def main(args):
graph_type = 'nodegraph'
report_on_config(args, graphtype=graph_type)
base = args.output_filename
filenames = args.input_filenames
for fname in args.input_filenames:
check_input_files(fname, args.force)
graphsize = calculate_graphsize(args, graph_type)
space_needed = (args.n_tables * graphsize /
khmer._buckets_per_byte[graph_type])
check_space_for_graph(args.output_filename, space_needed, args.force)
print('Saving k-mer nodegraph to %s' % base, file=sys.stderr)
print('Loading kmers from sequences in %s' % repr(filenames),
file=sys.stderr)
if args.no_build_tagset:
print('We WILL NOT build the tagset.', file=sys.stderr)
else:
print('We WILL build the tagset (for partitioning/traversal).',
file=sys.stderr)
print('making nodegraph', file=sys.stderr)
nodegraph = khmer_args.create_nodegraph(args)
oxfuncs.build_graph(filenames, nodegraph, args.threads,
not args.no_build_tagset)
print('Total number of unique k-mers: {0}'.format(
nodegraph.n_unique_kmers()),
file=sys.stderr)
print('saving k-mer nodegraph in', base, file=sys.stderr)
nodegraph.save(base)
if not args.no_build_tagset:
print('saving tagset in', base + '.tagset', file=sys.stderr)
nodegraph.save_tagset(base + '.tagset')
info_fp = open(base + '.info', 'w')
info_fp.write('%d unique k-mers' % nodegraph.n_unique_kmers())
fp_rate = \
khmer.calc_expected_collisions(
nodegraph, args.force, max_false_pos=.15)
# 0.18 is ACTUAL MAX. Do not change.
print('false positive rate estimated to be %1.3f' % fp_rate,
file=sys.stderr)
print('\nfalse positive rate estimated to be %1.3f' % fp_rate,
file=info_fp)
print('wrote to ' + base + '.info and ' + base, file=sys.stderr)
if not args.no_build_tagset:
print('and ' + base + '.tagset', file=sys.stderr)
sys.exit(0)
def main(args):
info('build-graph.py', ['graph', 'SeqAn'])
report_on_config(args, hashtype='nodegraph')
base = args.output_filename
filenames = args.input_filenames
for fname in args.input_filenames:
check_input_files(fname, args.force)
# if optimization args are given, do optimization
args = functions.do_sanity_checking(args, 0.01)
check_space(args.input_filenames, args.force)
check_space_for_hashtable(args, 'nodegraph', args.force)
print('Saving k-mer presence table to %s' % base, file=sys.stderr)
print('Loading kmers from sequences in %s' %
repr(filenames), file=sys.stderr)
if args.no_build_tagset:
print('We WILL NOT build the tagset.', file=sys.stderr)
else:
print('We WILL build the tagset (for partitioning/traversal).',
file=sys.stderr)
print('making nodegraph', file=sys.stderr)
htable = khmer_args.create_nodegraph(args)
functions.build_graph(filenames, htable, args.threads,
not args.no_build_tagset)
print('Total number of unique k-mers: {0}'.format(htable.n_unique_kmers()),
file=sys.stderr)
print('saving k-mer presence table in', base + '.pt', file=sys.stderr)
htable.save(base + '.pt')
if not args.no_build_tagset:
print('saving tagset in', base + '.tagset', file=sys.stderr)
htable.save_tagset(base + '.tagset')
info_fp = open(base + '.info', 'w')
info_fp.write('%d unique k-mers' % htable.n_unique_kmers())
fp_rate = \
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.15)
# 0.18 is ACTUAL MAX. Do not change.
print('false positive rate estimated to be %1.3f' % fp_rate,
file=sys.stderr)
print('\nfalse positive rate estimated to be %1.3f' % fp_rate,
file=info_fp)
print('wrote to', base + '.info and', base + '.pt', file=sys.stderr)
if not args.no_build_tagset:
print('and ' + base + '.tagset', file=sys.stderr)
sys.exit(0)
def main(args):
graph_type = 'nodegraph'
report_on_config(args, graphtype=graph_type)
base = args.output_filename
filenames = args.input_filenames
for fname in args.input_filenames:
check_input_files(fname, args.force)
graphsize = calculate_graphsize(args, graph_type)
space_needed = (args.n_tables * graphsize /
khmer._buckets_per_byte[graph_type])
check_space_for_graph(args.output_filename, space_needed, args.force)
print('Saving k-mer nodegraph to %s' % base, file=sys.stderr)
print('Loading kmers from sequences in %s' %
repr(filenames), file=sys.stderr)
if args.no_build_tagset:
print('We WILL NOT build the tagset.', file=sys.stderr)
else:
print('We WILL build the tagset (for partitioning/traversal).',
file=sys.stderr)
print('making nodegraph', file=sys.stderr)
nodegraph = khmer_args.create_nodegraph(args)
oxfuncs.build_graph(filenames, nodegraph, args.threads,
not args.no_build_tagset)
print('Total number of unique k-mers: {0}'.format(
nodegraph.n_unique_kmers()), file=sys.stderr)
print('saving k-mer nodegraph in', base, file=sys.stderr)
nodegraph.save(base)
if not args.no_build_tagset:
print('saving tagset in', base + '.tagset', file=sys.stderr)
nodegraph.save_tagset(base + '.tagset')
info_fp = open(base + '.info', 'w')
info_fp.write('%d unique k-mers' % nodegraph.n_unique_kmers())
fp_rate = \
khmer.calc_expected_collisions(
nodegraph, args.force, max_false_pos=.15)
# 0.18 is ACTUAL MAX. Do not change.
print('false positive rate estimated to be %1.3f' % fp_rate,
file=sys.stderr)
print('\nfalse positive rate estimated to be %1.3f' % fp_rate,
file=info_fp)
print('wrote to ' + base + '.info and ' + base, file=sys.stderr)
if not args.no_build_tagset:
print('and ' + base + '.tagset', file=sys.stderr)
sys.exit(0)
def main(args):
info('build-graph.py', ['graph', 'SeqAn'])
report_on_config(args, hashtype='hashbits')
base = args.output_filename
filenames = args.input_filenames
for fname in args.input_filenames:
check_input_files(fname, args.force)
check_space(args.input_filenames, args.force)
check_space_for_hashtable(
(float(args.n_tables * args.min_tablesize) / 8.), args.force)
print >>sys.stderr, 'Saving k-mer presence table to %s' % base
print >>sys.stderr, 'Loading kmers from sequences in %s' % repr(filenames)
if args.no_build_tagset:
print >>sys.stderr, 'We WILL NOT build the tagset.'
else:
print >>sys.stderr, 'We WILL build the tagset', \
' (for partitioning/traversal).'
print >>sys.stderr, 'making k-mer presence table'
htable = khmer.new_hashbits(args.ksize, args.min_tablesize, args.n_tables)
functions.build_graph(filenames, htable, args.threads,
not args.no_build_tagset)
print >> sys.stderr, 'Total number of unique k-mers: {0}'.format(
htable.n_unique_kmers())
print >>sys.stderr, 'saving k-mer presence table in', base + '.pt'
htable.save(base + '.pt')
if not args.no_build_tagset:
print >>sys.stderr, 'saving tagset in', base + '.tagset'
htable.save_tagset(base + '.tagset')
info_fp = open(base + '.info', 'w')
info_fp.write('%d unique k-mers' % htable.n_unique_kmers())
fp_rate = \
khmer.calc_expected_collisions(htable, args.force, max_false_pos=.15)
# 0.18 is ACTUAL MAX. Do not change.
print >>sys.stderr, 'false positive rate estimated to be %1.3f' % fp_rate
print >>info_fp, '\nfalse positive rate estimated to be %1.3f' % fp_rate
print >> sys.stderr, 'wrote to', base + '.info and', base + '.pt'
if not args.no_build_tagset:
print >> sys.stderr, 'and ' + base + '.tagset'
sys.exit(0)
def main(args):
info("build-graph.py", ["graph", "SeqAn"])
report_on_config(args, graphtype="nodegraph")
base = args.output_filename
filenames = args.input_filenames
for fname in args.input_filenames:
check_input_files(fname, args.force)
graphsize = calculate_graphsize(args, "nodegraph")
check_space_for_graph(args.output_filename, graphsize, args.force)
print("Saving k-mer nodegraph to %s" % base, file=sys.stderr)
print("Loading kmers from sequences in %s" % repr(filenames), file=sys.stderr)
if args.no_build_tagset:
print("We WILL NOT build the tagset.", file=sys.stderr)
else:
print("We WILL build the tagset (for partitioning/traversal).", file=sys.stderr)
print("making nodegraph", file=sys.stderr)
nodegraph = khmer_args.create_nodegraph(args)
oxfuncs.build_graph(filenames, nodegraph, args.threads, not args.no_build_tagset)
print("Total number of unique k-mers: {0}".format(nodegraph.n_unique_kmers()), file=sys.stderr)
print("saving k-mer nodegraph in", base, file=sys.stderr)
nodegraph.save(base)
if not args.no_build_tagset:
print("saving tagset in", base + ".tagset", file=sys.stderr)
nodegraph.save_tagset(base + ".tagset")
info_fp = open(base + ".info", "w")
info_fp.write("%d unique k-mers" % nodegraph.n_unique_kmers())
fp_rate = khmer.calc_expected_collisions(nodegraph, args.force, max_false_pos=0.15)
# 0.18 is ACTUAL MAX. Do not change.
print("false positive rate estimated to be %1.3f" % fp_rate, file=sys.stderr)
print("\nfalse positive rate estimated to be %1.3f" % fp_rate, file=info_fp)
print("wrote to " + base + ".info and " + base, file=sys.stderr)
if not args.no_build_tagset:
print("and " + base + ".tagset", file=sys.stderr)
sys.exit(0)
def main(args):
info("build-graph.py", ["graph", "SeqAn"])
report_on_config(args, hashtype="hashbits")
base = args.output_filename
filenames = args.input_filenames
for fname in args.input_filenames:
check_input_files(fname, args.force)
check_space(args.input_filenames, args.force)
check_space_for_hashtable((float(args.n_tables * args.min_tablesize) / 8.0), args.force)
print("Saving k-mer presence table to %s" % base, file=sys.stderr)
print("Loading kmers from sequences in %s" % repr(filenames), file=sys.stderr)
if args.no_build_tagset:
print("We WILL NOT build the tagset.", file=sys.stderr)
else:
print("We WILL build the tagset (for partitioning/traversal).", file=sys.stderr)
print("making k-mer presence table", file=sys.stderr)
htable = khmer.new_hashbits(args.ksize, args.min_tablesize, args.n_tables)
functions.build_graph(filenames, htable, args.threads, not args.no_build_tagset)
print("Total number of unique k-mers: {0}".format(htable.n_unique_kmers()), file=sys.stderr)
print("saving k-mer presence table in", base + ".pt", file=sys.stderr)
htable.save(base + ".pt")
if not args.no_build_tagset:
print("saving tagset in", base + ".tagset", file=sys.stderr)
htable.save_tagset(base + ".tagset")
info_fp = open(base + ".info", "w")
info_fp.write("%d unique k-mers" % htable.n_unique_kmers())
fp_rate = khmer.calc_expected_collisions(htable, args.force, max_false_pos=0.15)
# 0.18 is ACTUAL MAX. Do not change.
print("false positive rate estimated to be %1.3f" % fp_rate, file=sys.stderr)
print("\nfalse positive rate estimated to be %1.3f" % fp_rate, file=info_fp)
print("wrote to", base + ".info and", base + ".pt", file=sys.stderr)
if not args.no_build_tagset:
print("and " + base + ".tagset", file=sys.stderr)
sys.exit(0)
