def test_parse_illumina_line(self):
"""parse_illumina_line: functions with several lines """
illumina_line0 = illumina_read1[0]
illumina_line1 = illumina_read1[1]
actual = parse_illumina_line(illumina_line0,
barcode_length=6,
rev_comp_barcode=True)
expected = {\
'Full description':'HWI-6X_9267:1:1:4:1699#ACCACCC/1',\
'Machine Name':'HWI-6X_9267',\
'Channel Number':1,\
'Tile Number':1,\
'X Position':4,\
'Y Position':1699,\
'Barcode':'GGTGGT',\
'Full Y Position Field':'1699#ACCACCC/1',\
'Sequence':\
'TACGGAGGGTGCGAGCGTTAATCGCCCCCCCCCCCCCCCCCCCCCCCCCCCC'+\
'CCCCCCCCCCCCCCCCCCCCCCCGAAAAAAAAAAAAAAAAAAAAAAA',\
'Quality Score':\
'abbbbbbbbbb`_`bbbbbb`bb^aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'+\
'aaaaaaaaaaaaaDaabbBBBBBBBBBBBBBBBBBBB'}
self.assertEqual(actual, expected)
actual = parse_illumina_line(illumina_line0,
barcode_length=6,
rev_comp_barcode=False)
expected['Barcode'] = 'ACCACC'
actual = parse_illumina_line(illumina_line1,
barcode_length=6,
rev_comp_barcode=True)
expected = {\
'Full description':'HWI-6X_9267:1:1:4:390#ACCTCCC/1',\
'Machine Name':'HWI-6X_9267',\
'Channel Number':1,\
'Tile Number':1,\
'X Position':4,\
'Y Position':390,\
'Barcode':'GGAGGT',\
'Full Y Position Field':'390#ACCTCCC/1',\
'Sequence':\
'GACAGGAGGAGCAAGTGTTATTCAAATTATGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGG'+\
'GGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAA',\
'Quality Score':\
'aaaaaaaaaa```aa\^_aa``aVaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'+\
'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaBaaaaa'}
self.assertEqual(actual, expected)
actual = parse_illumina_line(illumina_line1,
barcode_length=6,
rev_comp_barcode=False)
expected['Barcode'] = 'ACCTCC'
def test_parse_illumina_line_barcode_in_header(self):
"""parse_illumina_line: handles barcode in header correctly """
illumina_line0 = illumina_read1[0]
illumina_line1 = illumina_read1[1]
actual = parse_illumina_line(
illumina_line0,barcode_length=6,rev_comp_barcode=True)
expected = {\
'Full description':'HWI-6X_9267:1:1:4:1699#ACCACCC/1',\
'Machine Name':'HWI-6X_9267',\
'Channel Number':1,\
'Tile Number':1,\
'X Position':4,\
'Y Position':1699,\
'Barcode':'GGTGGT',\
'Full Y Position Field':'1699#ACCACCC/1',\
'Sequence':\
'TACGGAGGGTGCGAGCGTTAATCGCCCCCCCCCCCCCCCCCCCCCCCCCCCC'+\
'CCCCCCCCCCCCCCCCCCCCCCCGAAAAAAAAAAAAAAAAAAAAAAA',\
'Quality Score':\
'abbbbbbbbbb`_`bbbbbb`bb^aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'+\
'aaaaaaaaaaaaaDaabbBBBBBBBBBBBBBBBBBBB'}
self.assertEqual(actual,expected)
actual = parse_illumina_line(
illumina_line0,barcode_length=6,rev_comp_barcode=False)
expected['Barcode'] = 'ACCACC'
actual = parse_illumina_line(
illumina_line1,barcode_length=6,rev_comp_barcode=True)
expected = {\
'Full description':'HWI-6X_9267:1:1:4:390#ACCTCCC/1',\
'Machine Name':'HWI-6X_9267',\
'Channel Number':1,\
'Tile Number':1,\
'X Position':4,\
'Y Position':390,\
'Barcode':'GGAGGT',\
'Full Y Position Field':'390#ACCTCCC/1',\
'Sequence':\
'GACAGGAGGAGCAAGTGTTATTCAAATTATGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGG'+\
'GGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAA',\
'Quality Score':\
'aaaaaaaaaa```aa\^_aa``aVaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'+\
'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaBaaaaa'}
self.assertEqual(actual,expected)
actual = parse_illumina_line(
illumina_line1,barcode_length=6,rev_comp_barcode=False)
expected['Barcode'] = 'ACCTCC'
def parse_illumina_paired_end_read_files(read1_file,read2_file,barcode_length,\
max_bad_run_length,quality_threshold,min_per_read_length,rev_comp_barcode,\
barcode_max_N=0,seq_max_N=0):
"""Parses Illumina paired-end read file pair
"""
for read1_line, read2_line in izip(read1_file, read2_file):
read1 = parse_illumina_line(read1_line, barcode_length,
rev_comp_barcode)
read2 = parse_illumina_line(read2_line, barcode_length,
rev_comp_barcode)
read1_desc = illumina_read_description_from_read_data(read1)
read2_desc = illumina_read_description_from_read_data(read2)
read1_barcode = read1['Barcode']
read2_barcode = read2['Barcode']
if (read1_barcode.count('N') > barcode_max_N) or \
(read2_barcode.count('N') > barcode_max_N):
continue
if read1_desc != read2_desc:
raise IlluminaParseError, \
"Error in sequence files, descriptions of"+\
" corresponding lines are not compatible: %s != %s" %\
(read1_desc, read2_desc)
assert read1_barcode == read2_barcode
seq1, qual1 = read_qual_score_filter(\
read1['Sequence'], read1['Quality Score'],\
max_bad_run_length, quality_threshold)
if (len(seq1) < min_per_read_length):
continue
seq2, qual2 = read_qual_score_filter(\
read2['Sequence'], read2['Quality Score'],\
max_bad_run_length, quality_threshold)
if (len(seq2) < min_per_read_length):
continue
seq = seq1 + revComp(seq2)
# If the total number of Ns is more than the max
# allowed ignore this sequence
if seq.count('N') > seq_max_N:
continue
qual = qual1 + qual2[::-1]
yield read1_desc, read1_barcode, seq, qual
def parse_illumina_single_end_read_file(read_file,barcode_length,\
max_bad_run_length,quality_threshold,min_per_read_length,
rev_comp,rev_comp_barcode,barcode_in_seq,barcode_max_N=0,seq_max_N=0):
"""Parses Illumina single-end read file
"""
for read_line in read_file:
read = parse_illumina_line(read_line, barcode_length, rev_comp_barcode,
barcode_in_seq)
read_desc = illumina_read_description_from_read_data(read)
read_barcode = read['Barcode']
if read_barcode.count('N') > barcode_max_N:
continue
seq, qual = read_qual_score_filter(\
read['Sequence'], read['Quality Score'],\
max_bad_run_length, quality_threshold)
if (len(seq) < min_per_read_length) or (seq.count('N') > seq_max_N):
continue
if rev_comp:
seq = revComp(seq)
qual = qual[::-1]
yield read_desc, read_barcode, seq, qual
def parse_illumina_single_end_read_file(read_file,barcode_length,\
max_bad_run_length,quality_threshold,min_per_read_length,
rev_comp,rev_comp_barcode,barcode_in_seq,barcode_max_N=0,seq_max_N=0):
"""Parses Illumina single-end read file
"""
for read_line in read_file:
read = parse_illumina_line(read_line,barcode_length,
rev_comp_barcode,barcode_in_seq)
read_desc = illumina_read_description_from_read_data(read)
read_barcode = read['Barcode']
if read_barcode.count('N') > barcode_max_N:
continue
seq, qual = read_qual_score_filter(\
read['Sequence'], read['Quality Score'],\
max_bad_run_length, quality_threshold)
if (len(seq) < min_per_read_length) or (seq.count('N') > seq_max_N):
continue
if rev_comp:
seq = DNA.rc(seq)
qual = qual[::-1]
yield read_desc, read_barcode, seq, qual
def parse_illumina_paired_end_read_files(read1_file,read2_file,barcode_length,\
max_bad_run_length,quality_threshold,min_per_read_length,rev_comp_barcode,\
barcode_max_N=0,seq_max_N=0):
"""Parses Illumina paired-end read file pair
"""
for read1_line, read2_line in izip(read1_file,read2_file):
read1 = parse_illumina_line(read1_line,barcode_length,rev_comp_barcode)
read2 = parse_illumina_line(read2_line,barcode_length,rev_comp_barcode)
read1_desc = illumina_read_description_from_read_data(read1)
read2_desc = illumina_read_description_from_read_data(read2)
read1_barcode = read1['Barcode']
read2_barcode = read2['Barcode']
if (read1_barcode.count('N') > barcode_max_N) or \
(read2_barcode.count('N') > barcode_max_N):
continue
if read1_desc != read2_desc:
raise IlluminaParseError, \
"Error in sequence files, descriptions of"+\
" corresponding lines are not compatible: %s != %s" %\
(read1_desc, read2_desc)
assert read1_barcode == read2_barcode
seq1, qual1 = read_qual_score_filter(\
read1['Sequence'], read1['Quality Score'],\
max_bad_run_length, quality_threshold)
if (len(seq1) < min_per_read_length):
continue
seq2, qual2 = read_qual_score_filter(\
read2['Sequence'], read2['Quality Score'],\
max_bad_run_length, quality_threshold)
if (len(seq2) < min_per_read_length):
continue
seq = seq1 + DNA.rc(seq2)
# If the total number of Ns is more than the max
# allowed ignore this sequence
if seq.count('N') > seq_max_N:
continue
qual = qual1 + qual2[::-1]
yield read1_desc, read1_barcode, seq, qual
def test_parse_illumina_line_barcode_in_sequence(self):
"""parse_illumina_line: handles barcode in sequence correctly """
illumina_line0 = illumina_read3[0]
actual = parse_illumina_line(
illumina_line0,barcode_length=12,
rev_comp_barcode=False,barcode_in_sequence=True)
expected = {\
'Full description':'HWI-EAS440_0386:1:23:19516:1031#0/1',
'Machine Name':'HWI-EAS440_0386',
'Channel Number':1,
'Tile Number':23,
'X Position':19516,
'Y Position':1031,
'Barcode':'ACAGCTAGCTTG',
'Full Y Position Field':'1031#0/1',
'Sequence':
'TACGNAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATT'
'GTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGT'
'ACAGTAGAGGCAGGCGGAATTCGTGGGG',
'Quality Score':
'fffcGddd\_``_gggggggggggfgggggegggggcgggggggggggeeffafdcdfgbdggdbe]fbf'
'dddddbdadadcddaf`abb`cVNRNUScaa``aOY]]]_[_BBBBBBBBBBB'
'BBBBBBBBBBBBBBBBBBBBBBBBBBBBB'}
self.assertEqual(actual,expected)
