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 test_get_file_writer_fail():
somefile = utils.get_temp_filename("potato")
somefile = open(somefile, "w")
stopped = True
try:
get_file_writer(somefile, True, True)
stopped = False
except ValueError as err:
assert "Cannot specify both bzip and gzip" in str(err), str(err)
assert stopped, "Expected exception"
def test_get_file_writer_fail():
somefile = utils.get_temp_filename("potato")
somefile = open(somefile, "w")
stopped = True
try:
get_file_writer(somefile, True, True)
stopped = False
except ValueError as err:
assert "Cannot specify both bzip and gzip" in str(err), str(err)
assert stopped, "Expected exception"
def main():
args = sanitize_help(get_parser()).parse_args()
if not args.quiet:
info('filter-abund.py', ['counting'])
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 = 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 = sanitize_help(get_parser()).parse_args()
print('fastq from ', args.input_sequence, file=sys.stderr)
outfp = get_file_writer(args.output, args.gzip, args.bzip)
n_count = 0
for n, record in enumerate(screed.open(args.input_sequence)):
if n % 10000 == 0:
print('...', n, file=sys.stderr)
sequence = record['sequence']
if 'N' in sequence:
if not args.n_keep:
n_count += 1
continue
del record['quality']
write_record(record, outfp)
print('\n' + 'lines from ' + args.input_sequence, file=sys.stderr)
if not args.n_keep:
print(str(n_count) + ' lines dropped.', file=sys.stderr)
else:
print('No lines dropped from file.', file=sys.stderr)
print('Wrote output to', describe_file_handle(args.output),
file=sys.stderr)
def main():
args = sanitize_help(get_parser()).parse_args()
print('fastq from ', args.input_sequence, file=sys.stderr)
outfp = get_file_writer(args.output, args.gzip, args.bzip)
n_count = 0
for n, record in enumerate(screed.open(args.input_sequence)):
if n % 10000 == 0:
print('...', n, file=sys.stderr)
sequence = record['sequence']
if 'N' in sequence:
if not args.n_keep:
n_count += 1
continue
del record['quality']
write_record(record, outfp)
print('\n' + 'lines from ' + args.input_sequence, file=sys.stderr)
if not args.n_keep:
print(str(n_count) + ' lines dropped.', file=sys.stderr)
else:
print('No lines dropped from file.', file=sys.stderr)
print('Wrote output to',
describe_file_handle(args.output),
file=sys.stderr)
def main():
args = sanitize_help(get_parser()).parse_args()
outfp = get_file_writer(args.output, args.gzip, args.bzip)
for filename in args.input_filenames:
for record in screed.open(filename):
if len(record['sequence']) >= args.length:
write_record(record, outfp)
print('wrote to: ' + args.output.name, file=sys.stderr)
def main():
args = sanitize_help(get_parser()).parse_args()
outfp = get_file_writer(args.output, args.gzip, args.bzip)
for filename in args.input_filenames:
for record in screed.open(filename):
if len(record['sequence']) >= args.length:
write_record(record, outfp)
print('wrote to: ' + args.output.name, file=sys.stderr)
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 = 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
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():
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()
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', '-'):
# seqan only treats '-' as "read from stdin"
infile = '-'
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
# walk through all the reads in broken-paired mode.
paired_iter = broken_paired_reader(ReadParser(infile),
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.read1.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)
# 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(): # pylint: disable=too-many-branches,too-many-statements
parser = sanitize_help(get_parser())
args = parser.parse_args()
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 is not None:
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 = Countgraph.load(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 = clean_input_reads(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 is not None:
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(): # pylint: disable=too-many-locals,too-many-branches
info('extract-partitions.py', ['graph'])
args = sanitize_help(get_parser()).parse_args()
distfilename = args.prefix + '.dist'
n_unassigned = 0
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 = '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:
ofile = open('%s.unassigned.%s' % (args.prefix, suffix), 'wb')
unassigned_fp = get_file_writer(ofile, args.gzip, args.bzip)
count = {}
for filename in args.part_filenames:
for index, read, pid in read_partition_file(filename):
if index % 100000 == 0:
print('...', index, file=sys.stderr)
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 list(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(list(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('%d groups' % group_n, file=sys.stderr)
if 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(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!
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('...x2', index, file=sys.stderr)
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('---', file=sys.stderr)
print('Of %d total seqs,' % total_seqs, file=sys.stderr)
print('extracted %d partitioned seqs into group files,' %
part_seqs, file=sys.stderr)
print('discarded %d sequences from small partitions (see -m),' %
toosmall_parts, file=sys.stderr)
print('and found %d unpartitioned sequences (see -U).' %
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():
parser = sanitize_help(get_parser())
args = parser.parse_args()
if not args.quiet:
info('trim-low-abund.py', ['streaming'])
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)
###
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:
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)
ct = khmer.load_countgraph(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 = 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:
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.
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:
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)
log_info('removing {pass2}', pass2=pass2filename)
os.unlink(pass2filename)
# if we created our own trimfps, close 'em.
if not args.output:
trimfp.close()
log_info('removing temp directory & contents ({temp})', temp=tempdir)
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
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)
log_info('output in *.abundtrim')
if args.savegraph:
log_info("Saving k-mer countgraph to {graph}", graph=args.savegraph)
ct.save(args.savegraph)
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():
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():
args = sanitize_help(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 in ('/dev/stdin', '-'):
# seqan only treats '-' as "read from stdin"
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 = get_file_writer(args.output_paired, args.gzip, args.bzip)
out2 = paired_fp.name
else:
# Don't override, just open the default filename from above
paired_fp = get_file_writer(open(out2, 'wb'), args.gzip, args.bzip)
if args.output_single:
single_fp = get_file_writer(args.output_single, args.gzip, args.bzip)
out1 = args.output_single.name
else:
# Don't override, just open the default filename from above
single_fp = get_file_writer(open(out1, 'wb'), args.gzip, args.bzip)
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 = ReadParser(infile)
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():
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(): # pylint: disable=too-many-branches,too-many-statements
start_time = time.time()
parser = sanitize_help(get_parser())
args = parser.parse_args()
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 is not None:
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)
countgraph1 = Countgraph.load(args.loadgraph)
# load second counting table.
if args.loadgraph2:
log_info('loading k-mer countgraph from {graph}',
graph=args.loadgraph2)
countgraph2 = Countgraph.load(args.loadgraph2)
# 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])
#
# 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)
screed_iter = clean_input_reads(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 _, is_paired, read0, read1 in reader:
for record in snarf(is_paired, read0, read1, countgraph1,
countgraph2):
if record is not None:
write_record(record, outfp)
print("--- %s seconds ---" % (time.time() - start_time))
def main(): # pylint: disable=too-many-branches,too-many-statements
parser = sanitize_help(get_parser())
args = parser.parse_args()
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 is not None:
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 = clean_input_reads(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 is not None:
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():
args = sanitize_help(get_parser()).parse_args()
if not args.quiet:
info('filter-abund.py', ['counting'])
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)
# 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:
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)
tsp = ThreadedSequenceProcessor(process_fn, n_workers=args.threads,
verbose=not args.quiet)
tsp.start(verbose_loader(infile), outfp)
log_info('output in {outfile}', outfile=outfile)
def main():
info('filter-abund-single.py', ['counting', 'SeqAn'])
args = sanitize_help(get_parser()).parse_args()
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)
print('making countgraph', file=sys.stderr)
graph = khmer_args.create_countgraph(args)
# first, load reads into graph
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=graph.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(cur_thread)
cur_thread.start()
for _ in threads:
_.join()
print('Total number of unique k-mers: {0}'.format(graph.n_unique_kmers()),
file=sys.stderr)
fp_rate = khmer.calc_expected_collisions(graph, 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 = 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
print('filtering', args.datafile, file=sys.stderr)
outfile = os.path.basename(args.datafile) + '.abundfilt'
outfile = open(outfile, 'wb')
outfp = get_file_writer(outfile, args.gzip, args.bzip)
tsp = ThreadedSequenceProcessor(process_fn)
tsp.start(verbose_loader(args.datafile), outfp)
print('output in', outfile.name, file=sys.stderr)
if args.savegraph:
print('Saving k-mer countgraph filename',
args.savegraph,
file=sys.stderr)
graph.save(args.savegraph)
def main():
sys.argv = parse_humanfriendly_mem(sys.argv)
info('filter-abund-single.py', ['counting', 'SeqAn'])
args = sanitize_help(get_parser()).parse_args()
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)
print('making countgraph', file=sys.stderr)
graph = khmer_args.create_countgraph(args)
# first, load reads into graph
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=graph.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(cur_thread)
cur_thread.start()
for _ in threads:
_.join()
print('Total number of unique k-mers: {0}'.format(
graph.n_unique_kmers()), file=sys.stderr)
fp_rate = khmer.calc_expected_collisions(graph, 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 = 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
print('filtering', args.datafile, file=sys.stderr)
outfile = os.path.basename(args.datafile) + '.abundfilt'
outfile = open(outfile, 'wb')
outfp = get_file_writer(outfile, args.gzip, args.bzip)
tsp = ThreadedSequenceProcessor(process_fn)
tsp.start(verbose_loader(args.datafile), outfp)
print('output in', outfile.name, file=sys.stderr)
if args.savegraph:
print('Saving k-mer countgraph filename',
args.savegraph, file=sys.stderr)
graph.save(args.savegraph)
def main(): # pylint: disable=too-many-locals,too-many-branches
info('extract-partitions.py', ['graph'])
args = sanitize_help(get_parser()).parse_args()
distfilename = args.prefix + '.dist'
n_unassigned = 0
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 = '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:
ofile = open('%s.unassigned.%s' % (args.prefix, suffix), 'wb')
unassigned_fp = get_file_writer(ofile, args.gzip, args.bzip)
count = {}
for filename in args.part_filenames:
for index, read, pid in read_partition_file(filename):
if index % 100000 == 0:
print('...', index, file=sys.stderr)
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 list(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(list(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('%d groups' % group_n, file=sys.stderr)
if 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(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!
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('...x2', index, file=sys.stderr)
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('---', file=sys.stderr)
print('Of %d total seqs,' % total_seqs, file=sys.stderr)
print('extracted %d partitioned seqs into group files,' % part_seqs,
file=sys.stderr)
print('discarded %d sequences from small partitions (see -m),' %
toosmall_parts,
file=sys.stderr)
print('and found %d unpartitioned sequences (see -U).' % 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():
parser = sanitize_help(get_parser())
args = parser.parse_args()
if not args.quiet:
info('trim-low-abund.py', ['streaming'])
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)
###
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:
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)
ct = khmer.load_countgraph(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 = 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:
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.
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:
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)
log_info('removing {pass2}', pass2=pass2filename)
os.unlink(pass2filename)
# if we created our own trimfps, close 'em.
if not args.output:
trimfp.close()
log_info('removing temp directory & contents ({temp})', temp=tempdir)
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
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)
log_info('output in *.abundtrim')
if args.savegraph:
log_info("Saving k-mer countgraph to {graph}", graph=args.savegraph)
ct.save(args.savegraph)
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.read1.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():
info('extract-partitions.py', ['graph'])
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():
parser = get_parser()
parser.epilog = parser.epilog.replace(
"`reservoir sampling\n"
"<http://en.wikipedia.org/wiki/Reservoir_sampling>`__ algorithm.",
"reservoir sampling algorithm. "
"http://en.wikipedia.org/wiki/Reservoir_sampling")
args = sanitize_help(parser).parse_args()
for name in args.filenames:
check_input_files(name, 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
if args.output_file:
output_filename = args.output_file.name
if num_samples > 1:
sys.stderr.write(
"Error: cannot specify -o with more than one sample.")
if not args.force:
print(
"NOTE: This can be overridden using the --force"
" argument",
file=sys.stderr)
sys.exit(1)
else:
filename = args.filenames[0]
if filename in ('/dev/stdin', '-'):
print(
"Accepting input from stdin; output filename must "
"be provided with '-o'.",
file=sys.stderr)
sys.exit(1)
output_filename = os.path.basename(filename) + '.subset'
filename = args.filenames[0]
if filename in ('/dev/stdin', '-'):
# seqan only treats '-' as "read from stdin"
filename = '-'
if num_samples == 1:
print('Subsampling %d reads using reservoir sampling.' %
args.num_reads,
file=sys.stderr)
print('Subsampled reads will be placed in %s' % output_filename,
file=sys.stderr)
print('', file=sys.stderr)
else: # > 1
print('Subsampling %d reads, %d times,' %
(args.num_reads, num_samples),
' using reservoir sampling.',
file=sys.stderr)
print('Subsampled reads will be placed in %s.N' % output_filename,
file=sys.stderr)
print('', file=sys.stderr)
reads = []
for _ in range(num_samples):
reads.append([])
# read through all the sequences and load/resample the reservoir
for filename in args.filenames:
print('opening', filename, 'for reading', file=sys.stderr)
for count, (_, _, rcrd1, rcrd2) in enumerate(
broken_paired_reader(ReadParser(filename),
force_single=args.force_single)):
if count % 10000 == 0:
print('...', count, 'reads scanned', file=sys.stderr)
if count >= args.max_reads:
print('reached upper limit of %d reads' % args.max_reads,
'(see -M); exiting',
file=sys.stderr)
break
# collect first N reads
if count < args.num_reads:
for sample in range(num_samples):
reads[sample].append((rcrd1, rcrd2))
else:
for sample in range(num_samples):
assert len(reads[sample]) <= 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('Writing %d sequences to %s' % (len(reads[0]), output_filename),
file=sys.stderr)
output_file = args.output_file
if not output_file:
output_file = open(output_filename, 'wb')
output_file = get_file_writer(output_file, args.gzip, args.bzip)
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('Writing %d sequences to %s' % (len(reads[n]), n_filename),
file=sys.stderr)
output_file = get_file_writer(open(n_filename, 'wb'), args.gzip,
args.bzip)
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():
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')
if args.variable_coverage: # only trim when sequence has high enough C
med, _, _ = graph.get_median_count(seqN)
if med < args.normalize_to:
return name, seq
_, 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('sample-reads-randomly.py')
args = get_parser().parse_args()
for _ in args.filenames:
check_input_files(_, 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
if args.output_file:
output_filename = args.output_file.name
if num_samples > 1:
sys.stderr.write(
"Error: cannot specify -o with more than one sample.")
if not args.force:
print("NOTE: This can be overridden using the --force"
" argument", file=sys.stderr)
sys.exit(1)
else:
filename = args.filenames[0]
if filename in ('/dev/stdin', '-'):
print("Accepting input from stdin; output filename must "
"be provided with '-o'.", file=sys.stderr)
sys.exit(1)
output_filename = os.path.basename(filename) + '.subset'
if num_samples == 1:
print('Subsampling %d reads using reservoir sampling.' %
args.num_reads, file=sys.stderr)
print('Subsampled reads will be placed in %s' %
output_filename, file=sys.stderr)
print('', file=sys.stderr)
else: # > 1
print('Subsampling %d reads, %d times,'
% (args.num_reads, num_samples), ' using reservoir sampling.',
file=sys.stderr)
print('Subsampled reads will be placed in %s.N'
% output_filename, file=sys.stderr)
print('', file=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('opening', filename, 'for reading', file=sys.stderr)
screed_iter = screed.open(filename)
for count, (_, ispair, rcrd1, rcrd2) in enumerate(broken_paired_reader(
screed_iter,
force_single=args.force_single)):
if count % 10000 == 0:
print('...', count, 'reads scanned', file=sys.stderr)
if count >= args.max_reads:
print('reached upper limit of %d reads' %
args.max_reads, '(see -M); exiting', file=sys.stderr)
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('Writing %d sequences to %s' %
(len(reads[0]), output_filename), file=sys.stderr)
output_file = args.output_file
if not output_file:
output_file = open(output_filename, 'wb')
output_file = get_file_writer(output_file, args.gzip, args.bzip)
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('Writing %d sequences to %s' %
(len(reads[n]), n_filename), file=sys.stderr)
output_file = get_file_writer(open(n_filename, 'wb'), args.gzip,
args.bzip)
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():
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)
