def write_summary(self, summary_fn, isoforms_fa, hq_fa=None, lq_fa=None):
"""Extract number of consensus isoforms predicted, and total
number of bases in all consensuus isoforms from isoforms_fa and write
the two attributes to summary_fn.
if hq_fa (polished high-quality isoforms) is not None, report
the number of polished hq clusters
if lq_fa (polished high-quality isoforms) is not None, report
the number of polished hq clusters
"""
self.add_log("Writing a summary to {f}".format(f=summary_fn),
level=logging.INFO)
try:
summary = ClusterSummary()
with FastaReader(isoforms_fa) as reader:
for r in reader:
summary.numConsensusIsoforms += 1
summary.numTotalBases += len(r.sequence)
if hq_fa is not None:
summary.num_polished_hq_isoforms = 0
with FastaReader(hq_fa) as reader:
for r in reader:
summary.num_polished_hq_isoforms += 1
if lq_fa is not None:
summary.num_polished_lq_isoforms = 0
with FastaReader(lq_fa) as reader:
for r in reader:
summary.num_polished_lq_isoforms += 1
summary.write(summary_fn)
except ZeroDivisionError:
errMsg = "No consensus isoforms predicted."
self.add_log(errMsg, level=logging.ERROR)
raise RuntimeError(errMsg)
def write_summary(self, summary_fn, isoforms_fa, hq_fa=None, lq_fa=None):
"""Extract number of consensus isoforms predicted, and total
number of bases in all consensuus isoforms from isoforms_fa and write
the two attributes to summary_fn.
if hq_fa (polished high-quality isoforms) is not None, report
the number of polished hq clusters
if lq_fa (polished high-quality isoforms) is not None, report
the number of polished hq clusters
"""
self.add_log("Writing a summary to {f}".format(f=summary_fn),
level=logging.INFO)
try:
summary = ClusterSummary()
with FastaReader(isoforms_fa) as reader:
for r in reader:
summary.numConsensusIsoforms += 1
summary.numTotalBases += len(r.sequence)
if hq_fa is not None:
summary.num_polished_hq_isoforms = 0
with FastaReader(hq_fa) as reader:
for r in reader:
summary.num_polished_hq_isoforms += 1
if lq_fa is not None:
summary.num_polished_lq_isoforms = 0
with FastaReader(lq_fa) as reader:
for r in reader:
summary.num_polished_lq_isoforms += 1
summary.write(summary_fn)
except ZeroDivisionError:
errMsg = "No consensus isoforms predicted."
self.add_log(errMsg, level=logging.ERROR)
raise RuntimeError(errMsg)
