def compare_mapping(oufilnam1, oufilnam2):
from formats import Cigar, openFile
infil1 = openFile(oufilnam1, 'r')
infil2 = openFile(oufilnam2, 'r')
cig1 = Cigar()
cig2 = Cigar()
ctr1 = 0
ctr2 = 0
while 1:
if cig1.next(infil1):
break
ctr1 = ctr1 + 1
if cig2.next(infil2):
break
ctr2 = ctr2 + 1
if cmp(cig1.qnam, cig2.qnam):
exit("readnames don't match: '%s' vs '%s'" % \
(cig1.qnam, cig2.qnam))
if cmp(cig1,cig2) and cig1.mapq > 5 and cig2.mapq > 5:
exit("mappings don't match for read '%s'" % \
cig1.qnam)
infil2.close()
infil1.close()
if ctr1 != ctr1:
exit("Expected the same number of mates, got %i (A) and %i (B)" % \
ctr1, ctr2)
if ctr1 != 20000:
exit("Expected 20,000 reads, got %i." % ctr1)
def cmpCigarFiles(cigfilA, cigfilB, is_verbose=True):
from formats import Cigar, openFile, getNextCigarPair
cigA1 = Cigar()
cigA2 = Cigar()
cigB1 = Cigar()
cigB2 = Cigar()
filA = openFile(cigfilA, 'r')
filB = openFile(cigfilB, 'r')
ctr = 0
while 1:
(isOK, isEOF) = getNextCigarPair(filA, cigA1, cigA2)
if not isOK:
break
(isOK, isEOF) = getNextCigarPair(filB, cigB1, cigB2)
if not isOK:
break
if cigA1 != cigB1:
if is_verbose:
print "Not matching:\n%s\n%s" % (cigA1.lin, cigB1.lin)
if cigA1.mapq > MAPQ_THRESH and cigB1.mapq > MAPQ_THRESH:
exit("Discrepancy:\n%s\n%s" % (cigA1.lin, cigB1.lin))
if cigA2 != cigB2:
if is_verbose:
print "Not matching:\n%s\n%s" % (cigA2.lin, cigB2.lin)
if cigA2.mapq > MAPQ_THRESH and cigB2.mapq > MAPQ_THRESH:
exit("Discrepancy:\n%s\n%s" % (cigA2.lin, cigB2.lin))
ctr = ctr + 1
if not isOK and isEOF:
isOK = True
return isOK, ctr
def cmpCigarFiles(cigfilA, cigfilB, is_verbose=True):
from formats import Cigar, openFile, getNextCigarPair
cigA1 = Cigar()
cigA2 = Cigar()
cigB1 = Cigar()
cigB2 = Cigar()
filA = openFile(cigfilA, 'r')
filB = openFile(cigfilB, 'r')
ctr = 0
while 1:
(isOK, isEOF) = getNextCigarPair(filA, cigA1, cigA2)
if not isOK:
break
(isOK, isEOF) = getNextCigarPair(filB, cigB1, cigB2)
if not isOK:
break
if cigA1 != cigB1:
if is_verbose:
print "Not matching:\n%s\n%s" % (cigA1.lin, cigB1.lin)
if cigA1.mapq > MAPQ_THRESH and cigB1.mapq > MAPQ_THRESH:
exit("Discrepancy:\n%s\n%s" % (cigA1.lin, cigB1.lin))
if cigA2 != cigB2:
if is_verbose:
print "Not matching:\n%s\n%s" % (cigA2.lin, cigB2.lin)
if cigA2.mapq > MAPQ_THRESH and cigB2.mapq > MAPQ_THRESH:
exit("Discrepancy:\n%s\n%s" % (cigA2.lin, cigB2.lin))
ctr = ctr + 1
if not isOK and isEOF:
isOK = True
return isOK, ctr
def assess_mapping(oufilnam):
from formats import Cigar, getNextCigarPair, openFile
infil = openFile(oufilnam, 'r')
cigA = Cigar()
cigB = Cigar()
pair_ctr = 0
nonproper_ctr = 0
(isOK, isEOF) = getNextCigarPair(infil, cigA, cigB)
while isOK:
pair_ctr = pair_ctr + 1
if cigA.mapcls != 'A':
nonproper_ctr = nonproper_ctr + 1
if cigB.mapcls != 'A':
nonproper_ctr = nonproper_ctr + 1
(isOK, isEOF) = getNextCigarPair(infil, cigA, cigB)
infil.close()
if pair_ctr != 10000:
exit("Found %i pairs, but expected 10,000." % pair_ctr)
if nonproper_ctr > MAXNUM_NONPROPER_PAIRS:
exit("Found %i non-proper pairs. Expected max. %i" %
(nonproper_ctr, MAXNUM_NONPROPER_PAIRS))
def prep_fasta(filnam):
from testdata import openFile
infil = openFile(filnam, 'w')
for seq in READSEQS:
for i in range(len(seq)):
infil.write("%c" % seq[i])
infil.close()
def prep_fasta(filnam):
from testdata import openFile
infil = openFile(filnam, 'w')
for seq in READSEQS:
for i in range(len(seq)):
infil.write("%c" % seq[i])
infil.close()
def checkLabels(cigfilnam, label_pairs, mateno_check=True):
from formats import Cigar, openFile, getNextCigarPair
cigA = Cigar()
cigB = Cigar()
infil = openFile(cigfilnam)
for lb in label_pairs:
(isOK, isEOF) = getNextCigarPair(infil, cigA, cigB, mateno_check)
if (not isOK) or isEOF:
exit("missing lines in cigar file %s" % cigfilnam)
if (cigA.mapcls != lb[0] and lb[0] != '?') or \
(cigB.mapcls != lb[1] and lb[1] != '?'):
exit("unexpeced cigar mapping labels %s%s (%s) for read pair %s" % \
(cigA.mapcls, cigB.mapcls, lb, cigA.qnam))
return
def checkLabels(cigfilnam, label_pairs, mateno_check=True):
from formats import Cigar, openFile, getNextCigarPair
cigA = Cigar()
cigB = Cigar()
infil = openFile(cigfilnam)
for lb in label_pairs:
(isOK, isEOF) = getNextCigarPair(infil, cigA, cigB, mateno_check)
if (not isOK) or isEOF:
exit("missing lines in cigar file %s" % cigfilnam)
if (cigA.mapcls != lb[0] and lb[0] != '?') or \
(cigB.mapcls != lb[1] and lb[1] != '?'):
exit("unexpeced cigar mapping labels %s%s (%s) for read pair %s" % \
(cigA.mapcls, cigB.mapcls, lb, cigA.qnam))
return
def compare_result(cigfilnam):
from formats import Cigar, openFile
from sys import exit
cig = Cigar()
infil = openFile(cigfilnam)
for result in RESULTS:
cig.next(infil)
if not cig.ok or \
cig.qseg != (result[0], result[1]) or \
cig.sense != result[2] or \
cig.snam != result[3] or \
cig.sseg != (result[4], result[5]) or \
cig.swatscor != result[6]:
exit("Unexpected result for read '%s'" % cig.qnam)
infil.close()
def compare_result(cigfilnam):
from formats import Cigar, openFile
from sys import exit
cig = Cigar()
infil = openFile(cigfilnam)
for result in RESULTS:
cig.next(infil)
if not cig.ok or \
cig.qseg != (result[0], result[1]) or \
cig.sense != result[2] or \
cig.snam != result[3] or \
cig.sseg != (result[4], result[5]) or \
cig.swatscor != result[6]:
exit("Unexpected result for read '%s'" % cig.qnam)
infil.close()