def parseCoverage(self, **kwargs):
# arguments
covLibObjs = kwargs['covLibObjs']
no_base_cov = kwargs['no_base_cov']
for covLib in covLibObjs:
self.addCovLib(covLib)
print BtLog.status_d['1'] % (covLib.name, covLib.f)
if covLib.fmt == 'bam' or covLib.fmt == 'sam':
base_cov_dict = {}
if covLib.fmt == 'bam':
base_cov_dict, covLib.reads_total, covLib.reads_mapped, read_cov_dict = BtIO.parseBam(
covLib.f, set(self.dict_of_blobs), no_base_cov)
else:
base_cov_dict, covLib.reads_total, covLib.reads_mapped, read_cov_dict = BtIO.parseSam(
covLib.f, set(self.dict_of_blobs), no_base_cov)
if covLib.reads_total == 0:
print BtLog.warn_d['4'] % covLib.f
for name, base_cov in base_cov_dict.items():
cov = base_cov / self.dict_of_blobs[name].agct_count
covLib.cov_sum += cov
self.dict_of_blobs[name].addCov(covLib.name, cov)
self.dict_of_blobs[name].addReadCov(
covLib.name, read_cov_dict[name])
# Create COV file for future use
out_f = BtIO.getOutFile(covLib.f, kwargs.get('prefix', None),
None)
covView = ViewObj(name="covlib",
out_f=out_f,
suffix="cov",
header="",
body=[])
self.view(viewObjs=[covView],
ranks=None,
taxrule=None,
hits_flag=None,
seqs=None,
cov_libs=[covLib.name],
progressbar=False)
elif covLib.fmt == 'cas':
cov_dict, covLib.reads_total, covLib.reads_mapped, read_cov_dict = BtIO.parseCas(
covLib.f, self.order_of_blobs)
if covLib.reads_total == 0:
print BtLog.warn_d['4'] % covLib.f
for name, cov in cov_dict.items():
covLib.cov_sum += cov
self.dict_of_blobs[name].addCov(covLib.name, cov)
self.dict_of_blobs[name].addReadCov(
covLib.name, read_cov_dict[name])
out_f = BtIO.getOutFile(covLib.f, kwargs.get('prefix', None),
None)
covView = ViewObj(name="covlib",
out_f=out_f,
suffix="cov",
header="",
body=[])
self.view(viewObjs=[covView],
ranks=None,
taxrule=None,
hits_flag=None,
seqs=None,
cov_libs=[covLib.name],
progressbar=False)
elif covLib.fmt == 'cov':
base_cov_dict, covLib.reads_total, covLib.reads_mapped, covLib.reads_unmapped, read_cov_dict = BtIO.parseCov(
covLib.f, set(self.dict_of_blobs))
#cov_dict = BtIO.readCov(covLib.f, set(self.dict_of_blobs))
if not len(base_cov_dict) == self.seqs:
print BtLog.warn_d['4'] % covLib.f
for name, cov in base_cov_dict.items():
covLib.cov_sum += cov
self.dict_of_blobs[name].addCov(covLib.name, cov)
if name in read_cov_dict:
self.dict_of_blobs[name].addReadCov(
covLib.name, read_cov_dict[name])
else:
pass
covLib.mean_cov = covLib.cov_sum / self.seqs
if covLib.cov_sum == 0.0:
print BtLog.warn_d['6'] % (covLib.name)
self.covLibs[covLib.name] = covLib
