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# Author: David Alexander
from pbcore.io.base import ReaderBase
__all__ = ["M4Record",
"M4Reader",
"M5Record",
"M5Reader"]
class MalformattedRecord(Exception):
pass
class M4Record:
"""
Record for alignment summary record output from BLASR -m 4 option
"""
@classmethod
def fromString(cls, s):
obj = cls()
try:
columns = s.strip().split()
obj.qName = columns[0]
obj.tName = columns[1]
obj.score = int(columns[2])
obj.percentSimilarity = float(columns[3])
obj.qStrand = int(columns[4])
obj.qStart = int(columns[5])
obj.qEnd = int(columns[6])
obj.qLength = int(columns[7])
obj.tStrand = int(columns[8])
obj.tStart = int(columns[9])
obj.tEnd = int(columns[10])
obj.tLength = int(columns[11])
obj.mapQV = int(columns[12])
return obj
except Exception:
raise MalformattedRecord(s)
class M4Reader(ReaderBase):
"""
Reader for -m 4 formatted alignment summary information from BLASR
"""
def __iter__(self):
for line in self.file:
yield M4Record.fromString(line)
class M5Record:
"""
Record for alignment summary record output from BLASR -m 5 option
"""
@classmethod
def fromString(cls, s):
obj = cls()
try:
columns = s.strip().split()
obj.qName = columns[0]
obj.qLength = int(columns[1])
obj.qStart = int(columns[2])
obj.qEnd = int(columns[3])
obj.qStrand = columns[4]
obj.tName = columns[5]
obj.tLength = int(columns[6])
obj.tStart = int(columns[7])
obj.tEnd = int(columns[8])
obj.tStrand = columns[9]
obj.score = float(columns[10])
obj.numMatch = int(columns[11])
obj.numMismatch = int(columns[12])
obj.numIns = int(columns[13])
obj.numDel = int(columns[14])
obj.mapQV = int(columns[15])
obj.qAlignedSeq = columns[16]
obj.matchPattern = columns[17]
obj.tAlignedSeq = columns[18]
return obj
except Exception:
raise MalformattedRecord(s)
class M5Reader(ReaderBase):
"""
Reader for -m 5 formatted alignment summary information from BLASR
"""
def __iter__(self):
for line in self.file:
yield M5Record.fromString(line)
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