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# parsing output formats
#############################################################################
#############################################################################
# #
# Copyright (C) 2013 - 2014 Genome Research Ltd. #
# #
# Author: Hannes Ponstingl (hp3@sanger.ac.uk) #
# #
# This file is part of SMALT. #
# #
# SMALT is free software: you can redistribute it and/or modify it under #
# the terms of the GNU General Public License as published by the Free #
# Software Foundation, either version 3 of the License, or (at your #
# option) any later version. #
# #
# This program is distributed in the hope that it will be useful, but #
# WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU #
# General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License along #
# with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
#############################################################################
#############################################################################
class Cigar:
from re import compile
DEBUG = False
CIGARSTR = compile("^cigar:([ABCDNRSP]):(\d{2})\s+(\S+)\s+(\d+)\s+(\d+)\s+([*+-])\s+" \
"(\S+)\s+(\d+)\s+(\d+)\s+\+\s+(\d+)\s+(.+)$")
def __init__(self):
self._blank()
def next(self, infil):
okflg = False
isEOF = False
while not okflg:
lin = infil.readline()
if not lin:
isEOF = True
break
self.parse(lin)
okflg = self.ok
if Cigar.DEBUG:
print "DEBUG:Cigar.next %s" % (okflg)
if Cigar.DEBUG:
print "DEBUG:Cigar.next returns %s" % (isEOF)
return isEOF
def parse(self, lin):
m = Cigar.CIGARSTR.match(lin)
if m:
self.lin = lin.strip()
self.mapcls = m.group(1) # class label (A,B,C,D,N,R,S)
self.mapq = int(m.group(2)) # mapping quality score
self.qnam = m.group(3) # name of query (read)
self.qseg = (int(m.group(4)), int(m.group(5)))
self.sense = m.group(6)
self.snam = m.group(7) # name of subject (reference)
self.sseg = (int(m.group(8)), int(m.group(9)))
self.swatscor = int(m.group(10))
self.cigar = m.group(11)
self.cigar.strip()
self.ok = True
if Cigar.DEBUG:
print "DEBUG:Cigar.parse('%s')::'%s'" % (self.lin, self.cigar)
else:
lin.strip()
if lin[0] != '#':
print "not parsed: %s" % (lin)
self._blank()
def getMateNo(self):
mateno = 0
if self.qnam[-2:] == "/1":
mateno = 1
elif self.qnam[-2:] == "/2":
mateno = 2
return mateno
def _blank(self):
self.mapcls = ""
self.mapq = 0
self.qnam = ""
self.qseg = (0,0)
self.sense = ''
self.snam = ""
self.sseg = (0,0)
self.swatscor = 0
self.lin = ""
self.ok = False
def __cmp__(self, other):
rv = cmp(self.snam, other.snam)
if rv: return rv
rv = cmp(self.sseg[0], other.sseg[0])
if rv: return rv
return cmp(other.sseg[1], self.sseg[1])
def getNextCigarPair(infil, cigA, cigB, mateno_check = True):
isOk = False
isEOF = cigA.next(infil)
if not isEOF:
if cigB.next(infil):
exit("ERROR EOF when reading 2nd mate ...")
if not cigA.ok:
exit("ERROR when parsing 1st mate")
if not cigB.ok:
exit("ERROR: when parsing 2nd mate")
isOk = True
if not isEOF and mateno_check:
if cigA.qnam[-2] != cigB.qnam[-2]:
print "ERROR: read names don't match %s, %s" % (cigA.qnam, cigB.qnam)
isOk = False
elif cigA.getMateNo() != 1 or cigB.getMateNo() != 2:
print "ERROR in mate number %s [1] and %s [2]" % (cigA.qnam, cigB.qnam)
isOk = False
return (isOk, isEOF)
def openFile(filnam, mode = 'r'):
import gzip
is_compressed = len(filnam) > 3 and filnam[-3:] == ".gz"
try:
if is_compressed:
fil = gzip.open(filnam, mode)
else:
fil = open(filnam, mode)
except:
exit("ERROR when opening file '%s'" % filnam)
return fil
if __name__ == "__main__":
from sys import argv, exit
if len(argv) < 2:
exit("usage: %s <cigar file>" % argv[0])
cig = Cigar()
infil = openFile(argv[1])
while not cig.next(infil):
print cig.qnam
infil.close()
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