def main():
args = docopt(__doc__)
fasta_f = args['--infile']
bam_fs = args['--bam']
cas_fs = args['--cas']
prefix = args['--output']
estimate_cov_flag = True if not args['--calculate_cov'] else False
# Make covLibs
cov_libs = [BtCore.CovLibObj('bam' + str(idx), 'bam', lib_f) for idx, lib_f in enumerate(bam_fs)] + \
[BtCore.CovLibObj('cas' + str(idx), 'cas', lib_f) for idx, lib_f in enumerate(cas_fs)]
if not (cov_libs):
BtLog.error('31')
blobDb = BtCore.BlobDb('cov')
blobDb.version = interface.__version__
blobDb.parseFasta(fasta_f, None)
blobDb.parseCoverage(covLibObjs=cov_libs, estimate_cov=estimate_cov_flag, prefix=prefix)
def main():
args = docopt(__doc__)
fasta_f = args['--infile']
bam_fs = args['--bam']
cas_fs = args['--cas']
sam_fs = args['--sam']
prefix = args['--output']
no_base_cov_flag = args['--no_base_cov']
# Make covLibs
cov_libs = [BtCore.CovLibObj('bam' + str(idx), 'bam', lib_f) for idx, lib_f in enumerate(bam_fs)] + \
[BtCore.CovLibObj('sam' + str(idx), 'sam', lib_f) for idx, lib_f in enumerate(sam_fs)] + \
[BtCore.CovLibObj('cas' + str(idx), 'cas', lib_f) for idx, lib_f in enumerate(cas_fs)]
if not (cov_libs):
BtLog.error('31')
blobDb = BtCore.BlobDb('cov')
blobDb.version = blobtools.__version__
blobDb.parseFasta(fasta_f, None)
blobDb.parseCoverage(covLibObjs=cov_libs, no_base_cov=no_base_cov_flag, prefix=prefix)
nodesDB_f = os.path.join(main_dir, nodesDB_f)
if not os.path.isfile(nodesDB_f) and not ((names_f) and (nodes_f)):
BtLog.error('3')
if not (hit_fs):
BtLog.error('18')
# can FASTA parser deal with assemblies
if not fasta_type in ASSEMBLY_TYPES:
BtLog.error('2', ",".join(ASSEMBLY_TYPES[1:]))
# Is coverage provided?
if not (fasta_type) and not bam_fs and not sam_fs and not cov_fs and not cas_fs:
BtLog.error('1')
cov_libs = [bt.CovLibObj('bam' + str(idx), 'bam', lib_f) for idx, lib_f in enumerate(bam_fs)] + \
[bt.CovLibObj('sam' + str(idx), 'sam', lib_f) for idx, lib_f in enumerate(sam_fs)] + \
[bt.CovLibObj('cas' + str(idx), 'cas', lib_f) for idx, lib_f in enumerate(cas_fs)] + \
[bt.CovLibObj('cov' + str(idx), 'cov', lib_f) for idx, lib_f in enumerate(cov_fs)]
# Create BlobDB object
blobDb = bt.BlobDb(title)
# Parse FASTA
blobDb.parseFasta(fasta_f, fasta_type)
# Parse coverage
blobDb.parseCovs(cov_libs)
# Parse Tax
hitLibs = [bt.hitLibObj('tax' + str(idx), 'tax', lib_f) for idx, lib_f in enumerate(hit_fs)]
blobDb.parseHits(hitLibs)
def validate_input_create(main_dir, args):
'''
Accepts:
- main_dir
- docopt args
Returns:
- title
- fasta_f
- fasta_type
- cov_libs
- hit_libs
- nodesDB_f
- taxrules
- out_f
'''
ASSEMBLY_TYPES = [None, 'spades', 'soap', 'abyss', 'velvet']
fasta_f = args['--infile']
fasta_type = args['--type']
sam_fs = args['--sam']
bam_fs = args['--bam']
cov_fs = args['--cov']
cas_fs = args['--cas']
hit_fs = args['--taxfile']
out_f = args['--out']
if (out_f):
out_f = "%s.%s" % (os.path.basename(out_f), "BlobDB.json")
else:
out_f = "%s" % ("BlobDB.json")
nodesDB_f = args['--db']
names_f = args['--names']
nodes_f = args['--nodes']
taxrules = args['--taxrule']
title = args['--title'] if (args['--title']) else out_f
# Do files exist ?
files = [
x for x in list([fasta_f] + sam_fs + bam_fs + cov_fs + cas_fs +
[names_f] + [nodes_f] + hit_fs) if x is not None
]
for f in files:
if not os.path.isfile(f):
BtLog.error('0', f)
# Is taxonomy provided?
if nodesDB_f == "data/nodesDB.txt":
nodesDB_f = os.path.join(main_dir, nodesDB_f)
if not os.path.isfile(nodesDB_f) and not ((names_f) and (nodes_f)):
BtLog.error('3')
if not (hit_fs):
BtLog.error('18')
# can FASTA parser deal with assemblies
if not fasta_type in ASSEMBLY_TYPES:
BtLog.error('2', ",".join(ASSEMBLY_TYPES[1:]))
# Is coverage provided?
if not (fasta_type
) and not bam_fs and not sam_fs and not cov_fs and not cas_fs:
BtLog.error('1')
cov_libs = [bt.CovLibObj('bam' + str(idx), 'bam', lib_f) for idx, lib_f in enumerate(bam_fs)] + \
[bt.CovLibObj('sam' + str(idx), 'sam', lib_f) for idx, lib_f in enumerate(sam_fs)] + \
[bt.CovLibObj('cas' + str(idx), 'cas', lib_f) for idx, lib_f in enumerate(cas_fs)] + \
[bt.CovLibObj('cov' + str(idx), 'cov', lib_f) for idx, lib_f in enumerate(cov_fs)]
hit_libs = [
bt.hitLibObj('tax' + str(idx), 'tax', lib_f)
for idx, lib_f in enumerate(hit_fs)
]
return title, fasta_f, fasta_type, cov_libs, hit_libs, taxrules, nodesDB_f, nodes_f, names_f, out_f
def main():
#main_dir = dirname(__file__)
args = docopt(__doc__)
fasta_f = args['--infile']
fasta_type = args['--type']
bam_fs = args['--bam']
cov_fs = args['--cov']
cas_fs = args['--cas']
hit_fs = args['--hitsfile']
prefix = args['--out']
nodesDB_f = args['--db']
names_f = args['--names']
estimate_cov_flag = True if not args['--calculate_cov'] else False
nodes_f = args['--nodes']
taxrules = args['--taxrule']
try:
min_bitscore_diff = float(args['--min_diff'])
min_score = float(args['--min_score'])
except ValueError():
BtLog.error('45')
tax_collision_random = args['--tax_collision_random']
title = args['--title']
# outfile
out_f = BtIO.getOutFile("blobDB", prefix, "json")
if not (title):
title = out_f
# coverage
if not (fasta_type) and not bam_fs and not cov_fs and not cas_fs:
BtLog.error('1')
cov_libs = [BtCore.CovLibObj('bam' + str(idx), 'bam', lib_f) for idx, lib_f in enumerate(bam_fs)] + \
[BtCore.CovLibObj('cas' + str(idx), 'cas', lib_f) for idx, lib_f in enumerate(cas_fs)] + \
[BtCore.CovLibObj('cov' + str(idx), 'cov', lib_f) for idx, lib_f in enumerate(cov_fs)]
# taxonomy
hit_libs = [
BtCore.HitLibObj('tax' + str(idx), 'tax', lib_f)
for idx, lib_f in enumerate(hit_fs)
]
# Create BlobDB object
blobDb = BtCore.BlobDb(title)
blobDb.version = interface.__version__
# Parse FASTA
blobDb.parseFasta(fasta_f, fasta_type)
# Parse nodesDB OR names.dmp, nodes.dmp
nodesDB_default = join(dirname(abspath(__file__)), "../data/nodesDB.txt")
nodesDB, nodesDB_f = BtIO.parseNodesDB(nodes=nodes_f,
names=names_f,
nodesDB=nodesDB_f,
nodesDBdefault=nodesDB_default)
blobDb.nodesDB_f = nodesDB_f
# Parse similarity hits
if (hit_libs):
blobDb.parseHits(hit_libs)
if not taxrules:
if len(hit_libs) > 1:
taxrules = ['bestsum', 'bestsumorder']
else:
taxrules = ['bestsum']
blobDb.computeTaxonomy(taxrules, nodesDB, min_score, min_bitscore_diff,
tax_collision_random)
else:
print(BtLog.warn_d['0'])
# Parse coverage
blobDb.parseCoverage(covLibObjs=cov_libs,
estimate_cov=estimate_cov_flag,
prefix=prefix)
# Generating BlobDB and writing to file
print(BtLog.status_d['7'] % out_f)
BtIO.writeJson(blobDb.dump(), out_f)