[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)
# Parse nodesDB
nodesDB, nodesDB_f = BtIO.getNodesDB(nodes=nodes_f, names=names_f, nodesDB=nodesDB_f)
blobDb.nodesDB_f = nodesDB_f
if not os.path.isfile(nodesDB_f):
print BtLog.status_d['5'] % nodesDB_f
BtIO.writeNodesDB(nodesDB, nodesDB_f)
# Computing taxonomy based on taxrules
print BtLog.status_d['6'] % ",".join(taxrules)
blobDb.computeTaxonomy(taxrules, nodesDB)
# Generating BlobDB and writing to file
print BtLog.status_d['7'] % out_f
BtIO.writeJson(blobDb.dump(), 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)
def output(self):
# meta
meta = self.get_meta()
meta_f = join(self.view_dir, "meta.json")
BtIO.writeJson(meta, meta_f, indent=2)
# gc
gc_f = join(self.view_dir, "gc.json")
print BtLog.status_d['13'] % (gc_f)
BtIO.writeJson(self.gc, gc_f, indent=1)
# length
length_f = join(self.view_dir, "length.json")
print BtLog.status_d['13'] % (length_f)
BtIO.writeJson(self.length, length_f, indent=1)
# names
names_f = join(self.view_dir, "names.json")
print BtLog.status_d['13'] % (names_f)
BtIO.writeJson(self.names, names_f, indent=1)
# cov
cov_d = join(self.view_dir, "covs")
BtIO.create_dir(directory=cov_d)
for cov_lib, cov in self.covs.items():
cov_f = join(cov_d, "%s.json" % cov_lib)
print BtLog.status_d['13'] % (cov_f)
BtIO.writeJson(cov, cov_f, indent=1)
# tax
taxrule_d = join(self.view_dir, "taxrule")
BtIO.create_dir(directory=taxrule_d)
for taxrule in self.tax:
tax_d = join(taxrule_d, taxrule)
BtIO.create_dir(directory=tax_d)
for rank in self.tax[taxrule]:
tax = self.tax[taxrule][rank]
rank_f = join(tax_d, "%s.json" % rank)
BtIO.writeJson(tax, rank_f, indent=1)
def output(self):
# meta
meta = self.get_meta()
meta_f = join(self.view_dir, "meta.json")
BtIO.writeJson(meta, meta_f, indent=2)
# gc
gc_f = join(self.view_dir, "gc.json")
print BtLog.status_d['13'] % (gc_f)
BtIO.writeJson({"values": self._format_float(self.gc)}, gc_f, indent=1)
# length
length_f = join(self.view_dir, "length.json")
print BtLog.status_d['13'] % (length_f)
BtIO.writeJson({"values": self.length}, length_f, indent=1)
# Ns
if max(self.n_count) > 0:
n_f = join(self.view_dir, "ncount.json")
print BtLog.status_d['13'] % (n_f)
BtIO.writeJson(
{"values": map(lambda x: max(x, 0.2), self.n_count)},
n_f,
indent=1)
# identifiers
ids_f = join(self.view_dir, "identifiers.json")
print BtLog.status_d['13'] % (ids_f)
BtIO.writeJson(self.names, ids_f, indent=1)
# cov
for cov_name, cov in self.covs.items():
name = self._remove_cov_suffix(cov_name, self.blobDb.covLibs)
cov_f = join(self.view_dir, "%s_cov.json" % name)
print BtLog.status_d['13'] % (cov_f)
BtIO.writeJson({"values": self._format_float(cov, 0.02)},
cov_f,
indent=1)
# read_cov
for cov_name, cov in self.read_covs.items():
name = self._remove_cov_suffix(cov_name, self.blobDb.covLibs)
cov_f = join(self.view_dir, "%s_read_cov.json" % name)
print BtLog.status_d['13'] % (cov_f)
BtIO.writeJson({"values": map(lambda x: max(x, 0.2), cov)},
cov_f,
indent=1)
# tax
for taxrule in self.tax:
for rank in self.tax[taxrule]:
tax = self._keyed_list(self.tax[taxrule][rank])
rank_f = join(self.view_dir, "%s_%s.json" % (taxrule, rank))
BtIO.writeJson(tax, rank_f, indent=1)
score = self.tax_scores[taxrule][rank]['score']
score_f = join(self.view_dir,
"%s_%s_score.json" % (taxrule, rank))
BtIO.writeJson({"values": map(lambda x: max(x, 0.2), score)},
score_f,
indent=1)
cindex = self.tax_scores[taxrule][rank]['c_index']
cindex_f = join(self.view_dir,
"%s_%s_cindex.json" % (taxrule, rank))
BtIO.writeJson({"values": cindex}, cindex_f, indent=1)
