def main():
args = docopt(__doc__)
#print(args)
bam_f = args['--bam']
include_f = args['--include']
exclude_f = args['--exclude']
out_prefix = args['--out']
read_format = args['--read_format']
if not read_format in set(['fq', 'fa']):
sys.exit("[X] Read format must be fq or fa!")
noninterleaved = args['--noninterleaved']
include_unmapped = True
if args['--exclude_unmapped']:
include_unmapped = False
out_f = BtIO.getOutFile(bam_f, out_prefix, None)
if include_f and exclude_f:
print(BtLog.error('43'))
elif include_f:
sequence_list = BtIO.parseList(include_f)
BtIO.parseBamForFilter(bam_f, include_unmapped, noninterleaved, out_f, sequence_list, None, read_format)
elif exclude_f:
sequence_list = BtIO.parseList(exclude_f)
BtIO.parseBamForFilter(bam_f, include_unmapped, noninterleaved, out_f, None, sequence_list, read_format)
else:
BtIO.parseBamForFilter(bam_f, include_unmapped, noninterleaved, out_f, None, None, read_format)
def main():
args = docopt(__doc__)
bam_f = args['--bam']
include_f = args['--include']
exclude_f = args['--exclude']
out_prefix = args['--out']
include_unmapped = args['--include_unmapped']
gzip = None
do_sort = args['--sort']
keep_sorted = args['--keep']
sort_threads = int(args['--threads'])
out_f = BtIO.getOutFile(bam_f, out_prefix, None)
if include_f and exclude_f:
print BtLog.error('43')
elif include_f:
sequence_list = BtIO.parseList(include_f)
BtIO.parseBamForFilter(bam_f, include_unmapped, out_f, sequence_list, None, gzip, do_sort, keep_sorted, sort_threads)
elif exclude_f:
sequence_list = BtIO.parseList(exclude_f)
BtIO.parseBamForFilter(bam_f, include_unmapped, out_f, None, sequence_list, gzip, do_sort, keep_sorted, sort_threads)
else:
BtIO.parseBamForFilter(bam_f, include_unmapped, out_f, None, None, gzip, do_sort, keep_sorted, sort_threads)
def main():
#print(data_dir)
args = docopt(__doc__)
blobdb_f = args['--input']
prefix = args['--out']
ranks = args['--rank']
taxrule = args['--taxrule']
hits_flag = args['--hits']
seq_list_f = args['--list']
concoct = args['--concoct']
cov = args['--cov']
notable = args['--notable']
experimental = args['--experimental']
# Does blobdb_f exist ?
if not isfile(blobdb_f):
BtLog.error('0', blobdb_f)
out_f = BtIO.getOutFile(blobdb_f, prefix, None)
# Are ranks sane ?
if 'all' in ranks:
temp_ranks = RANKS[0:-1]
ranks = temp_ranks[::-1]
else:
for rank in ranks:
if rank not in RANKS:
BtLog.error('9', rank)
# Does seq_list file exist?
seqs = []
if (seq_list_f):
if isfile(seq_list_f):
seqs = BtIO.parseList(seq_list_f)
else:
BtLog.error('0', seq_list_f)
# Load BlobDb
blobDb = BtCore.BlobDb('new')
print(BtLog.status_d['9'] % (blobdb_f))
blobDb.load(blobdb_f)
blobDb.version = interface.__version__
# Is taxrule sane and was it computed?
if (blobDb.hitLibs) and taxrule not in blobDb.taxrules:
BtLog.error('11', taxrule, blobDb.taxrules)
# view(s)
viewObjs = []
print(BtLog.status_d['14'])
if not (notable):
tableView = None
if len(blobDb.hitLibs) > 1:
tableView = BtCore.ViewObj(name="table",
out_f=out_f,
suffix="%s.table.txt" % (taxrule),
body=[])
else:
tableView = BtCore.ViewObj(name="table",
out_f=out_f,
suffix="table.txt",
body=[])
viewObjs.append(tableView)
if not experimental == 'False':
meta = {}
if isfile(experimental):
meta = BtIO.readYaml(experimental)
experimentalView = BtCore.ExperimentalViewObj(name="experimental",
view_dir=out_f,
blobDb=blobDb,
meta=meta)
viewObjs.append(experimentalView)
if (concoct):
concoctTaxView = None
concoctCovView = None
if len(blobDb.hitLibs) > 1:
concoctTaxView = BtCore.ViewObj(
name="concoct_tax",
out_f=out_f,
suffix="%s.concoct_taxonomy_info.csv" % (taxrule),
body=dict())
concoctCovView = BtCore.ViewObj(
name="concoct_cov",
out_f=out_f,
suffix="%s.concoct_coverage_info.tsv" % (taxrule),
body=[])
else:
concoctTaxView = BtCore.ViewObj(name="concoct_tax",
out_f=out_f,
suffix="concoct_taxonomy_info.csv",
body=dict())
concoctCovView = BtCore.ViewObj(name="concoct_cov",
out_f=out_f,
suffix="concoct_coverage_info.tsv",
body=[])
viewObjs.append(concoctTaxView)
viewObjs.append(concoctCovView)
if (cov):
for cov_lib_name, covLibDict in blobDb.covLibs.items():
out_f = BtIO.getOutFile(covLibDict['f'], prefix, None)
covView = BtCore.ViewObj(name="covlib",
out_f=out_f,
suffix="cov",
body=[])
blobDb.view(viewObjs=[covView],
ranks=None,
taxrule=None,
hits_flag=None,
seqs=None,
cov_libs=[cov_lib_name],
progressbar=True)
if (viewObjs):
#for viewObj in viewObjs:
# print(viewObj.name)
blobDb.view(viewObjs=viewObjs,
ranks=ranks,
taxrule=taxrule,
hits_flag=hits_flag,
seqs=seqs,
cov_libs=[],
progressbar=True)
print(BtLog.status_d['19'])
# Does blobdb_f exist ?
if not isfile(blobdb_f):
BtLog.error('0', blobdb_f)
# Are ranks sane ?
for rank in ranks:
if rank not in RANKS:
BtLog.error('9', rank)
if 'all' in ranks:
ranks = RANKS[0:-1]
# Is list a list of sequence names or a file?
seqs = []
if (seq_list):
if isfile(seq_list):
seqs = BtIO.parseList(seq_list)
elif "," in seq_list:
seqs = seq_list.split(",")
else:
seqs = [seq_list]
# Load BlobDb
blobDB = bt.BlobDb('new')
blobDB.load(blobdb_f)
# Is taxrule sane and was it computed?
if (blobDB.hitLibs) and taxrule not in blobDB.taxrules:
BtLog.error('11', taxrule, blobDB.taxrules)
blobDB.view(out_f, ranks, taxrule, hits_flag, seqs)
if not isfile(blobdb_f):
BtLog.error('0', blobdb_f)
# Are ranks sane ?
for rank in ranks:
if rank not in RANKS:
BtLog.error('9', rank)
if 'all' in ranks:
temp_ranks = RANKS[0:-1]
ranks = temp_ranks[::-1]
# Is list a list of sequence names or a file?
seqs = []
if (seq_list):
if isfile(seq_list):
seqs = BtIO.parseList(seq_list)
elif "," in seq_list:
seqs = seq_list.split(",")
else:
seqs = [seq_list]
# Load BlobDb
blobDB = bt.BlobDb('new')
blobDB.load(blobdb_f)
# Is taxrule sane and was it computed?
if (blobDB.hitLibs) and taxrule not in blobDB.taxrules:
BtLog.error('11', taxrule, blobDB.taxrules)
blobDB.view(out_f, ranks, taxrule, hits_flag, seqs)