def main():
#main_dir = dirname(__file__)
args = docopt(__doc__)
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['--hitsfile']
prefix = args['--out']
nodesDB_f = args['--db']
names_f = args['--names']
nodes_f = args['--nodes']
taxrules = args['--taxrule']
min_bitscore_diff = float(args['--min_diff'])
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 sam_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('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)] + \
[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 = blobtools.__version__
# Parse FASTA
blobDb.parseFasta(fasta_f, fasta_type)
# Parse nodesDB OR names.dmp, nodes.dmp
nodesDB_default = join(blobtools.DATADIR, "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)
blobDb.computeTaxonomy(taxrules, nodesDB, min_bitscore_diff, tax_collision_random)
else:
print BtLog.warn_d['0']
# Parse coverage
blobDb.parseCoverage(covLibObjs=cov_libs, no_base_cov=None)
# 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 main():
#main_dir = dirname(__file__)
args = docopt(__doc__)
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['--hitsfile']
prefix = args['--out']
nodesDB_f = args['--db']
names_f = args['--names']
nodes_f = args['--nodes']
taxrules = args['--taxrule']
min_bitscore_diff = float(args['--min_diff'])
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 sam_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('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)] + \
[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 = blobtools.__version__
# Parse FASTA
blobDb.parseFasta(fasta_f, fasta_type)
# Parse nodesDB OR names.dmp, nodes.dmp
nodesDB_default = join(blobtools.DATADIR, "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)
blobDb.computeTaxonomy(taxrules, nodesDB, min_bitscore_diff,
tax_collision_random)
else:
print BtLog.warn_d['0']
# Parse coverage
blobDb.parseCoverage(covLibObjs=cov_libs, no_base_cov=None)
# 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)
