def __init__(self, name='experimental', view_dir=''):
self.name = name
self.view_dir = view_dir
self.length = []
self.gc = []
self.names = []
self.tax = {}
self.covs = {}
self.meta = {}
BtIO.create_dir(self.view_dir)
def __init__(self, name='experimental', view_dir='', blobDb={}):
self.name = name
self.view_dir = re.sub(".blobDB", "", view_dir)
self.length = []
self.gc = []
self.n_count = []
self.names = []
self.tax = {}
self.covs = {}
self.read_covs = defaultdict(list)
self.tax_scores = {}
self.blobDb = blobDb
self.meta = {}
BtIO.create_dir(self.view_dir)
def _write_output(self):
primary = [
'meta', 'blob_id', 'length', 'gc', 'n_count', 'agct_count',
'tax_id'
]
secondary = ['cov_base', 'cov_read', 'tax', 'tax_hit']
directory = BtIO.create_dir(self.path)
out_fs = []
if (directory):
out_fs = []
strings = []
for key in self.files:
if key in primary:
out_f.append(self.files[key])
data.append(getattr(self, key))
elif key in secondary:
for key2 in self.files[key]:
out_f.append(self.files[key][key2])
data.append(getattr(self, key)[key2])
else:
pass
with tarfile.open(out_f, "a:gz") as tar:
for out_f, string in zip(out_fs, strings):
with open(out_f, 'w') as fh:
json.dump(string,
fh,
indent=1,
separators=(',', ' : '))
tar.add(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)
