def main():
args = parse_args()
global CONFIG
prophyle_conf_string = pro.load_prophyle_conf(CONFIG, args.config)
try:
assign_all_reads(
tree_fn=args.tree_fn,
inp_fo=args.input_file,
form=args.format,
k=args.k,
measure=args.measure,
annotate=args.annotate,
tie_lca=args.tie_lca,
kmer_lca=args.kmer_lca,
)
# Karel: I don't remember why I was considering also IOError here
# except (BrokenPipeError, IOError):
except BrokenPipeError:
# pipe error (e.g., when head is used)
sys.stderr.close()
sys.stdout.close()
exit(0)
except KeyboardInterrupt:
pro.message("Error: Keyboard interrupt")
pro.close_log()
exit(1)
finally:
try:
sys.stdout.flush()
except BrokenPipeError:
pass
finally:
try:
sys.stderr.flush()
except:
pass
def main():
try:
par = parser()
args = par.parse_args()
subcommand = args.subcommand
global CONFIG
prophyle_conf_string = pro.load_prophyle_conf(CONFIG, args.config)
if subcommand == "download":
pro.open_log(args.log_fn)
for single_lib in args.library:
pro.message('Downloading "{}" started'.format(single_lib))
prophyle_download(
library=single_lib,
library_dir=args.home_dir,
force=args.force,
)
pro.message('Downloading "{}" finished'.format(single_lib))
pro.close_log()
elif subcommand == "index":
if args.library_dir is None:
library_dir = os.path.dirname(args.tree[0])
else:
library_dir = args.library_dir
if args.log_fn is None:
args.log_fn = os.path.join(args.index_dir, "log.txt")
pro.open_log(args.log_fn)
pro.message('Index construction started')
prophyle_index(
index_dir=args.index_dir,
threads=args.threads,
k=args.k,
trees_fn=args.tree,
library_dir=library_dir,
force=args.force,
construct_klcp=args.klcp,
no_prefixes=args.no_prefixes,
mask_repeats=args.mask_repeats,
keep_tmp_files=args.keep_tmp_files,
sampling_rate=args.sampling_rate,
autocomplete=args.autocomplete,
)
pro.message('Index construction finished')
pro.close_log()
elif subcommand == "classify":
# if args.log_fn is None:
# args.log_fn = os.path.join(args.index_dir, "log.txt")
pro.open_log(args.log_fn)
pro.message('Classification started')
prophyle_classify(
index_dir=args.index_dir,
fq_fn=args.reads,
fq_pe_fn=args.reads_pe,
k=args.k,
out_format=args.oform,
mimic_kraken=args.mimic,
measure=args.measure,
tie_lca=args.tie_lca,
kmer_lca=args.kmer_lca,
annotate=args.annotate,
print_seq=args.print_seq,
cimpl=args.cimpl,
force_restarted_search=args.force_restarted_search,
prophyle_conf_string=prophyle_conf_string, # already preprocessed
)
pro.message('Classification finished')
pro.close_log()
elif subcommand == "analyze":
prophyle_analyze(
index_dir=args.index_dir,
out_prefix=args.out_prefix,
input_fns=args.input_fns,
stats=args.stats,
in_format=args.in_format,
)
elif subcommand == "compress":
if args.archive is None:
archive = args.index_dir.rstrip("/") + ".tar.gz"
else:
archive = args.archive
prophyle_compress(
index_dir=args.index_dir,
archive=archive,
)
elif subcommand == "decompress":
prophyle_decompress(
archive=args.archive,
output_dir=args.output_dir,
klcp=args.klcp,
)
elif subcommand == "compile":
prophyle_compile(
clean=args.clean,
parallel=args.parallel,
force=args.force,
)
else:
msg_lns = par.format_help().split("\n")[2:]
msg_lns = [x for x in msg_lns if x.find("optional arguments") == -1 and x.find("--") == -1]
msg = "\n".join(msg_lns)
msg = msg.replace("\n\n", '\n').replace("subcommands:\n", "Command:\n").replace("Usage", "\nUsage")
msg = msg.replace("\n compress", "\n\n compress")
print(file=sys.stderr)
print(msg, file=sys.stderr)
sys.exit(2)
except BrokenPipeError:
# pipe error (e.g., when head is used)
sys.stderr.close()
sys.stdout.close()
exit(0)
except KeyboardInterrupt:
pro.message("Error: Keyboard interrupt")
pro.close_log()
exit(1)
finally:
sys.stdout.flush()
sys.stderr.flush()
histogram, unique_histogram = compute_histogram(tree, asgs, args.stats)
otu_table = compute_otu_table(histogram, tree)
with open(args.out_prefix + '.rawhits.tsv', 'w') as f:
if args.stats.startswith('w'):
print_histogram(histogram, f, tree)
elif unique_histogram is not None:
print_histogram(unique_histogram, f, tree)
with open(args.out_prefix + '.otu.tsv', 'w') as f:
print_histogram(otu_table, f, tree)
with open(args.out_prefix + '.kraken.tsv', 'w') as f:
tot_count = print_kraken_report(otu_table, histogram, unclassified, tree, f)
with open(args.out_prefix + '.metaphlan.tsv', 'w') as f:
print_metaphlan_report(otu_table, tot_count, tree, f)
with open(args.out_prefix + '.centrifuge.tsv', 'w') as f:
print_centrifuge_report(otu_table, histogram, unique_histogram, tree, f)
if __name__ == "__main__":
try:
main()
except BrokenPipeError:
# pipe error (e.g., when head is used)
sys.stderr.close()
exit(0)
except KeyboardInterrupt:
pro.message("Error: Keyboard interrupt")
pro.close_log()
exit(1)