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#################################################################################
# Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#################################################################################
# Author: David Alexander
from pbcore.io.base import ReaderBase
__all__ = [ "M4Record",
"M4Reader",
"M5Record",
"M5Reader" ]
class MalformattedRecord(Exception): pass
class M4Record(object):
"""
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:
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(object):
"""
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:
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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