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()
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()
if not args.quiet:
info('load-into-counting.py', ['counting', 'SeqAn'])
configure_logging(args.quiet)
report_on_config(args)
base = args.output_countgraph_filename
filenames = args.input_sequence_filename
for name in args.input_sequence_filename:
check_input_files(name, args.force)
tablesize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(args.output_countgraph_filename, tablesize,
args.force)
info_filename = base + ".info"
check_file_writable(base)
check_file_writable(info_filename)
log_info('Saving k-mer countgraph to {base}', base=base)
log_info('Loading kmers from sequences in {filenames}',
filenames=repr(filenames))
# clobber the '.info' file now, as we always open in append mode below
with open(info_filename, 'w') as info_fp:
print('khmer version:', khmer.__version__, file=info_fp)
log_info('making countgraph')
countgraph = khmer_args.create_countgraph(args)
countgraph.set_use_bigcount(args.bigcount)
filename = None
total_num_reads = 0
for index, filename in enumerate(filenames):
rparser = khmer.ReadParser(filename)
threads = []
log_info('consuming input {input}', input=filename)
for _ in range(args.threads):
cur_thrd = \
threading.Thread(
target=countgraph.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:
tablesize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(base, tablesize, args.force)
log_info('mid-save {base}', base=base)
countgraph.save(base)
with open(info_filename, 'a') as info_fh:
print('through', filename, file=info_fh)
total_num_reads += rparser.num_reads
n_kmers = countgraph.n_unique_kmers()
log_info('Total number of unique k-mers: {nk}', nk=n_kmers)
with open(info_filename, 'a') as info_fp:
print('Total number of unique k-mers:', n_kmers, file=info_fp)
log_info('saving {base}', base=base)
countgraph.save(base)
# Change max_false_pos=0.2 only if you really grok it. HINT: You don't
fp_rate = \
khmer.calc_expected_collisions(
countgraph, args.force, max_false_pos=.2)
with open(info_filename, 'a') as info_fp:
print('fp rate estimated to be %1.3f\n' % fp_rate, file=info_fp)
if args.summary_info:
mr_fmt = args.summary_info.lower()
mr_file = base + '.info.' + mr_fmt
log_info("Writing summmary info to {mr_file}", mr_file=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")
log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
log_info('DONE.')
log_info('wrote to: {filename}', filename=info_filename)
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():
args = sanitize_help(get_parser()).parse_args()
configure_logging(args.quiet)
report_on_config(args)
base = args.output_countgraph_filename
filenames = args.input_sequence_filename
for name in args.input_sequence_filename:
check_input_files(name, args.force)
tablesize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(args.output_countgraph_filename, tablesize,
args.force)
info_filename = base + ".info"
check_file_writable(base)
check_file_writable(info_filename)
log_info('Saving k-mer countgraph to {base}', base=base)
log_info('Loading kmers from sequences in {filenames}',
filenames=repr(filenames))
# clobber the '.info' file now, as we always open in append mode below
with open(info_filename, 'w') as info_fp:
print('khmer version:', khmer.__version__, file=info_fp)
log_info('making countgraph')
countgraph = khmer_args.create_countgraph(args)
filename = None
total_num_reads = 0
for index, filename in enumerate(filenames):
rparser = khmer.ReadParser(filename)
threads = []
log_info('consuming input {input}', input=filename)
for _ in range(args.threads):
cur_thrd = \
threading.Thread(
target=countgraph.consume_seqfile_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:
tablesize = calculate_graphsize(args, 'countgraph')
check_space_for_graph(base, tablesize, args.force)
log_info('mid-save {base}', base=base)
countgraph.save(base)
with open(info_filename, 'a') as info_fh:
print('through', filename, file=info_fh)
total_num_reads += rparser.num_reads
n_kmers = countgraph.n_unique_kmers()
log_info('Total number of unique k-mers: {nk}', nk=n_kmers)
with open(info_filename, 'a') as info_fp:
print('Total number of unique k-mers:', n_kmers, file=info_fp)
log_info('saving {base}', base=base)
countgraph.save(base)
# Change max_false_pos=0.2 only if you really grok it. HINT: You don't
fp_rate = \
khmer.calc_expected_collisions(
countgraph, args.force, max_false_pos=.2)
with open(info_filename, 'a') as info_fp:
print('fp rate estimated to be %1.3f\n' % fp_rate, file=info_fp)
if args.summary_info:
mr_fmt = args.summary_info.lower()
mr_file = base + '.info.' + mr_fmt
log_info("Writing summmary info to {mr_file}", mr_file=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")
log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
log_info('DONE.')
log_info('wrote to: {filename}', filename=info_filename)
def main(): # pylint: disable=too-many-locals,too-many-branches
args = sanitize_help(get_parser()).parse_args()
graph_type = 'smallcountgraph' if args.small_count else 'countgraph'
configure_logging(args.quiet)
report_on_config(args, graph_type)
check_input_files(args.input_sequence_filename, args.force)
if args.savegraph is not None:
graphsize = calculate_graphsize(args, graph_type)
check_space_for_graph(args.savegraph, graphsize, args.force)
if (not args.squash_output
and os.path.exists(args.output_histogram_filename)):
log_error('ERROR: {output} exists; not squashing.',
output=args.output_histogram_filename)
sys.exit(1)
else:
hist_fp = open(args.output_histogram_filename, 'w')
hist_fp_csv = csv.writer(hist_fp)
# write headers:
hist_fp_csv.writerow(
['abundance', 'count', 'cumulative', 'cumulative_fraction'])
log_info('making countgraph')
# In case the user specified a maximum memory usage, use 8/(9+eps) of that
# for the countgraph and 1/(9+eps) for the tracking nodegraph
# `eps` is used to account for the memory used by the python interpreter
countgraph = khmer_args.create_countgraph(args, multiplier=8 / (9. + 0.3))
countgraph.set_use_bigcount(args.bigcount)
log_info('building k-mer tracking graph')
tracking = khmer_args.create_matching_nodegraph(countgraph)
log_info('kmer_size: {ksize}', ksize=countgraph.ksize())
log_info('k-mer countgraph sizes: {sizes}', sizes=countgraph.hashsizes())
log_info('outputting to {output}', output=args.output_histogram_filename)
# start loading
rparser = khmer.ReadParser(args.input_sequence_filename)
threads = []
log_info('consuming input, round 1 -- {input}',
input=args.input_sequence_filename)
for _ in range(args.threads):
thread = \
threading.Thread(
target=countgraph.consume_seqfile_with_reads_parser,
args=(rparser, )
)
threads.append(thread)
thread.start()
for thread in threads:
thread.join()
log_info('Total number of unique k-mers: {nk}',
nk=countgraph.n_unique_kmers())
abundance_lists = []
def __do_abundance_dist__(read_parser):
abundances = countgraph.abundance_distribution_with_reads_parser(
read_parser, tracking)
abundance_lists.append(abundances)
log_info('preparing hist from {seqfile}...',
seqfile=args.input_sequence_filename)
rparser = khmer.ReadParser(args.input_sequence_filename)
threads = []
log_info('consuming input, round 2 -- {filename}',
filename=args.input_sequence_filename)
for _ in range(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:
log_error("ERROR: abundance distribution is uniformly zero; "
"nothing to report.")
log_error("\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)
hist_fp_csv.writerow([_, i, sofar, round(frac, 3)])
if sofar == total:
break
if args.savegraph is not None:
log_info('Saving k-mer countgraph to {savegraph}',
savegraph=args.savegraph)
countgraph.save(args.savegraph)
log_info('wrote to: {output}', output=args.output_histogram_filename)
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():
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():
args = sanitize_help(get_parser()).parse_args()
if not args.quiet:
info('abundance-dist.py', ['counting'])
configure_logging(args.quiet)
infiles = [args.input_count_graph_filename,
args.input_sequence_filename]
for infile in infiles:
check_input_files(infile, False)
log_info('Loading counting graph from {graph}',
graph=args.input_count_graph_filename)
countgraph = khmer.load_countgraph(
args.input_count_graph_filename)
if not countgraph.get_use_bigcount() and args.bigcount:
log_warn("WARNING: The loaded graph has bigcount DISABLED while "
"bigcount reporting is ENABLED--counts higher than 255 will "
"not be reported.")
countgraph.set_use_bigcount(args.bigcount)
kmer_size = countgraph.ksize()
hashsizes = countgraph.hashsizes()
tracking = khmer._Nodegraph( # pylint: disable=protected-access
kmer_size, hashsizes)
log_info('K: {ksize}', ksize=kmer_size)
log_info('outputting to {output}', output=args.output_histogram_filename)
if args.output_histogram_filename in ('-', '/dev/stdout'):
pass
elif os.path.exists(args.output_histogram_filename):
if not args.squash_output:
log_error('ERROR: {output} exists; not squashing.',
output=args.output_histogram_filename)
sys.exit(1)
log_info('** squashing existing file {output}',
output=args.output_histogram_filename)
log_info('preparing hist...')
abundances = countgraph.abundance_distribution(
args.input_sequence_filename, tracking)
total = sum(abundances)
if 0 == total:
log_error("ERROR: abundance distribution is uniformly zero; "
"nothing to report.")
log_error("\tPlease verify that the input files are valid.")
sys.exit(1)
if args.output_histogram_filename in ('-', '/dev/stdout'):
countgraph_fp = sys.stdout
else:
countgraph_fp = open(args.output_histogram_filename, 'w')
countgraph_fp_csv = csv.writer(countgraph_fp)
# write headers:
countgraph_fp_csv.writerow(['abundance', 'count', 'cumulative',
'cumulative_fraction'])
sofar = 0
for _, i in enumerate(abundances):
if i == 0 and not args.output_zero:
continue
sofar += i
frac = sofar / float(total)
countgraph_fp_csv.writerow([_, i, sofar, round(frac, 3)])
if sofar == total:
break
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():
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():
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():
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(): # pylint: disable=too-many-locals,too-many-branches
args = sanitize_help(get_parser()).parse_args()
graph_type = 'smallcountgraph' if args.small_count else 'countgraph'
configure_logging(args.quiet)
report_on_config(args, graph_type)
check_input_files(args.input_sequence_filename, args.force)
if args.savegraph is not None:
graphsize = calculate_graphsize(args, graph_type)
check_space_for_graph(args.savegraph, graphsize, args.force)
if (not args.squash_output and
os.path.exists(args.output_histogram_filename)):
log_error('ERROR: {output} exists; not squashing.',
output=args.output_histogram_filename)
sys.exit(1)
else:
hist_fp = open(args.output_histogram_filename, 'w')
hist_fp_csv = csv.writer(hist_fp)
# write headers:
hist_fp_csv.writerow(['abundance', 'count', 'cumulative',
'cumulative_fraction'])
log_info('making countgraph')
# In case the user specified a maximum memory usage, use 8/(9+eps) of that
# for the countgraph and 1/(9+eps) for the tracking nodegraph
# `eps` is used to account for the memory used by the python interpreter
countgraph = khmer_args.create_countgraph(args, multiplier=8 / (9. + 0.3))
log_info('building k-mer tracking graph')
tracking = khmer_args.create_matching_nodegraph(countgraph)
log_info('kmer_size: {ksize}', ksize=countgraph.ksize())
log_info('k-mer countgraph sizes: {sizes}', sizes=countgraph.hashsizes())
log_info('outputting to {output}', output=args.output_histogram_filename)
# start loading
rparser = khmer.ReadParser(args.input_sequence_filename)
threads = []
log_info('consuming input, round 1 -- {input}',
input=args.input_sequence_filename)
for _ in range(args.threads):
thread = \
threading.Thread(
target=countgraph.consume_seqfile,
args=(rparser, )
)
threads.append(thread)
thread.start()
for thread in threads:
thread.join()
log_info('Total number of unique k-mers: {nk}',
nk=countgraph.n_unique_kmers())
abundance_lists = []
def __do_abundance_dist__(read_parser):
abundances = countgraph.abundance_distribution(
read_parser, tracking)
abundance_lists.append(abundances)
log_info('preparing hist from {seqfile}...',
seqfile=args.input_sequence_filename)
rparser = khmer.ReadParser(args.input_sequence_filename)
threads = []
log_info('consuming input, round 2 -- {filename}',
filename=args.input_sequence_filename)
for _ in range(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:
log_error("ERROR: abundance distribution is uniformly zero; "
"nothing to report.")
log_error("\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)
hist_fp_csv.writerow([_, i, sofar, round(frac, 3)])
if sofar == total:
break
if args.savegraph is not None:
log_info('Saving k-mer countgraph to {savegraph}',
savegraph=args.savegraph)
countgraph.save(args.savegraph)
log_info('wrote to: {output}', output=args.output_histogram_filename)
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(): # 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():
args = sanitize_help(get_parser()).parse_args()
configure_logging(args.quiet)
infiles = [args.input_count_graph_filename, args.input_sequence_filename]
for infile in infiles:
check_input_files(infile, False)
log_info('Loading counting graph from {graph}',
graph=args.input_count_graph_filename)
countgraph = khmer.load_countgraph(args.input_count_graph_filename)
if not countgraph.get_use_bigcount() and args.bigcount:
log_warn("WARNING: The loaded graph has bigcount DISABLED while "
"bigcount reporting is ENABLED--counts higher than 255 will "
"not be reported.")
countgraph.set_use_bigcount(args.bigcount)
kmer_size = countgraph.ksize()
hashsizes = countgraph.hashsizes()
tracking = khmer._Nodegraph( # pylint: disable=protected-access
kmer_size, hashsizes)
log_info('K: {ksize}', ksize=kmer_size)
log_info('outputting to {output}', output=args.output_histogram_filename)
if args.output_histogram_filename in ('-', '/dev/stdout'):
pass
elif os.path.exists(args.output_histogram_filename):
if not args.squash_output:
log_error('ERROR: {output} exists; not squashing.',
output=args.output_histogram_filename)
sys.exit(1)
log_info('** squashing existing file {output}',
output=args.output_histogram_filename)
log_info('preparing hist...')
abundances = countgraph.abundance_distribution(
args.input_sequence_filename, tracking)
total = sum(abundances)
if 0 == total:
log_error("ERROR: abundance distribution is uniformly zero; "
"nothing to report.")
log_error("\tPlease verify that the input files are valid.")
sys.exit(1)
if args.output_histogram_filename in ('-', '/dev/stdout'):
countgraph_fp = sys.stdout
else:
countgraph_fp = open(args.output_histogram_filename, 'w')
countgraph_fp_csv = csv.writer(countgraph_fp)
# write headers:
countgraph_fp_csv.writerow(
['abundance', 'count', 'cumulative', 'cumulative_fraction'])
sofar = 0
for _, i in enumerate(abundances):
if i == 0 and not args.output_zero:
continue
sofar += i
frac = sofar / float(total)
countgraph_fp_csv.writerow([_, i, sofar, round(frac, 3)])
if sofar == total:
break
