(records[1], output_file)
else:
for n in range(num_samples):
n_filename = output_filename + '.%d' % n
print >>sys.stderr, 'Writing %d sequences to %s' % \
(len(reads[n]), n_filename)
output_file = open(n_filename, 'w')
for records in reads[n]:
write_record(records[0], output_file)
if records[1] is not None:
write_record(records[1], output_file)
def main():
parser = sanitize_help(get_parser())
args = parser.parse_args()
configure_logging(args.quiet)
###
if len(set(args.input_filenames)) != len(args.input_filenames):
log_error("Error: Cannot input the same filename multiple times.")
sys.exit(1)
if args.trim_at_coverage != DEFAULT_TRIM_AT_COVERAGE and \
not args.variable_coverage:
log_error("Error: --trim-at-coverage/-Z given, but "
"--variable-coverage/-V not specified.")
sys.exit(1)
if args.diginorm_coverage != DEFAULT_DIGINORM_COVERAGE and \
not args.diginorm:
log_error("Error: --diginorm-coverage given, but "
"--diginorm not specified.")
sys.exit(1)
if args.diginorm and args.single_pass:
log_error("Error: --diginorm and --single-pass are incompatible!\n"
"You probably want to use normalize-by-median.py instead.")
sys.exit(1)
###
graphtype = 'countgraph' if not args.small_count else 'smallcountgraph'
report_on_config(args, graphtype=graphtype)
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, args.force)
if args.savegraph:
graphsize = calculate_graphsize(args, graphtype)
check_space_for_graph(args.savegraph, graphsize, args.force)
if ('-' in args.input_filenames or '/dev/stdin' in args.input_filenames) \
and not args.output:
log_error("Accepting input from stdin; output filename must "
"be provided with -o.")
sys.exit(1)
if args.loadgraph:
log_info('loading countgraph from {graph}', graph=args.loadgraph)
if args.small_count:
ct = SmallCountgraph.load(args.loadgraph)
else:
ct = Countgraph.load(args.loadgraph)
else:
log_info('making countgraph')
ct = khmer_args.create_countgraph(args)
K = ct.ksize()
tempdir = tempfile.mkdtemp('khmer', 'tmp', args.tempdir)
log_info('created temporary directory {temp};\n'
'use -T to change location', temp=tempdir)
trimmer = Trimmer(ct, not args.variable_coverage, args.cutoff,
args.trim_at_coverage)
if args.diginorm:
trimmer.set_diginorm(args.diginorm_coverage)
# ### FIRST PASS ###
save_pass2_total = 0
written_bp = 0
written_reads = 0
# only create the file writer once if outfp is specified; otherwise,
# create it for each file.
if args.output:
trimfp = get_file_writer(args.output, args.gzip, args.bzip)
pass2list = []
for filename in args.input_filenames:
# figure out temporary filename for 2nd pass
pass2filename = filename.replace(os.path.sep, '-') + '.pass2'
pass2filename = os.path.join(tempdir, pass2filename)
pass2fp = open(pass2filename, 'w')
# construct output filenames
if args.output is None:
# note: this will be saved in trimfp.
outfp = open(os.path.basename(filename) + '.abundtrim', 'wb')
# get file handle w/gzip, bzip
trimfp = get_file_writer(outfp, args.gzip, args.bzip)
# record all this info
pass2list.append((filename, pass2filename, trimfp))
# input file stuff: get a broken_paired reader.
paired_iter = broken_paired_reader(ReadParser(filename), min_length=K,
force_single=args.ignore_pairs)
# main loop through the file.
n_start = trimmer.n_reads
save_start = trimmer.n_saved
watermark = REPORT_EVERY_N_READS
for read in trimmer.pass1(paired_iter, pass2fp):
if (trimmer.n_reads - n_start) > watermark:
log_info("... {filename} {n_saved} {n_reads} {n_bp} "
"{w_reads} {w_bp}", filename=filename,
n_saved=trimmer.n_saved, n_reads=trimmer.n_reads,
n_bp=trimmer.n_bp, w_reads=written_reads,
w_bp=written_bp)
watermark += REPORT_EVERY_N_READS
# write out the trimmed/etc sequences that AREN'T going to be
# revisited in a 2nd pass.
write_record(read, trimfp)
written_bp += len(read)
written_reads += 1
pass2fp.close()
log_info("{filename}: kept aside {kept} of {total} from first pass",
filename=filename, kept=trimmer.n_saved - save_start,
total=trimmer.n_reads - n_start)
# first pass goes across all the data, so record relevant stats...
n_reads = trimmer.n_reads
n_bp = trimmer.n_bp
n_skipped = trimmer.n_skipped
bp_skipped = trimmer.bp_skipped
save_pass2_total = trimmer.n_saved
# ### SECOND PASS. ###
# nothing should have been skipped yet!
assert trimmer.n_skipped == 0
assert trimmer.bp_skipped == 0
if args.single_pass:
pass2list = []
# go back through all the files again.
for _, pass2filename, trimfp in pass2list:
log_info('second pass: looking at sequences kept aside in {pass2}',
pass2=pass2filename)
# note that for this second pass, we don't care about paired
# reads - they will be output in the same order they're read in,
# so pairs will stay together if not orphaned. This is in contrast
# to the first loop. Hence, force_single=True below.
read_parser = ReadParser(pass2filename)
paired_iter = broken_paired_reader(read_parser,
min_length=K,
force_single=True)
watermark = REPORT_EVERY_N_READS
for read in trimmer.pass2(paired_iter):
if (trimmer.n_reads - n_start) > watermark:
log_info('... x 2 {a} {b} {c} {d} {e} {f} {g}',
a=trimmer.n_reads - n_start,
b=pass2filename, c=trimmer.n_saved,
d=trimmer.n_reads, e=trimmer.n_bp,
f=written_reads, g=written_bp)
watermark += REPORT_EVERY_N_READS
write_record(read, trimfp)
written_reads += 1
written_bp += len(read)
read_parser.close()
log_info('removing {pass2}', pass2=pass2filename)
os.unlink(pass2filename)
# if we created our own trimfps, close 'em.
if not args.output:
trimfp.close()
try:
log_info('removing temp directory & contents ({temp})', temp=tempdir)
shutil.rmtree(tempdir)
except OSError as oe:
log_info('WARNING: unable to remove {temp} (probably an NFS issue); '
'please remove manually', temp=tempdir)
trimmed_reads = trimmer.trimmed_reads
n_passes = 1.0 + (float(save_pass2_total) / n_reads)
percent_reads_trimmed = float(trimmed_reads + (n_reads - written_reads)) /\
n_reads * 100.0
log_info('read {read} reads, {bp} bp', read=n_reads, bp=n_bp)
log_info('wrote {wr} reads, {wbp} bp', wr=written_reads, wbp=written_bp)
log_info('looked at {st} reads twice ({np:.2f} passes)',
st=save_pass2_total, np=n_passes)
log_info('removed {r} reads and trimmed {t} reads ({p:.2f}%)',
r=n_reads - written_reads, t=trimmed_reads,
p=percent_reads_trimmed)
log_info('trimmed or removed {p:.2f}%% of bases ({bp} total)',
p=(1 - (written_bp / float(n_bp))) * 100.0, bp=n_bp - written_bp)
if args.variable_coverage:
percent_reads_hicov = 100.0 * float(n_reads - n_skipped) / n_reads
log_info('{n} reads were high coverage ({p:.2f}%);',
n=n_reads - n_skipped, p=percent_reads_hicov)
log_info('skipped {r} reads/{bp} bases because of low coverage',
r=n_skipped, bp=bp_skipped)
fp_rate = \
khmer.calc_expected_collisions(ct, args.force, max_false_pos=.8)
# for max_false_pos see Zhang et al., http://arxiv.org/abs/1309.2975
log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
if args.output is None:
log_info('output in *.abundtrim')
elif args.output.name == 1:
log_info('output streamed to stdout')
elif args.output.name:
log_info('output in {}'.format(args.output.name))
if args.savegraph:
log_info("Saving k-mer countgraph to {graph}", graph=args.savegraph)
ct.save(args.savegraph)
if args.summary_info is not None:
# note that when streaming to stdout the name of args.output will
# be set to 1
if args.output is not None and args.output.name != 1:
base = args.output.name
# no explicit name or stdout stream -> use a default name
else:
base = 'trim-low-abund-{}'.format(
time.strftime("%Y-%m-%dT%H:%M:%S"))
info = {'fpr': fp_rate,
'reads': n_reads,
'basepairs': n_bp,
'reads_written': written_reads,
'basepairs_written': written_bp,
'reads_skipped': n_skipped,
'basepairs_skipped': bp_skipped,
'reads_removed': n_reads - written_reads,
'reads_trimmed': trimmed_reads,
'basepairs_removed_or_trimmed': n_bp - written_bp
}
store_provenance_info(info, fname=base, format=args.summary_info)
def main():
info('extract-paired-reads.py')
args = get_parser().parse_args()
infile = args.infile
check_input_files(infile, args.force)
check_space([infile], args.force)
# decide where to put output files - specific directory? or just default?
if infile == '/dev/stdin' or infile == '-':
if not (args.output_paired and args.output_single):
print(
"Accepting input from stdin; output filenames must be "
"provided.",
file=sys.stderr)
sys.exit(1)
elif args.output_dir:
if not os.path.exists(args.output_dir):
os.makedirs(args.output_dir)
out1 = args.output_dir + '/' + os.path.basename(infile) + '.se'
out2 = args.output_dir + '/' + os.path.basename(infile) + '.pe'
else:
out1 = os.path.basename(infile) + '.se'
out2 = os.path.basename(infile) + '.pe'
# OVERRIDE default output file locations with -p, -s
if args.output_paired:
paired_fp = args.output_paired
out2 = paired_fp.name
else:
# Don't override, just open the default filename from above
paired_fp = open(out2, 'w')
if args.output_single:
single_fp = args.output_single
out1 = single_fp.name
else:
# Don't override, just open the default filename from above
single_fp = open(out1, 'w')
print('reading file "%s"' % infile, file=sys.stderr)
print('outputting interleaved pairs to "%s"' % out2, file=sys.stderr)
print('outputting orphans to "%s"' % out1, file=sys.stderr)
n_pe = 0
n_se = 0
screed_iter = screed.open(infile, parse_description=False)
for index, is_pair, read1, read2 in broken_paired_reader(screed_iter):
if index % 100000 == 0 and index > 0:
print('...', index, file=sys.stderr)
if is_pair:
write_record_pair(read1, read2, paired_fp)
n_pe += 1
else:
write_record(read1, single_fp)
n_se += 1
single_fp.close()
paired_fp.close()
if n_pe == 0:
raise Exception("no paired reads!? check file formats...")
print('DONE; read %d sequences,'
' %d pairs and %d singletons' % (n_pe * 2 + n_se, n_pe, n_se),
file=sys.stderr)
print('wrote to: %s and %s' % (out2, out1), file=sys.stderr)
def main(): # pylint: disable=too-many-branches,too-many-statements
info('normalize-by-median.py', ['diginorm'])
args = get_parser().parse_args()
report_on_config(args)
report_fp = args.report
# check for similar filenames
filenames = []
for pathfilename in args.input_filenames:
filename = pathfilename.split('/')[-1]
if (filename in filenames):
print >>sys.stderr, "WARNING: At least two input files are named \
%s . (The script normalize-by-median.py can not handle this, only one .keep \
file for one of the input files will be generated.)" % filename
else:
filenames.append(filename)
# check for others
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, args.force)
if args.savetable:
check_space_for_hashtable(
args.n_tables * args.min_tablesize, args.force)
# list to save error files along with throwing exceptions
corrupt_files = []
if args.loadtable:
print 'loading k-mer counting table from', args.loadtable
htable = khmer.load_counting_hash(args.loadtable)
else:
print >> sys.stderr, 'making k-mer counting table'
htable = khmer.new_counting_hash(args.ksize, args.min_tablesize,
args.n_tables)
input_filename = None
for index, input_filename in enumerate(args.input_filenames):
total_acc, discarded_acc, corrupt_files = \
normalize_by_median_and_check(
input_filename, htable, args.single_output_file,
args.fail_save, args.paired, args.cutoff, args.force,
corrupt_files, report_fp)
if (args.dump_frequency > 0 and
index > 0 and index % args.dump_frequency == 0):
print 'Backup: Saving k-mer counting file through', input_filename
if args.savetable:
hashname = args.savetable
print '...saving to', hashname
else:
hashname = 'backup.ct'
print 'Nothing given for savetable, saving to', hashname
htable.save(hashname)
if args.paired and args.unpaired_reads:
args.paired = False
output_name = args.unpaired_reads
if not args.single_output_file:
output_name = os.path.basename(args.unpaired_reads) + '.keep'
outfp = open(output_name, 'w')
total_acc, discarded_acc, corrupt_files = \
normalize_by_median_and_check(
args.unpaired_reads, htable, args.single_output_file,
args.fail_save, args.paired, args.cutoff, args.force,
corrupt_files, report_fp)
if args.report_total_kmers:
print >> sys.stderr, 'Total number of unique k-mers: {0}'.format(
htable.n_unique_kmers())
if args.savetable:
print 'Saving k-mer counting table through', input_filename
print '...saving to', args.savetable
htable.save(args.savetable)
fp_rate = \
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.8)
# for max_false_pos see Zhang et al., http://arxiv.org/abs/1309.2975
print >> sys.stderr, \
'fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate)
if args.force and len(corrupt_files) > 0:
print >> sys.stderr, "** WARNING: Finished with errors!"
print >> sys.stderr, "** IOErrors occurred in the following files:"
print >> sys.stderr, "\t", " ".join(corrupt_files)
def main(): # pylint: disable=too-many-branches,too-many-statements
info('normalize-by-median.py', ['diginorm'])
args = get_parser().parse_args()
report_on_config(args)
report_fp = args.report
force_single = args.force_single
# if optimization args are given, do optimization
args = oxutils.do_sanity_checking(args, 0.1)
# check for similar filenames
# if we're using a single output file only check for identical filenames
# otherwise, check for identical BASE names as well.
filenames = []
basenames = []
for pathfilename in args.input_filenames:
filenames.append(pathfilename)
if args.single_output_file:
continue # nothing more to worry about
basename = os.path.basename(pathfilename)
if basename in basenames:
print('ERROR: Duplicate filename--Cannot handle this!',
file=sys.stderr)
print('** Exiting!', file=sys.stderr)
sys.exit(1)
basenames.append(basename)
# check that files exist and there is sufficient output disk space.
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, args.force)
if args.savetable:
check_space_for_hashtable(args, 'countgraph', args.force)
# load or create counting table.
if args.loadtable:
print('loading k-mer counting table from ' + args.loadtable,
file=sys.stderr)
htable = khmer.load_counting_hash(args.loadtable)
if args.unique_kmers != 0:
print('Warning: You have specified a number of unique kmers'
' but are loading a precreated counting table--'
'argument optimization will NOT be done.', file=sys.stderr)
else:
print('making countgraph', file=sys.stderr)
htable = khmer_args.create_countgraph(args)
# create an object to handle diginorm of all files
norm = Normalizer(args.cutoff, htable)
# make a list of all filenames and if they're paired or not;
# if we don't know if they're paired, default to allowing but not
# forcing pairing.
files = []
for element in filenames:
files.append([element, args.paired])
if args.unpaired_reads:
files.append([args.unpaired_reads, False])
corrupt_files = []
outfp = None
output_name = None
if args.single_output_file:
if args.single_output_file is sys.stdout:
output_name = '/dev/stdout'
else:
output_name = args.single_output_file.name
outfp = args.single_output_file
#
# main loop: iterate over all files given, do diginorm.
#
for filename, require_paired in files:
if not args.single_output_file:
output_name = os.path.basename(filename) + '.keep'
outfp = open(output_name, 'w')
# failsafe context manager in case an input file breaks
with catch_io_errors(filename, outfp, args.single_output_file,
args.force, corrupt_files):
screed_iter = screed.open(filename, parse_description=False)
reader = broken_paired_reader(screed_iter, min_length=args.ksize,
force_single=force_single,
require_paired=require_paired)
# actually do diginorm
for record in with_diagnostics(filename, norm, reader, report_fp):
if record is not None:
write_record(record, outfp)
print('output in ' + output_name, file=sys.stderr)
if output_name is not '/dev/stdout':
outfp.close()
# finished - print out some diagnostics.
print('Total number of unique k-mers: {0}'
.format(htable.n_unique_kmers()),
file=sys.stderr)
if args.savetable:
print('...saving to ' + args.savetable, file=sys.stderr)
htable.save(args.savetable)
fp_rate = \
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.8)
# for max_false_pos see Zhang et al., http://arxiv.org/abs/1309.2975
print('fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate),
file=sys.stderr)
if args.force and len(corrupt_files) > 0:
print("** WARNING: Finished with errors!", file=sys.stderr)
print("** I/O Errors occurred in the following files:",
file=sys.stderr)
print("\t", " ".join(corrupt_files), file=sys.stderr)
def main():
info('sweep-reads-buffered.py', ['sweep'])
parser = get_parser()
args = parser.parse_args()
if args.min_tablesize < MIN_HSIZE:
args.min_tablesize = MIN_HSIZE
if args.ksize < MIN_KSIZE:
args.ksize = MIN_KSIZE
report_on_config(args, hashtype='hashbits')
K = args.ksize
HT_SIZE = args.min_tablesize
N_HT = args.n_tables
traversal_range = args.traversal_range
input_fastp = args.input_fastp
if not args.outdir:
outdir = os.path.dirname(input_fastp)
else:
outdir = args.outdir
max_buffers = args.max_buffers
output_pref = args.output_prefix
buf_size = args.buffer_size
max_reads = args.max_reads
check_input_files(args.input_fastp, args.force)
check_valid_file_exists(args.input_files)
all_input_files = [input_fastp]
all_input_files.extend(args.input_files)
# Check disk space availability
check_space(all_input_files, args.force)
# figure out input file type (FA/FQ) -- based on first file
ix = iter(screed.open(args.input_files[0]))
record = ix.next()
del ix
extension = 'fa'
if hasattr(record, 'quality'): # fastq!
extension = 'fq'
output_buffer = ReadBufferManager(
max_buffers, max_reads, buf_size, output_pref, outdir, extension)
# consume the partitioned fasta with which to label the graph
ht = khmer.LabelHash(K, HT_SIZE, N_HT)
try:
print >>sys.stderr, 'consuming input sequences...'
if args.label_by_pid:
print >>sys.stderr, '...labeling by partition id (pid)'
ht.consume_partitioned_fasta_and_tag_with_labels(input_fastp)
elif args.label_by_seq:
print >>sys.stderr, '...labeling by sequence'
for n, record in enumerate(screed.open(input_fastp)):
if n % 50000 == 0:
print >>sys.stderr, \
'...consumed {n} sequences...'.format(n=n)
ht.consume_sequence_and_tag_with_labels(record.sequence, n)
else:
print >>sys.stderr, \
'...labeling to create groups of size {s}'.format(
s=args.group_size)
label = -1
g = 0
try:
outfp = open('{pref}_base_{g}.{ext}'.format(pref=output_pref,
g=g,
ext=extension
), 'wb')
for n, record in enumerate(screed.open(input_fastp)):
if n % args.group_size == 0:
label += 1
if label > g:
g = label
outfp = open('{pref}_base_{g}.{ext}'.format(
pref=output_pref, g=g,
ext=extension), 'wb')
if n % 50000 == 0:
print >>sys.stderr, \
'...consumed {n} sequences...'.format(n=n)
ht.consume_sequence_and_tag_with_labels(record.sequence,
label)
write_record(record, outfp)
except IOError as e:
print >>sys.stderr, '!! ERROR !!', e
print >>sys.stderr, '...error splitting input. exiting...'
except IOError as e:
print >>sys.stderr, '!! ERROR: !!', e
print >>sys.stderr, '...error consuming \
{i}. exiting...'.format(i=input_fastp)
print >>sys.stderr, 'done consuming input sequence. \
added {t} tags and {l} \
labels...'.format(t=ht.n_tags(), l=ht.n_labels())
label_dict = defaultdict(int)
label_number_dist = []
n_orphaned = 0
n_labeled = 0
n_mlabeled = 0
total_t = time.clock()
start_t = time.clock()
for read_file in args.input_files:
print >>sys.stderr, '** sweeping {read_file} for labels...'.format(
read_file=read_file)
file_t = 0.0
try:
read_fp = screed.open(read_file)
except IOError as error:
print >>sys.stderr, '!! ERROR: !!', error
print >>sys.stderr, '*** Could not open {fn}, skipping...'.format(
fn=read_file)
else:
for _, record in enumerate(read_fp):
if _ % 50000 == 0:
end_t = time.clock()
batch_t = end_t - start_t
file_t += batch_t
print >>sys.stderr, '\tswept {n} reads [{nc} labeled, \
{no} orphaned] \
** {sec}s ({sect}s total)' \
.format(n=_, nc=n_labeled,
no=n_orphaned,
sec=batch_t, sect=file_t)
start_t = time.clock()
seq = record.sequence
name = record.name
try:
labels = ht.sweep_label_neighborhood(seq, traversal_range)
except ValueError as e:
pass
else:
if hasattr(record, 'quality'):
seq_str = fmt_fastq(name, seq, record.quality, labels)
else:
seq_str = fmt_fasta(name, seq, labels)
label_number_dist.append(len(labels))
if labels:
n_labeled += 1
if len(labels) > 1:
output_buffer.queue(seq_str, 'multi')
n_mlabeled += 1
label_dict['multi'] += 1
else:
output_buffer.queue(seq_str, labels[0])
label_dict[labels[0]] += 1
else:
n_orphaned += 1
output_buffer.queue(seq_str, 'orphaned')
label_dict['orphaned'] += 1
print >>sys.stderr, '** End of file {fn}...'.format(fn=read_file)
output_buffer.flush_all()
read_fp.close()
# gotta output anything left in the buffers at the end!
print >>sys.stderr, '** End of run...'
output_buffer.flush_all()
total_t = time.clock() - total_t
if output_buffer.num_write_errors > 0 or output_buffer.num_file_errors > 0:
print >>sys.stderr, '! WARNING: Sweep finished with errors !'
print >>sys.stderr, '** {writee} reads not written'.format(
writee=output_buffer.num_write_errors)
print >>sys.stderr, '** {filee} errors opening files'.format(
filee=output_buffer.num_file_errors)
print >>sys.stderr, 'swept {n_reads} for labels...'.format(
n_reads=n_labeled + n_orphaned)
print >>sys.stderr, '...with {nc} labeled and {no} orphaned'.format(
nc=n_labeled, no=n_orphaned)
print >>sys.stderr, '...and {nmc} multilabeled'.format(nmc=n_mlabeled)
print >>sys.stderr, '** outputting label number distribution...'
fn = os.path.join(outdir, '{pref}.dist.txt'.format(pref=output_pref))
with open(fn, 'wb') as outfp:
for nc in label_number_dist:
outfp.write('{nc}\n'.format(nc=nc))
fn = os.path.join(outdir, '{pref}.counts.csv'.format(pref=output_pref))
print >>sys.stderr, '** outputting label read counts...'
with open(fn, 'wb') as outfp:
for k in label_dict:
outfp.write('{l},{c}\n'.format(l=k, c=label_dict[k]))
def main():
info('trim-low-abund.py', ['streaming'])
parser = sanitize_help(get_parser())
args = parser.parse_args()
###
if len(set(args.input_filenames)) != len(args.input_filenames):
print("Error: Cannot input the same filename multiple times.",
file=sys.stderr)
sys.exit(1)
###
report_on_config(args)
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, args.force)
if args.savegraph:
graphsize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(args.savegraph, graphsize, args.force)
if ('-' in args.input_filenames or '/dev/stdin' in args.input_filenames) \
and not args.output:
print(
"Accepting input from stdin; output filename must "
"be provided with -o.",
file=sys.stderr)
sys.exit(1)
if args.loadgraph:
print('loading countgraph from', args.loadgraph, file=sys.stderr)
ct = khmer.load_countgraph(args.loadgraph)
else:
print('making countgraph', file=sys.stderr)
ct = khmer_args.create_countgraph(args)
K = ct.ksize()
CUTOFF = args.cutoff
NORMALIZE_LIMIT = args.normalize_to
tempdir = tempfile.mkdtemp('khmer', 'tmp', args.tempdir)
print('created temporary directory %s; '
'use -T to change location' % tempdir,
file=sys.stderr)
# ### FIRST PASS ###
save_pass2_total = 0
n_bp = 0
n_reads = 0
written_bp = 0
written_reads = 0
trimmed_reads = 0
pass2list = []
for filename in args.input_filenames:
pass2filename = os.path.basename(filename) + '.pass2'
pass2filename = os.path.join(tempdir, pass2filename)
if args.output is None:
trimfp = get_file_writer(
open(os.path.basename(filename) + '.abundtrim', 'wb'),
args.gzip, args.bzip)
else:
trimfp = get_file_writer(args.output, args.gzip, args.bzip)
pass2list.append((filename, pass2filename, trimfp))
screed_iter = screed.open(filename)
pass2fp = open(pass2filename, 'w')
save_pass2 = 0
n = 0
paired_iter = broken_paired_reader(screed_iter,
min_length=K,
force_single=args.ignore_pairs)
for n, is_pair, read1, read2 in paired_iter:
if n % 10000 == 0:
print('...',
n,
filename,
save_pass2,
n_reads,
n_bp,
written_reads,
written_bp,
file=sys.stderr)
# we want to track paired reads here, to make sure that pairs
# are not split between first pass and second pass.
if is_pair:
n_reads += 2
n_bp += len(read1.sequence) + len(read2.sequence)
seq1 = read1.sequence.replace('N', 'A')
seq2 = read2.sequence.replace('N', 'A')
med1, _, _ = ct.get_median_count(seq1)
med2, _, _ = ct.get_median_count(seq2)
if med1 < NORMALIZE_LIMIT or med2 < NORMALIZE_LIMIT:
ct.consume(seq1)
ct.consume(seq2)
write_record_pair(read1, read2, pass2fp)
save_pass2 += 2
else:
_, trim_at1 = ct.trim_on_abundance(seq1, CUTOFF)
_, trim_at2 = ct.trim_on_abundance(seq2, CUTOFF)
if trim_at1 >= K:
read1 = trim_record(read1, trim_at1)
if trim_at2 >= K:
read2 = trim_record(read2, trim_at2)
if trim_at1 != len(seq1):
trimmed_reads += 1
if trim_at2 != len(seq2):
trimmed_reads += 1
write_record_pair(read1, read2, trimfp)
written_reads += 2
written_bp += trim_at1 + trim_at2
else:
n_reads += 1
n_bp += len(read1.sequence)
seq = read1.sequence.replace('N', 'A')
med, _, _ = ct.get_median_count(seq)
# has this portion of the graph saturated? if not,
# consume & save => pass2.
if med < NORMALIZE_LIMIT:
ct.consume(seq)
write_record(read1, pass2fp)
save_pass2 += 1
else: # trim!!
_, trim_at = ct.trim_on_abundance(seq, CUTOFF)
if trim_at >= K:
new_read = trim_record(read1, trim_at)
write_record(new_read, trimfp)
written_reads += 1
written_bp += trim_at
if trim_at != len(read1.sequence):
trimmed_reads += 1
pass2fp.close()
print('%s: kept aside %d of %d from first pass, in %s' %
(filename, save_pass2, n, filename),
file=sys.stderr)
save_pass2_total += save_pass2
# ### SECOND PASS. ###
skipped_n = 0
skipped_bp = 0
for _, pass2filename, trimfp in pass2list:
print('second pass: looking at sequences kept aside in %s' %
pass2filename,
file=sys.stderr)
# note that for this second pass, we don't care about paired
# reads - they will be output in the same order they're read in,
# so pairs will stay together if not orphaned. This is in contrast
# to the first loop.
for n, read in enumerate(screed.open(pass2filename)):
if n % 10000 == 0:
print('... x 2',
n,
pass2filename,
written_reads,
written_bp,
file=sys.stderr)
seq = read.sequence.replace('N', 'A')
med, _, _ = ct.get_median_count(seq)
# do we retain low-abundance components unchanged?
if med < NORMALIZE_LIMIT and args.variable_coverage:
write_record(read, trimfp)
written_reads += 1
written_bp += len(read.sequence)
skipped_n += 1
skipped_bp += len(read.sequence)
# otherwise, examine/trim/truncate.
else: # med >= NORMALIZE LIMIT or not args.variable_coverage
_, trim_at = ct.trim_on_abundance(seq, CUTOFF)
if trim_at >= K:
new_read = trim_record(read, trim_at)
write_record(new_read, trimfp)
written_reads += 1
written_bp += trim_at
if trim_at != len(read.sequence):
trimmed_reads += 1
print('removing %s' % pass2filename, file=sys.stderr)
os.unlink(pass2filename)
print('removing temp directory & contents (%s)' % tempdir, file=sys.stderr)
shutil.rmtree(tempdir)
n_passes = 1.0 + (float(save_pass2_total) / n_reads)
percent_reads_trimmed = float(trimmed_reads + (n_reads - written_reads)) /\
n_reads * 100.0
print('read %d reads, %d bp' % (
n_reads,
n_bp,
), file=sys.stderr)
print('wrote %d reads, %d bp' % (
written_reads,
written_bp,
),
file=sys.stderr)
print('looked at %d reads twice (%.2f passes)' %
(save_pass2_total, n_passes),
file=sys.stderr)
print('removed %d reads and trimmed %d reads (%.2f%%)' %
(n_reads - written_reads, trimmed_reads, percent_reads_trimmed),
file=sys.stderr)
print('trimmed or removed %.2f%% of bases (%d total)' %
((1 - (written_bp / float(n_bp))) * 100.0, n_bp - written_bp),
file=sys.stderr)
if args.variable_coverage:
percent_reads_hicov = 100.0 * float(n_reads - skipped_n) / n_reads
print('%d reads were high coverage (%.2f%%);' %
(n_reads - skipped_n, percent_reads_hicov),
file=sys.stderr)
print('skipped %d reads/%d bases because of low coverage' %
(skipped_n, skipped_bp),
file=sys.stderr)
fp_rate = \
khmer.calc_expected_collisions(ct, args.force, max_false_pos=.8)
# for max_false_pos see Zhang et al., http://arxiv.org/abs/1309.2975
print('fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate),
file=sys.stderr)
print('output in *.abundtrim', file=sys.stderr)
if args.savegraph:
print("Saving k-mer countgraph to", args.savegraph, file=sys.stderr)
ct.save(args.savegraph)
def main(): # pylint: disable=too-many-locals,too-many-statements
info('do-partition.py', ['graph'])
args = get_parser().parse_args()
report_on_config(args, hashtype='hashbits')
for infile in args.input_filenames:
check_file_status(infile, args.force)
check_space(args.input_filenames, args.force)
print >>sys.stderr, 'Saving k-mer presence table to %s' % args.graphbase
print >>sys.stderr, 'Loading kmers from sequences in %s' % \
repr(args.input_filenames)
print >>sys.stderr, '--'
print >>sys.stderr, 'SUBSET SIZE', args.subset_size
print >>sys.stderr, 'N THREADS', args.threads
print >>sys.stderr, '--'
# load-graph
print >>sys.stderr, 'making k-mer presence table'
htable = khmer.new_hashbits(args.ksize, args.min_tablesize, args.n_tables)
for _, filename in enumerate(args.input_filenames):
print >>sys.stderr, 'consuming input', filename
htable.consume_fasta_and_tag(filename)
fp_rate = khmer.calc_expected_collisions(htable)
print >>sys.stderr, 'fp rate estimated to be %1.3f' % fp_rate
if fp_rate > 0.15: # 0.18 is ACTUAL MAX. Do not change.
print >> sys.stderr, "**"
print >> sys.stderr, ("** ERROR: the graph structure is too small for"
" this data set. Increase k-mer presence table "
"size/num of tables.")
print >> sys.stderr, "**"
if not args.force:
sys.exit(1)
# partition-graph
# do we want to exhaustively traverse the graph?
stop_big_traversals = args.no_big_traverse
if stop_big_traversals:
print >>sys.stderr, '** This script brakes for lumps: ', \
'stop_big_traversals is true.'
else:
print >>sys.stderr, '** Traverse all the things:', \
' stop_big_traversals is false.'
#
# now, partition!
#
# divide the tags up into subsets
divvy = htable.divide_tags_into_subsets(int(args.subset_size))
n_subsets = len(divvy)
divvy.append(0)
# build a queue of tasks:
worker_q = Queue.Queue()
# break up the subsets into a list of worker tasks
for _ in range(0, n_subsets):
start = divvy[_]
end = divvy[_ + 1]
worker_q.put((htable, _, start, end))
print >>sys.stderr, 'enqueued %d subset tasks' % n_subsets
open('%s.info' % args.graphbase, 'w').write('%d subsets total\n'
% (n_subsets))
if n_subsets < args.threads:
args.threads = n_subsets
# start threads!
print >>sys.stderr, 'starting %d threads' % args.threads
print >>sys.stderr, '---'
threads = []
for _ in range(args.threads):
cur_thread = threading.Thread(target=worker,
args=(worker_q, args.graphbase,
stop_big_traversals))
threads.append(cur_thread)
cur_thread.start()
assert threading.active_count() == args.threads + 1
print >>sys.stderr, 'done starting threads'
# wait for threads
for _ in threads:
_.join()
print >>sys.stderr, '---'
print >>sys.stderr, 'done making subsets! see %s.subset.*.pmap' % \
(args.graphbase,)
# merge-partitions
pmap_files = glob.glob(args.graphbase + '.subset.*.pmap')
print >>sys.stderr, 'loading %d pmap files (first one: %s)' % \
(len(pmap_files), pmap_files[0])
htable = khmer.new_hashbits(args.ksize, 1, 1)
for pmap_file in pmap_files:
print >>sys.stderr, 'merging', pmap_file
htable.merge_subset_from_disk(pmap_file)
if args.remove_subsets:
print >>sys.stderr, 'removing pmap files'
for pmap_file in pmap_files:
os.unlink(pmap_file)
# annotate-partitions
for infile in args.input_filenames:
print >>sys.stderr, 'outputting partitions for', infile
outfile = os.path.basename(infile) + '.part'
part_count = htable.output_partitions(infile, outfile)
print >>sys.stderr, 'output %d partitions for %s' % (
part_count, infile)
print >>sys.stderr, 'partitions are in', outfile
def main():
info('filter-abund-single.py', ['counting', 'SeqAn'])
args = get_parser().parse_args()
check_input_files(args.datafile, args.force)
check_space([args.datafile], args.force)
if args.savetable:
check_space_for_hashtable(args.n_tables * args.min_tablesize,
args.force)
report_on_config(args)
print('making k-mer counting table', file=sys.stderr)
htable = khmer.new_counting_hash(args.ksize, args.min_tablesize,
args.n_tables)
# first, load reads into hash table
rparser = khmer.ReadParser(args.datafile)
threads = []
print('consuming input, round 1 --', args.datafile, file=sys.stderr)
for _ in range(args.threads):
cur_thread = \
threading.Thread(
target=htable.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(cur_thread)
cur_thread.start()
for _ in threads:
_.join()
if args.report_total_kmers:
print('Total number of unique k-mers: {0}'.format(
htable.n_unique_kmers()),
file=sys.stderr)
fp_rate = khmer.calc_expected_collisions(htable, args.force)
print('fp rate estimated to be %1.3f' % fp_rate, file=sys.stderr)
# now, trim.
# the filtering function.
def process_fn(record):
name = record.name
seq = record.sequence
seqN = seq.replace('N', 'A')
_, trim_at = htable.trim_on_abundance(seqN, args.cutoff)
if trim_at >= args.ksize:
# be sure to not to change the 'N's in the trimmed sequence -
# so, return 'seq' and not 'seqN'.
return name, seq[:trim_at]
return None, None
# the filtering loop
print('filtering', args.datafile, file=sys.stderr)
outfile = os.path.basename(args.datafile) + '.abundfilt'
outfp = open(outfile, 'w')
tsp = ThreadedSequenceProcessor(process_fn)
tsp.start(verbose_loader(args.datafile), outfp)
print('output in', outfile, file=sys.stderr)
if args.savetable:
print('Saving k-mer counting table filename',
args.savetable,
file=sys.stderr)
print('...saving to', args.savetable, file=sys.stderr)
htable.save(args.savetable)
print('wrote to: ', outfile, file=sys.stderr)
