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():
info('load-into-counting.py', ['counting', 'SeqAn'])
args = get_parser().parse_args()
report_on_config(args)
base = args.output_countingtable_filename
filenames = args.input_sequence_filename
for name in args.input_sequence_filename:
check_input_files(name, args.force)
check_space(args.input_sequence_filename, args.force)
check_space_for_hashtable(args.n_tables * args.min_tablesize, args.force)
check_file_writable(base)
check_file_writable(base + ".info")
print >>sys.stderr, 'Saving k-mer counting table to %s' % base
print >>sys.stderr, 'Loading kmers from sequences in %s' % repr(filenames)
# clobber the '.info' file now, as we always open in append mode below
if os.path.exists(base + '.info'):
os.remove(base + '.info')
print >>sys.stderr, 'making k-mer counting table'
htable = khmer.new_counting_hash(args.ksize, args.min_tablesize,
args.n_tables)
htable.set_use_bigcount(args.bigcount)
filename = None
for index, filename in enumerate(filenames):
rparser = khmer.ReadParser(filename)
threads = []
print >>sys.stderr, 'consuming input', filename
for _ in xrange(args.threads):
cur_thrd = \
threading.Thread(
target=htable.consume_fasta_with_reads_parser,
args=(rparser, )
)
threads.append(cur_thrd)
cur_thrd.start()
for thread in threads:
thread.join()
if index > 0 and index % 10 == 0:
check_space_for_hashtable(args.n_tables * args.min_tablesize,
args.force)
print >>sys.stderr, 'mid-save', base
htable.save(base)
with open(base + '.info', 'a') as info_fh:
print >> info_fh, 'through', filename
n_kmers = htable.n_unique_kmers()
if args.report_total_kmers:
print >> sys.stderr, 'Total number of unique k-mers:', n_kmers
with open(base + '.info', 'a') as info_fp:
print >>info_fp, 'Total number of unique k-mers:', n_kmers
print >>sys.stderr, 'saving', base
htable.save(base)
# Change max_false_pos=0.2 only if you really grok it. HINT: You don't
fp_rate = \
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.2)
with open(base + '.info', 'a') as info_fp:
print >> info_fp, 'fp rate estimated to be %1.3f\n' % fp_rate
if args.summary_info:
mr_fmt = args.summary_info.lower()
mr_file = base + '.info.' + mr_fmt
print >> sys.stderr, "Writing summmary info to", mr_file
with open(mr_file, 'w') as mr_fh:
if mr_fmt == 'json':
mr_data = {
"ht_name": os.path.basename(base),
"fpr": fp_rate,
"num_kmers": n_kmers,
"files": filenames,
"mrinfo_version": "0.1.0",
}
json.dump(mr_data, mr_fh)
mr_fh.write('\n')
elif mr_fmt == 'tsv':
mr_fh.write("ht_name\tfpr\tnum_kmers\tfiles\n")
mr_fh.write("{b:s}\t{fpr:1.3f}\t{k:d}\t{fls:s}\n".format(
b=os.path.basename(base), fpr=fp_rate, k=n_kmers,
fls=";".join(filenames)))
print >> sys.stderr, 'fp rate estimated to be %1.3f' % fp_rate
print >>sys.stderr, 'DONE.'
print >>sys.stderr, 'wrote to:', base + '.info'
def main():
info('load-into-counting.py', ['counting', 'SeqAn'])
args = sanitize_help(get_parser()).parse_args()
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)
check_file_writable(base)
check_file_writable(base + ".info")
print('Saving k-mer countgraph to %s' % base, file=sys.stderr)
print('Loading kmers from sequences in %s' % repr(filenames),
file=sys.stderr)
# clobber the '.info' file now, as we always open in append mode below
if os.path.exists(base + '.info'):
os.remove(base + '.info')
print('making countgraph', file=sys.stderr)
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 = []
print('consuming input', filename, file=sys.stderr)
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)
print('mid-save', base, file=sys.stderr)
countgraph.save(base)
with open(base + '.info', 'a') as info_fh:
print('through', filename, file=info_fh)
total_num_reads += rparser.num_reads
n_kmers = countgraph.n_unique_kmers()
print('Total number of unique k-mers:', n_kmers, file=sys.stderr)
with open(base + '.info', 'a') as info_fp:
print('Total number of unique k-mers:', n_kmers, file=info_fp)
print('saving', base, file=sys.stderr)
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(base + '.info', '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
print("Writing summmary info to", mr_file, file=sys.stderr)
with open(mr_file, 'w') as mr_fh:
if mr_fmt == 'json':
mr_data = {
"ht_name": os.path.basename(base),
"fpr": fp_rate,
"num_kmers": n_kmers,
"files": filenames,
"mrinfo_version": "0.2.0",
"num_reads": total_num_reads,
}
json.dump(mr_data, mr_fh)
mr_fh.write('\n')
elif mr_fmt == 'tsv':
mr_fh.write("ht_name\tfpr\tnum_kmers\tnum_reads\tfiles\n")
vals = [
os.path.basename(base),
"{:1.3f}".format(fp_rate),
str(n_kmers),
str(total_num_reads),
";".join(filenames),
]
mr_fh.write("\t".join(vals) + "\n")
print('fp rate estimated to be %1.3f' % fp_rate, file=sys.stderr)
print('DONE.', file=sys.stderr)
print('wrote to:', base + '.info', file=sys.stderr)
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():
info("load-into-counting.py", ["counting", "SeqAn"])
args = get_parser().parse_args()
report_on_config(args)
base = args.output_countingtable_filename
filenames = args.input_sequence_filename
for name in args.input_sequence_filename:
check_input_files(name, args.force)
check_space(args.input_sequence_filename, args.force)
check_space_for_hashtable(args.n_tables * args.min_tablesize, args.force)
check_file_writable(base)
check_file_writable(base + ".info")
print("Saving k-mer counting table to %s" % base, file=sys.stderr)
print("Loading kmers from sequences in %s" % repr(filenames), file=sys.stderr)
# clobber the '.info' file now, as we always open in append mode below
if os.path.exists(base + ".info"):
os.remove(base + ".info")
print("making k-mer counting table", file=sys.stderr)
htable = khmer.new_counting_hash(args.ksize, args.min_tablesize, args.n_tables)
htable.set_use_bigcount(args.bigcount)
filename = None
total_num_reads = 0
for index, filename in enumerate(filenames):
rparser = khmer.ReadParser(filename)
threads = []
print("consuming input", filename, file=sys.stderr)
for _ in range(args.threads):
cur_thrd = threading.Thread(target=htable.consume_fasta_with_reads_parser, args=(rparser,))
threads.append(cur_thrd)
cur_thrd.start()
for thread in threads:
thread.join()
if index > 0 and index % 10 == 0:
check_space_for_hashtable(args.n_tables * args.min_tablesize, args.force)
print("mid-save", base, file=sys.stderr)
htable.save(base)
with open(base + ".info", "a") as info_fh:
print("through", filename, file=info_fh)
total_num_reads += rparser.num_reads
n_kmers = htable.n_unique_kmers()
if args.report_total_kmers:
print("Total number of unique k-mers:", n_kmers, file=sys.stderr)
with open(base + ".info", "a") as info_fp:
print("Total number of unique k-mers:", n_kmers, file=info_fp)
print("saving", base, file=sys.stderr)
htable.save(base)
# Change max_false_pos=0.2 only if you really grok it. HINT: You don't
fp_rate = khmer.calc_expected_collisions(htable, args.force, max_false_pos=0.2)
with open(base + ".info", "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
print("Writing summmary info to", mr_file, file=sys.stderr)
with open(mr_file, "w") as mr_fh:
if mr_fmt == "json":
mr_data = {
"ht_name": os.path.basename(base),
"fpr": fp_rate,
"num_kmers": n_kmers,
"files": filenames,
"mrinfo_version": "0.2.0",
"num_reads": total_num_reads,
}
json.dump(mr_data, mr_fh)
mr_fh.write("\n")
elif mr_fmt == "tsv":
mr_fh.write("ht_name\tfpr\tnum_kmers\tnum_reads\tfiles\n")
vals = [
os.path.basename(base),
"{:1.3f}".format(fp_rate),
str(n_kmers),
str(total_num_reads),
";".join(filenames),
]
mr_fh.write("\t".join(vals) + "\n")
print("fp rate estimated to be %1.3f" % fp_rate, file=sys.stderr)
print("DONE.", file=sys.stderr)
print("wrote to:", base + ".info", file=sys.stderr)