def callable(lines):
num_lines = 0
header = None
for line in lines:
if is_empty(line):
continue
line = line.strip('\n').split(sep)
if strip_wspace and by_column:
line = [field.strip() for field in line]
if with_header and not header:
header = True
yield line
continue
if converter:
line = converter(line)
if ignore(line):
continue
yield line
num_lines += 1
if limit is not None and num_lines >= limit:
break
def callable(lines):
num_lines = 0
header = None
for line in lines:
if is_empty(line):
continue
line = line.strip('\n').split(sep)
if strip_wspace and by_column:
line = [field.strip() for field in line]
if with_header and not header:
header = True
yield line
continue
if converter:
line = converter(line)
if ignore(line):
continue
yield line
num_lines += 1
if limit is not None and num_lines >= limit:
break
def parse_otu_list(lines, precision=0.0049):
"""Parser for mothur *.list file
To ensure all distances are of type float, the parser returns a
distance of 0.0 for the unique groups. However, if some sequences
are very similar, mothur may return a grouping at zero distance.
What Mothur really means by this, however, is that the clustering
is at the level of Mothur's precision. In this case, the parser
returns the distance explicitly.
If you are parsing otu's with a non-default precision, you must
specify the precision here to ensure that the parsed distances are
in order.
Returns an iterator over (distance, otu_list)
"""
for line in lines:
if is_empty(line):
continue
tokens = line.strip().split('\t')
distance_str = tokens.pop(0)
if distance_str.lstrip().lower().startswith('u'):
distance = 0.0
elif distance_str == '0.0':
distance = float(precision)
else:
distance = float(distance_str)
num_otus = int(tokens.pop(0))
otu_list = [t.split(',') for t in tokens]
yield (distance, otu_list)
def parse_otu_list(lines, precision=0.0049):
"""Parser for mothur *.list file
To ensure all distances are of type float, the parser returns a
distance of 0.0 for the unique groups. However, if some sequences
are very similar, mothur may return a grouping at zero distance.
What Mothur really means by this, however, is that the clustering
is at the level of Mothur's precision. In this case, the parser
returns the distance explicitly.
If you are parsing otu's with a non-default precision, you must
specify the precision here to ensure that the parsed distances are
in order.
Returns an iterator over (distance, otu_list)
"""
for line in lines:
if is_empty(line):
continue
tokens = line.strip().split('\t')
distance_str = tokens.pop(0)
if distance_str.lstrip().lower().startswith('u'):
distance = 0.0
elif distance_str == '0.0':
distance = float(precision)
else:
distance = float(distance_str)
num_otus = int(tokens.pop(0))
otu_list = [t.split(',') for t in tokens]
yield (distance, otu_list)
