elif opt in ("-m", "--meta"):
pass
elif opt in ["--no-plots"]:
pass
elif opt in ["--no-html"]:
pass
else:
logger.error('Unknown option: %s. Use -h for help.' %
(opt + (' ' + arg) if arg else ''),
to_stderr=True)
sys.exit(2)
for c_fpath in contigs_fpaths:
assert_file_exists(c_fpath, 'contigs')
labels = quast.process_labels(contigs_fpaths, labels, all_labels_from_dirs)
for contigs_fpath in contigs_fpaths:
quast_py_args.remove(contigs_fpath)
# # Removing outout dir if exists
# if output_dirpath: # 'output dir was specified with -o option'
# if os.path.isdir(output_dirpath):
# shutil.rmtree(output_dirpath)
# Directories
output_dirpath, _, _ = quast._set_up_output_dir(output_dirpath,
None,
make_latest_symlink,
save_json=False,
remove_old=True)
def main(args):
if ' ' in quast_dirpath:
logger.error('QUAST does not support spaces in paths. \n'
'You are trying to run it from ' + str(quast_dirpath) + '\n'
'Please, put QUAST in a different directory, then try again.\n',
to_stderr=True,
exit_with_code=3)
if not args:
qconfig.usage(meta=True)
sys.exit(0)
min_contig = qconfig.min_contig
genes = []
operons = []
draw_plots = qconfig.draw_plots
html_report = qconfig.html_report
make_latest_symlink = True
try:
options, contigs_fpaths = getopt.gnu_getopt(args, qconfig.short_options, qconfig.long_options)
except getopt.GetoptError:
_, exc_value, _ = sys.exc_info()
print >> sys.stderr, exc_value
print >> sys.stderr
qconfig.usage(meta=True)
sys.exit(2)
quast_py_args = args[:]
test_mode = False
for opt, arg in options:
if opt in ('-d', '--debug'):
options.remove((opt, arg))
qconfig.debug = True
logger.set_up_console_handler(debug=True)
elif opt == '--test':
options.remove((opt, arg))
quast_py_args.remove(opt)
options += [('-o', 'quast_test_output'),
('-R', 'test_data/meta_ref_1.fasta,'
'test_data/meta_ref_2.fasta,'
'test_data/meta_ref_3.fasta')]
contigs_fpaths += ['test_data/meta_contigs_1.fasta',
'test_data/meta_contigs_2.fasta']
test_mode = True
elif opt.startswith('--help'):
qconfig.usage(opt == "--help-hidden", meta=True)
sys.exit(0)
if not contigs_fpaths:
logger.error("You should specify at least one file with contigs!\n")
qconfig.usage(meta=True)
sys.exit(2)
ref_fpaths = []
combined_ref_fpath = ''
output_dirpath = None
labels = None
all_labels_from_dirs = False
for opt, arg in options:
if opt in ('-o', "--output-dir"):
# Removing output dir arg in order to further
# construct other quast calls from this options
if opt in quast_py_args and arg in quast_py_args:
quast_py_args.remove(opt)
quast_py_args.remove(arg)
output_dirpath = os.path.abspath(arg)
make_latest_symlink = False
elif opt in ('-G', "--genes"):
assert_file_exists(arg, 'genes')
genes += arg
elif opt in ('-O', "--operons"):
assert_file_exists(arg, 'operons')
operons += arg
elif opt in ('-R', "--reference"):
# Removing reference args in order to further
# construct quast calls from this args with other reference options
if opt in quast_py_args and arg in quast_py_args:
quast_py_args.remove(opt)
quast_py_args.remove(arg)
ref_fpaths = arg.split(',')
for i, ref_fpath in enumerate(ref_fpaths):
assert_file_exists(ref_fpath, 'reference')
ref_fpaths[i] = ref_fpath
elif opt in ('-M', "--min-contig"):
min_contig = int(arg)
elif opt in ('-T', "--threads"):
pass
elif opt in ('-l', '--labels'):
quast_py_args.remove(opt)
quast_py_args.remove(arg)
labels = quast.parse_labels(arg, contigs_fpaths)
elif opt == '-L':
quast_py_args.remove(opt)
all_labels_from_dirs = True
elif opt in ('-j', '--save-json'):
pass
elif opt in ('-J', '--save-json-to'):
pass
elif opt in ('-t', "--contig-thresholds"):
pass
elif opt in ('-c', "--mincluster"):
pass
elif opt == "--est-ref-size":
pass
elif opt in ('-S', "--gene-thresholds"):
pass
elif opt in ('-s', "--scaffolds"):
pass
elif opt == "--gage":
pass
elif opt == "--debug":
pass
elif opt in ('-e', "--eukaryote"):
pass
elif opt in ('-f', "--gene-finding"):
pass
elif opt in ('-a', "--ambiguity-usage"):
pass
elif opt in ('-u', "--use-all-alignments"):
pass
elif opt in ('-n', "--strict-NA"):
pass
elif opt in ("-m", "--meta"):
pass
elif opt in ["--no-plots"]:
pass
elif opt in ["--no-html"]:
pass
else:
logger.error('Unknown option: %s. Use -h for help.' % (opt + ' ' + arg), to_stderr=True, exit_with_code=2)
for c_fpath in contigs_fpaths:
assert_file_exists(c_fpath, 'contigs')
labels = quast.process_labels(contigs_fpaths, labels, all_labels_from_dirs)
for contigs_fpath in contigs_fpaths:
if contigs_fpath in quast_py_args:
quast_py_args.remove(contigs_fpath)
# Directories
output_dirpath, _, _ = quast._set_up_output_dir(
output_dirpath, None, make_latest_symlink,
save_json=False)
corrected_dirpath = os.path.join(output_dirpath, qconfig.corrected_dirname)
logger.set_up_file_handler(output_dirpath)
logger.print_command_line([os.path.realpath(__file__)] + args, wrap_after=None)
logger.start()
########################################################################
from libs import reporting
reload(reporting)
if os.path.isdir(corrected_dirpath):
shutil.rmtree(corrected_dirpath)
os.mkdir(corrected_dirpath)
# PROCESSING REFERENCES
common_ref_fasta_ext = ''
if ref_fpaths:
logger.info()
logger.info('Reference(s):')
ref_fpaths, common_ref_fasta_ext, combined_ref_fpath =\
_correct_refrences(ref_fpaths, corrected_dirpath)
# PROCESSING CONTIGS
logger.info()
logger.info('Contigs:')
assemblies = _correct_contigs(contigs_fpaths, corrected_dirpath, min_contig, labels)
if not assemblies:
logger.error("None of the assembly files contains correct contigs. "
"Please, provide different files or decrease --min-contig threshold.")
return 4
# Running QUAST(s)
quast_py_args += ['--meta']
if not ref_fpaths:
# No references, running regular quast with MetaGenemark gene finder
logger.info()
logger.notice('No references provided, starting quast.py with MetaGeneMark gene finder')
_start_quast_main(
None,
quast_py_args,
assemblies=assemblies,
output_dirpath=os.path.join(output_dirpath, 'quast_output'),
exit_on_exception=True)
exit(0)
# Running combined reference
run_name = 'for the combined reference'
logger.info()
logger.info('Starting quast.py ' + run_name + '...')
total_num_notices = 0
total_num_warnings = 0
total_num_nf_errors = 0
total_num_notifications = (total_num_notices, total_num_warnings, total_num_nf_errors)
return_code, total_num_notifications = _start_quast_main(run_name, quast_py_args,
assemblies=assemblies,
reference_fpath=combined_ref_fpath,
output_dirpath=os.path.join(output_dirpath, 'combined_quast_output'),
num_notifications_tuple=total_num_notifications)
# Partitioning contigs into bins aligned to each reference
assemblies_by_reference, not_aligned_assemblies = _partition_contigs(
assemblies, ref_fpaths, corrected_dirpath,
os.path.join(output_dirpath, 'combined_quast_output', 'contigs_reports', 'alignments_%s.tsv'))
for ref_name, ref_assemblies in assemblies_by_reference.iteritems():
logger.info('')
if not ref_assemblies:
logger.info('No contigs were aligned to the reference ' + ref_name)
else:
run_name = 'for the contigs aligned to ' + ref_name
logger.info('Starting quast.py ' + run_name)
return_code, total_num_notifications = _start_quast_main(run_name, quast_py_args,
assemblies=ref_assemblies,
reference_fpath=os.path.join(corrected_dirpath, ref_name) + common_ref_fasta_ext,
output_dirpath=os.path.join(output_dirpath, ref_name + '_quast_output'),
exit_on_exception=False, num_notifications_tuple=total_num_notifications)
# Finally running for the contigs that has not been aligned to any reference
run_name = 'for the contigs not alined anywhere'
logger.info()
logger.info('Starting quast.py ' + run_name + '...')
return_code, total_num_notifications = _start_quast_main(run_name, quast_py_args,
assemblies=not_aligned_assemblies,
output_dirpath=os.path.join(output_dirpath, 'not_aligned_quast_output'),
exit_on_exception=False, num_notifications_tuple=total_num_notifications)
if return_code not in [0, 4]:
logger.error('Error running quast.py for the contigs not aligned anywhere')
quast._cleanup(corrected_dirpath)
logger.info('')
logger.info('MetaQUAST finished.')
logger.finish_up(numbers=tuple(total_num_notifications), check_test=test_mode)
def main(args):
if ' ' in qconfig.QUAST_HOME:
logger.error(
'QUAST does not support spaces in paths. \n'
'You are trying to run it from ' + str(qconfig.QUAST_HOME) + '\n'
'Please, put QUAST in a different directory, then try again.\n',
to_stderr=True,
exit_with_code=3)
if not args:
qconfig.usage(meta=True)
sys.exit(0)
genes = []
operons = []
html_report = qconfig.html_report
make_latest_symlink = True
ref_txt_fpath = None
try:
options, contigs_fpaths = getopt.gnu_getopt(args,
qconfig.short_options,
qconfig.long_options)
except getopt.GetoptError:
_, exc_value, _ = sys.exc_info()
print >> sys.stderr, exc_value
print >> sys.stderr
qconfig.usage(meta=True)
sys.exit(2)
quast_py_args = args[:]
test_mode = False
for opt, arg in options:
if opt in ('-d', '--debug'):
options.remove((opt, arg))
qconfig.debug = True
logger.set_up_console_handler(debug=True)
elif opt == '--test' or opt == '--test-no-ref':
options.remove((opt, arg))
quast_py_args = __remove_from_quast_py_args(quast_py_args, opt)
options += [('-o', 'quast_test_output')]
if opt == '--test':
options += [('-R', ','.join([
os.path.join(qconfig.QUAST_HOME, 'test_data',
'meta_ref_1.fasta'),
os.path.join(qconfig.QUAST_HOME, 'test_data',
'meta_ref_2.fasta'),
os.path.join(qconfig.QUAST_HOME, 'test_data',
'meta_ref_3.fasta')
]))]
contigs_fpaths += [
os.path.join(qconfig.QUAST_HOME, 'test_data',
'meta_contigs_1.fasta'),
os.path.join(qconfig.QUAST_HOME, 'test_data',
'meta_contigs_2.fasta')
]
test_mode = True
elif opt.startswith('--help') or opt == '-h':
qconfig.usage(opt == "--help-hidden", meta=True, short=False)
sys.exit(0)
elif opt.startswith('--version') or opt == '-v':
qconfig.print_version(meta=True)
sys.exit(0)
if not contigs_fpaths:
logger.error("You should specify at least one file with contigs!\n")
qconfig.usage(meta=True)
sys.exit(2)
ref_fpaths = []
combined_ref_fpath = ''
reads_fpath_f = ''
reads_fpath_r = ''
output_dirpath = None
labels = None
all_labels_from_dirs = False
for opt, arg in options:
if opt in ('-o', "--output-dir"):
# Removing output dir arg in order to further
# construct other quast calls from this options
if opt in quast_py_args and arg in quast_py_args:
quast_py_args = __remove_from_quast_py_args(
quast_py_args, opt, arg)
output_dirpath = os.path.abspath(arg)
make_latest_symlink = False
elif opt in ('-G', "--genes"):
assert_file_exists(arg, 'genes')
genes += arg
elif opt in ('-O', "--operons"):
assert_file_exists(arg, 'operons')
operons += arg
elif opt in ('-R', "--reference"):
# Removing reference args in order to further
# construct quast calls from this args with other reference options
if opt in quast_py_args and arg in quast_py_args:
quast_py_args = __remove_from_quast_py_args(
quast_py_args, opt, arg)
if os.path.isdir(arg):
ref_fpaths = [
os.path.join(path, file)
for (path, dirs, files) in os.walk(arg) for file in files
if qutils.check_is_fasta_file(file)
]
ref_fpaths.sort()
else:
ref_fpaths = arg.split(',')
for i, ref_fpath in enumerate(ref_fpaths):
assert_file_exists(ref_fpath, 'reference')
ref_fpaths[i] = ref_fpath
elif opt == '--max-ref-number':
quast_py_args = __remove_from_quast_py_args(
quast_py_args, opt, arg)
qconfig.max_references = int(arg)
if qconfig.max_references < 0:
qconfig.max_references = 0
elif opt in ('-m', "--min-contig"):
qconfig.min_contig = int(arg)
elif opt in ('-t', "--threads"):
qconfig.max_threads = int(arg)
if qconfig.max_threads < 1:
qconfig.max_threads = 1
elif opt in ('-l', '--labels'):
quast_py_args = __remove_from_quast_py_args(
quast_py_args, opt, arg)
labels = quast.parse_labels(arg, contigs_fpaths)
elif opt == '-L':
quast_py_args = __remove_from_quast_py_args(quast_py_args, opt)
all_labels_from_dirs = True
elif opt in ('-j', '--save-json'):
pass
elif opt in ('-J', '--save-json-to'):
pass
elif opt == "--contig-thresholds":
pass
elif opt in ('-c', "--mincluster"):
pass
elif opt == "--est-ref-size":
pass
elif opt == "--gene-thresholds":
pass
elif opt in ('-s', "--scaffolds"):
pass
elif opt == "--gage":
pass
elif opt == "--debug":
pass
elif opt in ('-e', "--eukaryote"):
pass
elif opt in ('-f', "--gene-finding"):
pass
elif opt in ('-i', "--min-alignment"):
pass
elif opt in ('-c', "--min-cluster"):
pass
elif opt in ('-a', "--ambiguity-usage"):
pass
elif opt in ('-u', "--use-all-alignments"):
pass
elif opt == "--strict-NA":
pass
elif opt in ('-x', "--extensive-mis-size"):
pass
elif opt == "--meta":
pass
elif opt == '--references-list':
ref_txt_fpath = arg
elif opt == '--glimmer':
pass
elif opt == '--no-snps':
pass
elif opt == '--no-check':
pass
elif opt == '--no-gc':
pass
elif opt == '--no-plots':
pass
elif opt == '--no-html':
html_report = False
elif opt == '--fast': # --no-check, --no-gc, --no-snps will automatically set in QUAST runs
html_report = False
elif opt == '--plots-format':
pass
elif opt == '--memory-efficient':
pass
elif opt == '--silent':
qconfig.silent = True
elif opt in ('-1', '--reads1'):
reads_fpath_f = arg
quast_py_args = __remove_from_quast_py_args(
quast_py_args, opt, arg)
elif opt in ('-2', '--reads2'):
reads_fpath_r = arg
quast_py_args = __remove_from_quast_py_args(
quast_py_args, opt, arg)
elif opt == '--contig-alignment-html':
qconfig.create_contig_alignment_html = True
else:
logger.error('Unknown option: %s. Use -h for help.' %
(opt + ' ' + arg),
to_stderr=True,
exit_with_code=2)
for c_fpath in contigs_fpaths:
assert_file_exists(c_fpath, 'contigs')
labels = quast.process_labels(contigs_fpaths, labels, all_labels_from_dirs)
for contigs_fpath in contigs_fpaths:
if contigs_fpath in quast_py_args:
quast_py_args.remove(contigs_fpath)
# Directories
output_dirpath, _, _ = quast._set_up_output_dir(output_dirpath,
None,
make_latest_symlink,
save_json=False)
corrected_dirpath = os.path.join(output_dirpath, qconfig.corrected_dirname)
logger.set_up_file_handler(output_dirpath)
args = [os.path.realpath(__file__)]
for k, v in options:
args.extend([k, v])
args.extend(contigs_fpaths)
logger.print_command_line(args, wrap_after=None)
logger.start()
qconfig.set_max_threads(logger)
########################################################################
from libs import reporting
reload(reporting)
if os.path.isdir(corrected_dirpath):
shutil.rmtree(corrected_dirpath)
os.mkdir(corrected_dirpath)
# PROCESSING REFERENCES
if ref_fpaths:
logger.main_info()
logger.main_info('Reference(s):')
corrected_ref_fpaths, combined_ref_fpath, chromosomes_by_refs, ref_names =\
_correct_references(ref_fpaths, corrected_dirpath)
# PROCESSING CONTIGS
logger.main_info()
logger.main_info('Contigs:')
assemblies, correct_assemblies = _correct_contigs(contigs_fpaths,
output_dirpath, labels)
if not assemblies:
logger.error(
"None of the assembly files contains correct contigs. "
"Please, provide different files or decrease --min-contig threshold."
)
return 4
# Running QUAST(s)
quast_py_args += ['--meta']
downloaded_refs = False
# SEARCHING REFERENCES
if not ref_fpaths:
logger.main_info()
if qconfig.max_references == 0:
logger.notice(
"Maximum number of references (--max-ref-number) is set to 0, search in SILVA 16S rRNA database is disabled"
)
else:
if ref_txt_fpath:
logger.main_info(
"List of references was provided, starting to download reference genomes from NCBI..."
)
else:
logger.main_info(
"No references are provided, starting to search for reference genomes in SILVA 16S rRNA database "
"and to download them from NCBI...")
downloaded_dirpath = os.path.join(output_dirpath,
qconfig.downloaded_dirname)
if not os.path.isdir(downloaded_dirpath):
os.mkdir(downloaded_dirpath)
ref_fpaths = search_references_meta.do(assemblies, labels,
downloaded_dirpath,
ref_txt_fpath)
if ref_fpaths:
search_references_meta.is_quast_first_run = True
if not ref_txt_fpath:
downloaded_refs = True
logger.main_info()
logger.main_info('Downloaded reference(s):')
corrected_ref_fpaths, combined_ref_fpath, chromosomes_by_refs, ref_names =\
_correct_references(ref_fpaths, corrected_dirpath)
elif test_mode and ref_fpaths is None:
logger.error(
'Failed to download or setup SILVA 16S rRNA database for working without '
'references on metagenome datasets!',
to_stderr=True,
exit_with_code=4)
if not ref_fpaths:
# No references, running regular quast with MetaGenemark gene finder
logger.main_info()
logger.notice(
'No references are provided, starting regular QUAST with MetaGeneMark gene finder'
)
_start_quast_main(None,
quast_py_args,
assemblies=assemblies,
output_dirpath=output_dirpath,
exit_on_exception=True)
exit(0)
# Running combined reference
combined_output_dirpath = os.path.join(output_dirpath,
qconfig.combined_output_name)
reads_fpaths = []
if reads_fpath_f:
reads_fpaths.append(reads_fpath_f)
if reads_fpath_r:
reads_fpaths.append(reads_fpath_r)
if reads_fpaths:
bed_fpath = reads_analyzer.do(combined_ref_fpath,
contigs_fpaths,
reads_fpaths,
corrected_ref_fpaths,
os.path.join(combined_output_dirpath,
qconfig.variation_dirname),
external_logger=logger)
if bed_fpath:
quast_py_args += ['--bed-file']
quast_py_args += [bed_fpath]
quast_py_args += ['--combined-ref']
run_name = 'for the combined reference'
logger.main_info()
logger.main_info('Starting quast.py ' + run_name + '...')
total_num_notices = 0
total_num_warnings = 0
total_num_nf_errors = 0
total_num_notifications = (total_num_notices, total_num_warnings,
total_num_nf_errors)
if qconfig.html_report:
from libs.html_saver import json_saver
json_texts = []
else:
json_texts = None
return_code, total_num_notifications, assemblies, labels = _start_quast_main(
run_name,
quast_py_args + ["--ambiguity-usage"] + ['all'],
assemblies=assemblies,
reference_fpath=combined_ref_fpath,
output_dirpath=combined_output_dirpath,
num_notifications_tuple=total_num_notifications,
is_first_run=True)
for arg in args:
if arg in ('-s', "--scaffolds"):
quast_py_args.remove(arg)
if json_texts is not None:
json_texts.append(json_saver.json_text)
search_references_meta.is_quast_first_run = False
genome_info_dirpath = os.path.join(output_dirpath,
qconfig.combined_output_name,
'genome_stats')
genome_info_fpath = os.path.join(genome_info_dirpath, 'genome_info.txt')
if not os.path.exists(genome_info_fpath):
logger.main_info('')
logger.main_info(
'Failed aligning the contigs for all the references. ' +
('Try to restart MetaQUAST with another references.'
if not downloaded_refs else
'Try to use option --max-ref-number to change maximum number of references '
'(per each assembly) to download.'))
logger.main_info('')
quast._cleanup(corrected_dirpath)
logger.main_info('MetaQUAST finished.')
logger.finish_up(numbers=tuple(total_num_notifications),
check_test=test_mode)
return
if downloaded_refs:
logger.main_info()
logger.main_info(
'Excluding downloaded references with low genome fraction from further analysis..'
)
corr_ref_fpaths = remove_unaligned_downloaded_refs(
genome_info_fpath, ref_fpaths, chromosomes_by_refs)
if corr_ref_fpaths and corr_ref_fpaths != ref_fpaths:
logger.main_info()
logger.main_info('Filtered reference(s):')
os.remove(combined_ref_fpath)
contigs_analyzer.ref_labels_by_chromosomes = {}
corrected_ref_fpaths, combined_ref_fpath, chromosomes_by_refs, ref_names =\
_correct_references(corr_ref_fpaths, corrected_dirpath)
run_name = 'for the corrected combined reference'
logger.main_info()
logger.main_info('Starting quast.py ' + run_name + '...')
return_code, total_num_notifications, assemblies, labels = _start_quast_main(
run_name,
quast_py_args + ["--ambiguity-usage"] + ['all'],
assemblies=assemblies,
reference_fpath=combined_ref_fpath,
output_dirpath=combined_output_dirpath,
num_notifications_tuple=total_num_notifications,
is_first_run=True)
if json_texts is not None:
json_texts = json_texts[:-1]
json_texts.append(json_saver.json_text)
elif corr_ref_fpaths == ref_fpaths:
logger.main_info(
'All downloaded references have genome fraction more than 10%. Nothing was excluded.'
)
else:
logger.main_info(
'All downloaded references have low genome fraction. Nothing was excluded for now.'
)
quast_py_args += ['--no-check-meta']
qconfig.contig_thresholds = ','.join([
str(threshold) for threshold in qconfig.contig_thresholds
if threshold > qconfig.min_contig
])
if not qconfig.contig_thresholds:
qconfig.contig_thresholds = 'None'
quast_py_args = __remove_from_quast_py_args(quast_py_args,
'--contig-thresholds',
qconfig.contig_thresholds)
quast_py_args += ['--contig-thresholds']
quast_py_args += [qconfig.contig_thresholds]
quast_py_args.remove('--combined-ref')
logger.main_info()
logger.main_info(
'Partitioning contigs into bins aligned to each reference..')
assemblies_by_reference, not_aligned_assemblies = _partition_contigs(
assemblies, corrected_ref_fpaths, corrected_dirpath,
os.path.join(combined_output_dirpath, 'contigs_reports',
'alignments_%s.tsv'), labels)
ref_names = []
output_dirpath_per_ref = os.path.join(output_dirpath,
qconfig.per_ref_dirname)
for ref_fpath, ref_assemblies in assemblies_by_reference:
ref_name = qutils.name_from_fpath(ref_fpath)
logger.main_info('')
if not ref_assemblies:
logger.main_info('No contigs were aligned to the reference ' +
ref_name + ', skipping..')
else:
ref_names.append(ref_name)
run_name = 'for the contigs aligned to ' + ref_name
logger.main_info('Starting quast.py ' + run_name)
return_code, total_num_notifications = _start_quast_main(
run_name,
quast_py_args,
assemblies=ref_assemblies,
reference_fpath=ref_fpath,
output_dirpath=os.path.join(output_dirpath_per_ref, ref_name),
exit_on_exception=False,
num_notifications_tuple=total_num_notifications)
if json_texts is not None:
json_texts.append(json_saver.json_text)
# Finally running for the contigs that has not been aligned to any reference
no_unaligned_contigs = True
for assembly in not_aligned_assemblies:
if os.path.isfile(
assembly.fpath) and os.stat(assembly.fpath).st_size != 0:
no_unaligned_contigs = False
break
run_name = 'for the contigs not aligned anywhere'
logger.main_info()
if no_unaligned_contigs:
logger.main_info('Skipping quast.py ' + run_name +
' (everything is aligned!)')
else:
logger.main_info('Starting quast.py ' + run_name + '...')
return_code, total_num_notifications = _start_quast_main(
run_name,
quast_py_args,
assemblies=not_aligned_assemblies,
output_dirpath=os.path.join(output_dirpath,
qconfig.not_aligned_name),
exit_on_exception=False,
num_notifications_tuple=total_num_notifications)
if return_code not in [0, 4]:
logger.error(
'Error running quast.py for the contigs not aligned anywhere')
elif return_code == 4: # no unaligned contigs, i.e. everything aligned
no_unaligned_contigs = True
if not no_unaligned_contigs:
if json_texts is not None:
json_texts.append(json_saver.json_text)
if ref_names:
logger.print_timestamp()
logger.main_info("Summarizing results...")
summary_output_dirpath = os.path.join(output_dirpath,
qconfig.meta_summary_dir)
if not os.path.isdir(summary_output_dirpath):
os.makedirs(summary_output_dirpath)
if html_report and json_texts:
from libs.html_saver import html_saver
html_summary_report_fpath = html_saver.init_meta_report(
output_dirpath)
else:
html_summary_report_fpath = None
from libs import create_meta_summary
metrics_for_plots = reporting.Fields.main_metrics
misassembl_metrics = [
reporting.Fields.MIS_RELOCATION,
reporting.Fields.MIS_TRANSLOCATION, reporting.Fields.MIS_INVERTION,
reporting.Fields.MIS_ISTRANSLOCATIONS
]
create_meta_summary.do(
html_summary_report_fpath, summary_output_dirpath,
combined_output_dirpath, output_dirpath_per_ref, metrics_for_plots,
misassembl_metrics,
ref_names if no_unaligned_contigs else ref_names +
[qconfig.not_aligned_name])
if html_report and json_texts:
from libs import plotter
html_saver.save_colors(output_dirpath,
contigs_fpaths,
plotter.dict_color_and_ls,
meta=True)
html_saver.create_meta_report(output_dirpath, json_texts)
quast._cleanup(corrected_dirpath)
logger.main_info('')
logger.main_info('MetaQUAST finished.')
logger.finish_up(numbers=tuple(total_num_notifications),
check_test=test_mode)
def main(args):
if ' ' in qconfig.QUAST_HOME:
logger.error('QUAST does not support spaces in paths. \n'
'You are trying to run it from ' + str(qconfig.QUAST_HOME) + '\n'
'Please, put QUAST in a different directory, then try again.\n',
to_stderr=True,
exit_with_code=3)
if not args:
qconfig.usage(meta=True)
sys.exit(0)
genes = []
operons = []
html_report = qconfig.html_report
make_latest_symlink = True
ref_txt_fpath = None
try:
options, contigs_fpaths = getopt.gnu_getopt(args, qconfig.short_options, qconfig.long_options)
except getopt.GetoptError:
_, exc_value, _ = sys.exc_info()
print >> sys.stderr, exc_value
print >> sys.stderr
qconfig.usage(meta=True)
sys.exit(2)
quast_py_args = args[:]
test_mode = False
for opt, arg in options:
if opt in ('-d', '--debug'):
options.remove((opt, arg))
qconfig.debug = True
logger.set_up_console_handler(debug=True)
elif opt == '--test' or opt == '--test-no-ref':
options.remove((opt, arg))
quast_py_args = __remove_from_quast_py_args(quast_py_args, opt)
options += [('-o', 'quast_test_output')]
if opt == '--test':
options += [('-R', ','.join([os.path.join(qconfig.QUAST_HOME, 'test_data', 'meta_ref_1.fasta'),
os.path.join(qconfig.QUAST_HOME, 'test_data', 'meta_ref_2.fasta'),
os.path.join(qconfig.QUAST_HOME, 'test_data', 'meta_ref_3.fasta')]))]
contigs_fpaths += [os.path.join(qconfig.QUAST_HOME, 'test_data', 'meta_contigs_1.fasta'),
os.path.join(qconfig.QUAST_HOME, 'test_data', 'meta_contigs_2.fasta')]
test_mode = True
elif opt.startswith('--help') or opt == '-h':
qconfig.usage(opt == "--help-hidden", meta=True, short=False)
sys.exit(0)
elif opt.startswith('--version') or opt == '-v':
qconfig.print_version(meta=True)
sys.exit(0)
if not contigs_fpaths:
logger.error("You should specify at least one file with contigs!\n")
qconfig.usage(meta=True)
sys.exit(2)
ref_fpaths = []
combined_ref_fpath = ''
reads_fpath_f = ''
reads_fpath_r = ''
output_dirpath = None
labels = None
all_labels_from_dirs = False
for opt, arg in options:
if opt in ('-o', "--output-dir"):
# Removing output dir arg in order to further
# construct other quast calls from this options
if opt in quast_py_args and arg in quast_py_args:
quast_py_args = __remove_from_quast_py_args(quast_py_args, opt, arg)
output_dirpath = os.path.abspath(arg)
make_latest_symlink = False
elif opt in ('-G', "--genes"):
assert_file_exists(arg, 'genes')
genes += arg
elif opt in ('-O', "--operons"):
assert_file_exists(arg, 'operons')
operons += arg
elif opt in ('-R', "--reference"):
# Removing reference args in order to further
# construct quast calls from this args with other reference options
if opt in quast_py_args and arg in quast_py_args:
quast_py_args = __remove_from_quast_py_args(quast_py_args, opt, arg)
if os.path.isdir(arg):
ref_fpaths = [os.path.join(path,file) for (path, dirs, files) in os.walk(arg) for file in files if qutils.check_is_fasta_file(file)]
ref_fpaths.sort()
else:
ref_fpaths = arg.split(',')
for i, ref_fpath in enumerate(ref_fpaths):
assert_file_exists(ref_fpath, 'reference')
ref_fpaths[i] = ref_fpath
elif opt == '--max-ref-number':
quast_py_args = __remove_from_quast_py_args(quast_py_args, opt, arg)
qconfig.max_references = int(arg)
if qconfig.max_references < 0:
qconfig.max_references = 0
elif opt in ('-m', "--min-contig"):
qconfig.min_contig = int(arg)
elif opt in ('-t', "--threads"):
qconfig.max_threads = int(arg)
if qconfig.max_threads < 1:
qconfig.max_threads = 1
elif opt in ('-l', '--labels'):
quast_py_args = __remove_from_quast_py_args(quast_py_args, opt, arg)
labels = quast.parse_labels(arg, contigs_fpaths)
elif opt == '-L':
quast_py_args = __remove_from_quast_py_args(quast_py_args, opt)
all_labels_from_dirs = True
elif opt in ('-j', '--save-json'):
pass
elif opt in ('-J', '--save-json-to'):
pass
elif opt == "--contig-thresholds":
pass
elif opt in ('-c', "--mincluster"):
pass
elif opt == "--est-ref-size":
pass
elif opt == "--gene-thresholds":
pass
elif opt in ('-s', "--scaffolds"):
pass
elif opt == "--gage":
pass
elif opt == "--debug":
pass
elif opt in ('-e', "--eukaryote"):
pass
elif opt in ('-f', "--gene-finding"):
pass
elif opt in ('-i', "--min-alignment"):
pass
elif opt in ('-c', "--min-cluster"):
pass
elif opt in ('-a', "--ambiguity-usage"):
pass
elif opt in ('-u', "--use-all-alignments"):
pass
elif opt == "--strict-NA":
pass
elif opt in ('-x', "--extensive-mis-size"):
pass
elif opt == "--meta":
pass
elif opt == '--references-list':
ref_txt_fpath = arg
elif opt == '--glimmer':
pass
elif opt == '--no-snps':
pass
elif opt == '--no-check':
pass
elif opt == '--no-gc':
pass
elif opt == '--no-plots':
pass
elif opt == '--no-html':
html_report = False
elif opt == '--fast': # --no-check, --no-gc, --no-snps will automatically set in QUAST runs
html_report = False
elif opt == '--plots-format':
pass
elif opt == '--memory-efficient':
pass
elif opt == '--silent':
qconfig.silent = True
elif opt in ('-1', '--reads1'):
reads_fpath_f = arg
quast_py_args = __remove_from_quast_py_args(quast_py_args, opt, arg)
elif opt in ('-2', '--reads2'):
reads_fpath_r = arg
quast_py_args = __remove_from_quast_py_args(quast_py_args, opt, arg)
elif opt == '--contig-alignment-html':
qconfig.create_contig_alignment_html = True
else:
logger.error('Unknown option: %s. Use -h for help.' % (opt + ' ' + arg), to_stderr=True, exit_with_code=2)
for c_fpath in contigs_fpaths:
assert_file_exists(c_fpath, 'contigs')
labels = quast.process_labels(contigs_fpaths, labels, all_labels_from_dirs)
for contigs_fpath in contigs_fpaths:
if contigs_fpath in quast_py_args:
quast_py_args.remove(contigs_fpath)
# Directories
output_dirpath, _, _ = quast._set_up_output_dir(
output_dirpath, None, make_latest_symlink,
save_json=False)
corrected_dirpath = os.path.join(output_dirpath, qconfig.corrected_dirname)
logger.set_up_file_handler(output_dirpath)
args = [os.path.realpath(__file__)]
for k, v in options: args.extend([k, v])
args.extend(contigs_fpaths)
logger.print_command_line(args, wrap_after=None)
logger.start()
qconfig.set_max_threads(logger)
########################################################################
from libs import reporting
reload(reporting)
if os.path.isdir(corrected_dirpath):
shutil.rmtree(corrected_dirpath)
os.mkdir(corrected_dirpath)
# PROCESSING REFERENCES
if ref_fpaths:
logger.main_info()
logger.main_info('Reference(s):')
corrected_ref_fpaths, combined_ref_fpath, chromosomes_by_refs, ref_names =\
_correct_references(ref_fpaths, corrected_dirpath)
# PROCESSING CONTIGS
logger.main_info()
logger.main_info('Contigs:')
assemblies, correct_assemblies = _correct_contigs(contigs_fpaths, output_dirpath, labels)
if not assemblies:
logger.error("None of the assembly files contains correct contigs. "
"Please, provide different files or decrease --min-contig threshold.")
return 4
# Running QUAST(s)
quast_py_args += ['--meta']
downloaded_refs = False
# SEARCHING REFERENCES
if not ref_fpaths:
logger.main_info()
if qconfig.max_references == 0:
logger.notice("Maximum number of references (--max-ref-number) is set to 0, search in SILVA 16S rRNA database is disabled")
else:
if ref_txt_fpath:
logger.main_info("List of references was provided, starting to download reference genomes from NCBI...")
else:
logger.main_info("No references are provided, starting to search for reference genomes in SILVA 16S rRNA database "
"and to download them from NCBI...")
downloaded_dirpath = os.path.join(output_dirpath, qconfig.downloaded_dirname)
if not os.path.isdir(downloaded_dirpath):
os.mkdir(downloaded_dirpath)
ref_fpaths = search_references_meta.do(assemblies, labels, downloaded_dirpath, ref_txt_fpath)
if ref_fpaths:
search_references_meta.is_quast_first_run = True
if not ref_txt_fpath:
downloaded_refs = True
logger.main_info()
logger.main_info('Downloaded reference(s):')
corrected_ref_fpaths, combined_ref_fpath, chromosomes_by_refs, ref_names =\
_correct_references(ref_fpaths, corrected_dirpath)
elif test_mode and ref_fpaths is None:
logger.error('Failed to download or setup SILVA 16S rRNA database for working without '
'references on metagenome datasets!', to_stderr=True, exit_with_code=4)
if not ref_fpaths:
# No references, running regular quast with MetaGenemark gene finder
logger.main_info()
logger.notice('No references are provided, starting regular QUAST with MetaGeneMark gene finder')
_start_quast_main(
None,
quast_py_args,
assemblies=assemblies,
output_dirpath=output_dirpath,
exit_on_exception=True)
exit(0)
# Running combined reference
combined_output_dirpath = os.path.join(output_dirpath, qconfig.combined_output_name)
reads_fpaths = []
if reads_fpath_f:
reads_fpaths.append(reads_fpath_f)
if reads_fpath_r:
reads_fpaths.append(reads_fpath_r)
if reads_fpaths:
bed_fpath = reads_analyzer.do(combined_ref_fpath, contigs_fpaths, reads_fpaths, corrected_ref_fpaths,
os.path.join(combined_output_dirpath, qconfig.variation_dirname),
external_logger=logger)
if bed_fpath:
quast_py_args += ['--bed-file']
quast_py_args += [bed_fpath]
quast_py_args += ['--combined-ref']
run_name = 'for the combined reference'
logger.main_info()
logger.main_info('Starting quast.py ' + run_name + '...')
total_num_notices = 0
total_num_warnings = 0
total_num_nf_errors = 0
total_num_notifications = (total_num_notices, total_num_warnings, total_num_nf_errors)
if qconfig.html_report:
from libs.html_saver import json_saver
json_texts = []
else:
json_texts = None
return_code, total_num_notifications, assemblies, labels = _start_quast_main(run_name, quast_py_args + ["--ambiguity-usage"] + ['all'],
assemblies=assemblies,
reference_fpath=combined_ref_fpath,
output_dirpath=combined_output_dirpath,
num_notifications_tuple=total_num_notifications, is_first_run=True)
for arg in args:
if arg in ('-s', "--scaffolds"):
quast_py_args.remove(arg)
if json_texts is not None:
json_texts.append(json_saver.json_text)
search_references_meta.is_quast_first_run = False
genome_info_dirpath = os.path.join(output_dirpath, qconfig.combined_output_name, 'genome_stats')
genome_info_fpath = os.path.join(genome_info_dirpath, 'genome_info.txt')
if not os.path.exists(genome_info_fpath):
logger.main_info('')
logger.main_info('Failed aligning the contigs for all the references. ' + ('Try to restart MetaQUAST with another references.'
if not downloaded_refs else 'Try to use option --max-ref-number to change maximum number of references '
'(per each assembly) to download.'))
logger.main_info('')
quast._cleanup(corrected_dirpath)
logger.main_info('MetaQUAST finished.')
logger.finish_up(numbers=tuple(total_num_notifications), check_test=test_mode)
return
if downloaded_refs:
logger.main_info()
logger.main_info('Excluding downloaded references with low genome fraction from further analysis..')
corr_ref_fpaths = remove_unaligned_downloaded_refs(genome_info_fpath, ref_fpaths, chromosomes_by_refs)
if corr_ref_fpaths and corr_ref_fpaths != ref_fpaths:
logger.main_info()
logger.main_info('Filtered reference(s):')
os.remove(combined_ref_fpath)
contigs_analyzer.ref_labels_by_chromosomes = {}
corrected_ref_fpaths, combined_ref_fpath, chromosomes_by_refs, ref_names =\
_correct_references(corr_ref_fpaths, corrected_dirpath)
run_name = 'for the corrected combined reference'
logger.main_info()
logger.main_info('Starting quast.py ' + run_name + '...')
return_code, total_num_notifications, assemblies, labels = _start_quast_main(run_name, quast_py_args + ["--ambiguity-usage"] + ['all'],
assemblies=assemblies,
reference_fpath=combined_ref_fpath,
output_dirpath=combined_output_dirpath,
num_notifications_tuple=total_num_notifications, is_first_run=True)
if json_texts is not None:
json_texts = json_texts[:-1]
json_texts.append(json_saver.json_text)
elif corr_ref_fpaths == ref_fpaths:
logger.main_info('All downloaded references have genome fraction more than 10%. Nothing was excluded.')
else:
logger.main_info('All downloaded references have low genome fraction. Nothing was excluded for now.')
quast_py_args += ['--no-check-meta']
qconfig.contig_thresholds = ','.join([str(threshold) for threshold in qconfig.contig_thresholds if threshold > qconfig.min_contig])
if not qconfig.contig_thresholds:
qconfig.contig_thresholds = 'None'
quast_py_args = __remove_from_quast_py_args(quast_py_args, '--contig-thresholds', qconfig.contig_thresholds)
quast_py_args += ['--contig-thresholds']
quast_py_args += [qconfig.contig_thresholds]
quast_py_args.remove('--combined-ref')
logger.main_info()
logger.main_info('Partitioning contigs into bins aligned to each reference..')
assemblies_by_reference, not_aligned_assemblies = _partition_contigs(
assemblies, corrected_ref_fpaths, corrected_dirpath,
os.path.join(combined_output_dirpath, 'contigs_reports', 'alignments_%s.tsv'), labels)
ref_names = []
output_dirpath_per_ref = os.path.join(output_dirpath, qconfig.per_ref_dirname)
for ref_fpath, ref_assemblies in assemblies_by_reference:
ref_name = qutils.name_from_fpath(ref_fpath)
logger.main_info('')
if not ref_assemblies:
logger.main_info('No contigs were aligned to the reference ' + ref_name + ', skipping..')
else:
ref_names.append(ref_name)
run_name = 'for the contigs aligned to ' + ref_name
logger.main_info('Starting quast.py ' + run_name)
return_code, total_num_notifications = _start_quast_main(run_name, quast_py_args,
assemblies=ref_assemblies,
reference_fpath=ref_fpath,
output_dirpath=os.path.join(output_dirpath_per_ref, ref_name),
exit_on_exception=False, num_notifications_tuple=total_num_notifications)
if json_texts is not None:
json_texts.append(json_saver.json_text)
# Finally running for the contigs that has not been aligned to any reference
no_unaligned_contigs = True
for assembly in not_aligned_assemblies:
if os.path.isfile(assembly.fpath) and os.stat(assembly.fpath).st_size != 0:
no_unaligned_contigs = False
break
run_name = 'for the contigs not aligned anywhere'
logger.main_info()
if no_unaligned_contigs:
logger.main_info('Skipping quast.py ' + run_name + ' (everything is aligned!)')
else:
logger.main_info('Starting quast.py ' + run_name + '...')
return_code, total_num_notifications = _start_quast_main(run_name, quast_py_args,
assemblies=not_aligned_assemblies,
output_dirpath=os.path.join(output_dirpath, qconfig.not_aligned_name),
exit_on_exception=False, num_notifications_tuple=total_num_notifications)
if return_code not in [0, 4]:
logger.error('Error running quast.py for the contigs not aligned anywhere')
elif return_code == 4: # no unaligned contigs, i.e. everything aligned
no_unaligned_contigs = True
if not no_unaligned_contigs:
if json_texts is not None:
json_texts.append(json_saver.json_text)
if ref_names:
logger.print_timestamp()
logger.main_info("Summarizing results...")
summary_output_dirpath = os.path.join(output_dirpath, qconfig.meta_summary_dir)
if not os.path.isdir(summary_output_dirpath):
os.makedirs(summary_output_dirpath)
if html_report and json_texts:
from libs.html_saver import html_saver
html_summary_report_fpath = html_saver.init_meta_report(output_dirpath)
else:
html_summary_report_fpath = None
from libs import create_meta_summary
metrics_for_plots = reporting.Fields.main_metrics
misassembl_metrics = [reporting.Fields.MIS_RELOCATION, reporting.Fields.MIS_TRANSLOCATION, reporting.Fields.MIS_INVERTION,
reporting.Fields.MIS_ISTRANSLOCATIONS]
create_meta_summary.do(html_summary_report_fpath, summary_output_dirpath, combined_output_dirpath, output_dirpath_per_ref, metrics_for_plots, misassembl_metrics,
ref_names if no_unaligned_contigs else ref_names + [qconfig.not_aligned_name])
if html_report and json_texts:
from libs import plotter
html_saver.save_colors(output_dirpath, contigs_fpaths, plotter.dict_color_and_ls, meta=True)
html_saver.create_meta_report(output_dirpath, json_texts)
quast._cleanup(corrected_dirpath)
logger.main_info('')
logger.main_info('MetaQUAST finished.')
logger.finish_up(numbers=tuple(total_num_notifications), check_test=test_mode)