def parse(self, fp, separator):
con_names = []
con_bins = []
reader = CSVReader()
for (cid, bid) in reader.readCSV(fp, separator):
con_names.append(cid)
con_bins.append(bid)
return (con_names, con_bins)
def parse(self, fp, separator):
con_names = []
con_bins = []
reader = CSVReader()
for (cid, bid) in reader.readCSV(fp, separator):
con_names.append(cid)
con_bins.append(bid)
return (con_names, con_bins)
def readOtuTable_(self, otu_file):
"""Parse singleM otu table"""
reader = CSVReader()
cols = None
for l in reader.readCSV(otu_file, "\t"):
if cols is None:
cols = [l.index('read_names'), l.index('gene')]
try:
cols += [l.index('taxonomy')]
except ValueError:
pass
continue
yield tuple(l[i] for i in cols)
def readTaxTable(self, otu_file):
"""Parse graftm taxonomy table"""
reader = CSVReader()
for (cname, taxstring) in reader.readCSV(otu_file, "\t"):
# strip _(num)_(num)_(num) suffix
parsed = cname
for _ in range(3):
parsed = parsed.rstrip('1234567890')
if not parsed.endswith('_') or len(parsed) < 2:
raise ValueError(
'Error encountered when parsing contig name: %s' %
cname)
parsed = parsed[:-1]
yield (parsed, taxstring)