def test_extractCigarSeq_ref_and_N(self):
"""Test a cigar sequence that has the reference allele on forward and N"""
sequence = ".N"
phred = "EI"
mapq = "[\\"
info = dict([('chr', "2"), ('pos', "3423"), ('ref', "T"), ('NB', "4")])
lettersCount = extractCigarSeq(sequence, phred, mapq, info)
self.assertTrue(len(lettersCount) == 6)
self.assertTrue(lettersCount['A'] == [])
self.assertTrue(lettersCount['C'] == [])
self.assertTrue(lettersCount['G'] == [])
self.assertTrue(lettersCount['T'] == [(36, 58)])
self.assertTrue(lettersCount['N'] == [(40, 59)])
self.assertTrue(lettersCount['O'] == [])
def test_extractCigarSeq_one_insertion(self):
"""Test a cigar sequence that has the reference allele and one insertion"""
sequence = ".+2AC,"
phred = "EI"
mapq = "[\\"
info = dict([('chr', "2"), ('pos', "3423"), ('ref', "T"), ('NB', "4")])
lettersCount = extractCigarSeq(sequence, phred, mapq, info)
self.assertTrue(len(lettersCount) == 6)
self.assertTrue(lettersCount['A'] == [])
self.assertTrue(lettersCount['C'] == [])
self.assertTrue(lettersCount['G'] == [])
self.assertTrue(lettersCount['T'] == [(36, 58), (40, 59)])
self.assertTrue(lettersCount['N'] == [])
self.assertTrue(lettersCount['O'] == [(-1, -1)])
def test_extractCigarSeq_ref_and_two_alternative_alleles(self):
"""Test a cigar sequence that has the reference allele on forward and reverse strand and two alternative alleles"""
sequence = ".AG.,"
phred = "!F!DG"
mapq = "]hacb"
info = dict([('chr', "2"), ('pos', "3423"), ('ref', "T"), ('NB', "4")])
lettersCount = extractCigarSeq(sequence, phred, mapq, info)
self.assertTrue(len(lettersCount) == 6)
self.assertTrue(lettersCount['A'] == [(37, 71)])
self.assertTrue(lettersCount['C'] == [])
self.assertTrue(lettersCount['G'] == [(0, 64)])
self.assertTrue(lettersCount['T'] == [(0, 60), (35, 66), (38, 65)])
self.assertTrue(lettersCount['N'] == [])
self.assertTrue(lettersCount['O'] == [])
def test_extractCigarSeq_only_ref_allele(self):
"""Test a cigar sequence that has only the reference allele on forward and reverse strand"""
sequence = ".,,."
phred = "DF!D"
mapq = "]]ac"
info = dict([('chr', "2"), ('pos', "323"), ('ref', "A"), ('NB', "4")])
lettersCount = extractCigarSeq(sequence, phred, mapq, info)
self.assertTrue(len(lettersCount) == 6)
self.assertTrue(lettersCount['A'] == [(35, 60), (37, 60), (0, 64), (35, 66)])
self.assertTrue(lettersCount['C'] == [])
self.assertTrue(lettersCount['G'] == [])
self.assertTrue(lettersCount['T'] == [])
self.assertTrue(lettersCount['N'] == [])
self.assertTrue(lettersCount['O'] == [])
def test_extractCigarSeq_start_of_read(self):
"""Test a cigar sequence that has reference and alternative alleles, indels, end and start of reads"""
sequence = "+3CTT-1T$.^D-4ATAT$a"
phred = "UB"
mapq = "!["
info = dict([('chr', "2"), ('pos', "3423"), ('ref', "C"), ('NB', "4")])
lettersCount = extractCigarSeq(sequence, phred, mapq, info)
self.assertTrue(len(lettersCount) == 6)
self.assertTrue(lettersCount['A'] == [(33, 58)])
self.assertTrue(lettersCount['C'] == [(52, 0)])
self.assertTrue(lettersCount['G'] == [])
self.assertTrue(lettersCount['T'] == [])
self.assertTrue(lettersCount['N'] == [])
self.assertTrue(lettersCount['O'] == [(-1, -1), (-1, -1), (-1, -1)])
def test_extractCigarSeq_end_of_read(self):
"""Test a cigar sequence that has the reference allele and two deletions"""
sequence = "+2CT-1T$.-2AT$,"
phred = "UT"
mapq = "!!"
info = dict([('chr', "2"), ('pos', "3423"), ('ref', "G"), ('NB', "4")])
lettersCount = extractCigarSeq(sequence, phred, mapq, info)
self.assertTrue(len(lettersCount) == 6)
self.assertTrue(lettersCount['A'] == [])
self.assertTrue(lettersCount['C'] == [])
self.assertTrue(lettersCount['G'] == [(52, 0), (51, 0)])
self.assertTrue(lettersCount['T'] == [])
self.assertTrue(lettersCount['N'] == [])
self.assertTrue(lettersCount['O'] == [(-1, -1), (-1, -1), (-1, -1)])
def test_extractCigarSeq_two_deletions(self):
"""Test a cigar sequence that has the reference allele and two deletions"""
sequence = ".-1T,-2AT"
phred = "QI"
mapq = "!E"
info = dict([('chr', "2"), ('pos', "3423"), ('ref', "G"), ('NB', "4")])
lettersCount = extractCigarSeq(sequence, phred, mapq, info)
self.assertTrue(len(lettersCount) == 6)
self.assertTrue(lettersCount['A'] == [])
self.assertTrue(lettersCount['C'] == [])
self.assertTrue(lettersCount['G'] == [(48, 0), (40, 36)])
self.assertTrue(lettersCount['T'] == [])
self.assertTrue(lettersCount['N'] == [])
self.assertTrue(lettersCount['O'] == [(-1, -1), (-1, -1)])
