def write(self, outfile):
csv_file = open(outfile, 'w')
self.writer = CSVWriter(csv_file)
# Header
self.writer.write_row([
'Query', 'Name', 'Length', 'Score', 'Expect', 'QueryStart',
'QueryEnd', 'SubjectStart', 'SubjectEnd'
])
# Body
for row in self.parse():
self.writer.write_row(row)
def filterByExpect(self, outfile, threshold=1.0):
csv_file = open(outfile, 'w')
self.writer = CSVWriter(csv_file)
# Header
self.writer.write_row([
'Query', 'Name', 'Length', 'Score', 'Expect', 'QueryStart',
'QueryEnd', 'SubjectStart', 'SubjectEnd'
])
# Body
for row in self.parse():
if row[self.EXPECT_COLUMN] <= threshold:
self.writer.write_row(row)
def write(self, outfile):
csv_file = open(outfile, 'w')
self.writer = CSVWriter(csv_file)
# Header
self.writer.write_row([
'Query',
'Name', 'Length', 'Score', 'Expect',
'QueryStart', 'QueryEnd',
'SubjectStart', 'SubjectEnd'
])
# Body
for row in self.parse():
self.writer.write_row(row)
def filterByExpect(self, outfile, threshold=1.0):
csv_file = open(outfile, 'w')
self.writer = CSVWriter(csv_file)
# Header
self.writer.write_row([
'Query',
'Name', 'Length', 'Score', 'Expect',
'QueryStart', 'QueryEnd',
'SubjectStart', 'SubjectEnd'
])
# Body
for row in self.parse():
if row[self.EXPECT_COLUMN] <= threshold:
self.writer.write_row(row)
class PhageDBReader:
EXPECT_COLUMN = 4 # zero-based
def __init__(self, infile, **kwargs):
blast_file = open(infile, 'r')
self.reader = blast_file.read()
def write(self, outfile):
csv_file = open(outfile, 'w')
self.writer = CSVWriter(csv_file)
# Header
self.writer.write_row([
'Query', 'Name', 'Length', 'Score', 'Expect', 'QueryStart',
'QueryEnd', 'SubjectStart', 'SubjectEnd'
])
# Body
for row in self.parse():
self.writer.write_row(row)
def filterByExpect(self, outfile, threshold=1.0):
csv_file = open(outfile, 'w')
self.writer = CSVWriter(csv_file)
# Header
self.writer.write_row([
'Query', 'Name', 'Length', 'Score', 'Expect', 'QueryStart',
'QueryEnd', 'SubjectStart', 'SubjectEnd'
])
# Body
for row in self.parse():
if row[self.EXPECT_COLUMN] <= threshold:
self.writer.write_row(row)
def queries(self):
# split file up into queries
queries = re.split(r'Query= ', self.reader)
# queries[0] will be the header and not needed
queries.pop(0)
for query in queries:
yield query
def sequences(self):
for query in self.queries():
queryNumber = float(query.splitlines()[0])
# split query into matches
matches = re.split(r'>', query)
matches.pop(0)
for match in matches:
yield (queryNumber, match)
def parse(self):
for (queryNumber, sequence) in self.sequences():
pattern = re.compile(
r"(?P<Sequence>\w+)[^~]*(Length=)(?P<Length>\d*.\d*)(\s*)(Score = )(?P<Score>\d*.\d*)[^~]*(Expect = )(?P<Expect>\d*.\d*-*\d*)[^~]*(Query\s*)(?P<QStart>\d*)\s*[ACGT-]*\s*(?P<QEnd>\d*)[^~]*(Sbjct\s*)(?P<SubStart>\d*)\s*[ACGT-]*\s*(?P<SubEnd>\d*)[^~]*",
re.MULTILINE)
iterator = pattern.finditer(sequence)
for data in iterator:
yield [
float(queryNumber),
data.group('Sequence'),
int(data.group('Length')),
float(data.group('Score')),
float(data.group('Expect')),
int(data.group('QStart')),
int(data.group('QEnd')),
int(data.group('SubStart')),
int(data.group('SubEnd'))
]
class PhageDBReader:
EXPECT_COLUMN = 4 # zero-based
def __init__(self, infile, **kwargs):
blast_file = open(infile, 'r')
self.reader = blast_file.read()
def write(self, outfile):
csv_file = open(outfile, 'w')
self.writer = CSVWriter(csv_file)
# Header
self.writer.write_row([
'Query',
'Name', 'Length', 'Score', 'Expect',
'QueryStart', 'QueryEnd',
'SubjectStart', 'SubjectEnd'
])
# Body
for row in self.parse():
self.writer.write_row(row)
def filterByExpect(self, outfile, threshold=1.0):
csv_file = open(outfile, 'w')
self.writer = CSVWriter(csv_file)
# Header
self.writer.write_row([
'Query',
'Name', 'Length', 'Score', 'Expect',
'QueryStart', 'QueryEnd',
'SubjectStart', 'SubjectEnd'
])
# Body
for row in self.parse():
if row[self.EXPECT_COLUMN] <= threshold:
self.writer.write_row(row)
def queries(self):
# split file up into queries
queries = re.split(r'Query= ', self.reader)
# queries[0] will be the header and not needed
queries.pop(0)
for query in queries:
yield query
def sequences(self):
for query in self.queries():
queryNumber = float(query.splitlines()[0])
# split query into matches
matches = re.split(r'>', query)
matches.pop(0)
for match in matches:
yield (queryNumber, match)
def parse(self):
for (queryNumber, sequence) in self.sequences():
pattern = re.compile(
r"(?P<Sequence>\w+)[^~]*(Length = )(?P<Length>\d*.\d*)(\s*)(Score = )(?P<Score>\d*.\d*)[^~]*(Expect = )(?P<Expect>\d*.\d*)[^~]*(Query: )(?P<QStart>\d*)[ acgt]*(?P<QEnd>\d*)[^~]*(Sbjct: )(?P<SubStart>\d*)[ acgt]*(?P<SubEnd>\d*)[^~]*",
re.MULTILINE)
iterator = pattern.finditer(sequence)
for data in iterator:
yield [
float(queryNumber),
data.group('Sequence'),
int(data.group('Length')),
float(data.group('Score')),
float(data.group('Expect')),
int(data.group('QStart')),
int(data.group('QEnd')),
int(data.group('SubStart')),
int(data.group('SubEnd'))
]
