def CmalignScoreParser(lines):
"""Parser for tabfile format cmalign score result.
- IMPORTANT: Will only parse standard output from cmalign.
- NOTE: Will only work with search result files with a single CM
as a query. Will not work with multiple alignment result files
that have been concatenated.
- Result will be list of hits with following order:
[seq idx, seq name, seq len, total bit score, struct bit score,
avg prob, elapsed time]
"""
# Converting indices and %GC to integers and bit score to float.
# Since E-value is only present if CM is calibrated, leaving as string.
conversion_fields = [(0,int),(2,int),(3,float),(4,float),(5,float)]
cmalign_score_converter = ConvertFields(conversion_fields)
#Ignore hash characters
good_lines = []
for l in lines:
line = l.strip()
if line.startswith('# STOCKHOLM 1.0'):
break
if line and (not line.startswith('#')):
good_lines.append(l)
#make parser
cmalign_score_parser = SeparatorFormatParser(with_header=False,\
converter=cmalign_score_converter,\
ignore=None,\
sep=None)
return cmalign_score_parser(good_lines)
def CmsearchParser(lines):
"""Parser for tabfile format cmsearch result.
- IMPORTANT: Will not parse standard output from cmsearch. You must
use --tabfile with cmsearch to get correct format to use this
parser.
- NOTE: Will only work with search result files with a single CM
as a query. Will not work with multiple search result files
that have been concatenated.
- Result will be list of hits with following order:
[target name, target start, target stop, query start, query stop,
bit score, E-value, GC%]
"""
# Converting indices and %GC to integers and bit score to float.
# Since E-value is only present if CM is calibrated, leaving as string.
conversion_fields = [(2,int),(3,int),(4,int),(5,int),(6,float),(8,int)]
cmsearch_converter = ConvertFields(conversion_fields)
#Ignore hash characters
good_lines = []
for l in lines:
if not l.startswith('#'):
good_lines.append(l)
#make parser
cmsearch_parser = SeparatorFormatParser(with_header=False,\
converter=cmsearch_converter,\
ignore=None,\
sep=None)
return cmsearch_parser(good_lines)
def MinimalBedParser(data, converter=converter):
"""returns data lines from a BED file
NOTE: BED uses 0-based numbering"""
# If given a filename for the data
if type(data) == str:
if data.endswith('.bed.gz'):
data = gzip.GzipFile(data, 'rb')
else:
data = open(data, 'r')
header_lines = 0
data_lines = []
for row in data:
if not row.startswith('chr'):
header_lines += 1
else:
data_lines.append(row)
parser = SeparatorFormatParser(converter=converter,
with_header=False,
sep="\t")
for row in parser(data_lines):
yield row
def MinimalSamParser(data, converter=converter):
"""returns records from a sam file
NOTE: the default converter turns the 1-based numbering of POS into
0-based numbering"""
# If given a filename for the data
if type(data) == str:
data = open(data)
# get the lengths dict
lengths = {}
header_lines = 0
for row in data:
header_lines += 1
if not row.startswith('@'):
yield lengths
break
elif not row.startswith('@SQ'):
continue
line = row.split()[1:]
name = line[0].split(':')[1]
length = int(line[1].split(':')[1])
lengths[name] = length
# reset file pointer and move to first data line
data.seek(0)
for i, line in enumerate(data):
if i == header_lines - 2:
break
parser = SeparatorFormatParser(converter=converter,
with_header=False,
sep="\t")
for row in parser(data):
yield row