def test_illumina_data_to_fastq(self):
"""illumina_data_to_fastq functions as expected """
in1 = ("M10","68","1","1","28680","29475","0","1","AACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACG.","BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB","0")
expected = """@M10_68:1:1:28680:29475#0/1\nAACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACGN\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB"""
self.assertEqual(illumina_data_to_fastq(in1),expected)
expected12 = """@M10_68:1:1:28680:29475#0/1\nAACGAAAGGCAG\n+\nBBBBBBBBBBBB"""
self.assertEqual(illumina_data_to_fastq(in1,number_of_bases=12),expected12)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
input_fps = opts.input_fps
output_dir = opts.output_dir
create_dir(output_dir)
barcode_length = opts.barcode_length
barcode_in_header = opts.barcode_in_header
barcode_qual_c = opts.barcode_qual_c
for input_fp in input_fps:
if input_fp.endswith('.gz'):
open_f = gzip_open
input_basename = split(splitext(splitext(input_fp)[0])[0])[1]
else:
input_basename = split(splitext(input_fp)[0])[1]
open_f = open
sequence_output_fp = '%s/%s.fastq' % (output_dir,input_basename)
sequence_output_f = open(sequence_output_fp,'w')
barcode_output_fp = '%s/%s_barcodes.fastq' % (output_dir,input_basename)
barcode_output_f = open(barcode_output_fp,'w')
for line in open_f(input_fp):
common_fields, sequence, sequence_qual, barcode, barcode_qual =\
iseq_to_qseq_fields(line, barcode_in_header, barcode_length, barcode_qual_c)
sequence_s, pass_filter_s = illumina_data_to_fastq((common_fields[0],
common_fields[1],
common_fields[2],
common_fields[3],
common_fields[4],
common_fields[5],
common_fields[6],
common_fields[7],
sequence,
sequence_qual))
barcode_s, pass_filter_b = illumina_data_to_fastq((common_fields[0],
common_fields[1],
common_fields[2],
common_fields[3],
common_fields[4],
common_fields[5],
common_fields[6],
common_fields[7],
barcode,
barcode_qual),barcode_length)
if pass_filter_s != 0:
sequence_output_f.write('%s\n' % sequence_s)
barcode_output_f.write('%s\n' % barcode_s)
sequence_output_f.close()
barcode_output_f.close()
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
input_fps = opts.input_fps
output_dir = opts.output_dir
create_dir(output_dir)
barcode_length = opts.barcode_length
barcode_in_header = opts.barcode_in_header
barcode_qual_c = opts.barcode_qual_c
for input_fp in input_fps:
if input_fp.endswith('.gz'):
open_f = gzip_open
input_basename = split(splitext(splitext(input_fp)[0])[0])[1]
else:
input_basename = split(splitext(input_fp)[0])[1]
open_f = open
sequence_output_fp = '%s/%s.fastq' % (output_dir,input_basename)
sequence_output_f = open(sequence_output_fp,'w')
barcode_output_fp = '%s/%s_barcodes.fastq' % (output_dir,input_basename)
barcode_output_f = open(barcode_output_fp,'w')
for line in open_f(input_fp):
common_fields, sequence, sequence_qual, barcode, barcode_qual =\
iseq_to_qseq_fields(line, barcode_in_header, barcode_length, barcode_qual_c)
sequence_s, pass_filter_s = illumina_data_to_fastq((common_fields[0],
common_fields[1],
common_fields[2],
common_fields[3],
common_fields[4],
common_fields[5],
common_fields[6],
common_fields[7],
sequence,
sequence_qual))
barcode_s, pass_filter_b = illumina_data_to_fastq((common_fields[0],
common_fields[1],
common_fields[2],
common_fields[3],
common_fields[4],
common_fields[5],
common_fields[6],
common_fields[7],
barcode,
barcode_qual),barcode_length)
if pass_filter_s != 0:
sequence_output_f.write('%s\n' % sequence_s)
barcode_output_f.write('%s\n' % barcode_s)
sequence_output_f.close()
barcode_output_f.close()
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
input_dir = opts.input_dir
output_dir = opts.output_dir
create_dir(output_dir)
lanes = opts.lanes.split(',')
bases = opts.bases
read = opts.read
for lane in lanes:
read1_fps = glob('%s/s_%s_%d_*qseq.txt' % (input_dir,
lane.replace(',',''),
read))
# sort so results will be consistent across different runs (important
# so amplicon and barcodes read headers will match)
read1_fps.sort()
for read1_fp in read1_fps:
output_fp = '%s/s_%s_%s_sequences.fastq' % (output_dir,lane,read)
output_f = open(output_fp,'w')
for record in iter_split_lines(open(read1_fp,'U')):
fastq_s = illumina_data_to_fastq(record,
number_of_bases=bases)
output_f.write('%s\n' % fastq_s)
output_f.close()
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
input_dir = opts.input_dir
output_dir = opts.output_dir
create_dir(output_dir)
lanes = opts.lanes.split(',')
bases = opts.bases
read = opts.read
ignore_pass_filter = opts.ignore_pass_filter
for lane in lanes:
read1_fps = sorted(
glob('%s/s_%s_%d_*qseq.txt' %
(input_dir, lane.replace(',', ''), read)))
# sort so results will be consistent across different runs (important
# so amplicon and barcodes read headers will match)
output_fp = '%s/s_%s_%s_sequences.fastq' % (output_dir, lane, read)
output_f = open(output_fp, 'w')
for read1_fp in read1_fps:
for record in iter_split_lines(open(read1_fp, 'U')):
fastq_s, pass_filter = illumina_data_to_fastq(
record, number_of_bases=bases)
if ignore_pass_filter or pass_filter != 0:
output_f.write('%s\n' % fastq_s)
output_f.close()
def test_illumina_data_to_fastq_no_pass_filter_field(self):
"""illumina_data_to_fastq functions as expected with no pass filter field"""
in1 = (
"M10", "68", "1", "1", "28680", "29475", "0", "1",
"AACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACG.",
"BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB"
)
expected = """@M10_68:1:1:28680:29475#0/1\nAACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACGN\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB""", 2
self.assertEqual(illumina_data_to_fastq(in1), expected)
def test_illumina_data_to_fastq(self):
"""illumina_data_to_fastq functions as expected """
in1 = (
"M10",
"68",
"1",
"1",
"28680",
"29475",
"0",
"1",
"AACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACG.",
"BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB",
"0")
expected = """@M10_68:1:1:28680:29475#0/1\nAACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACGN\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB""", 0
self.assertEqual(illumina_data_to_fastq(in1), expected)
expected12 = """@M10_68:1:1:28680:29475#0/1\nAACGAAAGGCAG\n+\nBBBBBBBBBBBB""", 0
self.assertEqual(
illumina_data_to_fastq(
in1,
number_of_bases=12),
expected12)
# different value in the pass filter field
in2 = (
"M10",
"68",
"1",
"1",
"28680",
"29475",
"0",
"1",
"AACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACG.",
"BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB",
"1")
expected = """@M10_68:1:1:28680:29475#0/1\nAACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACGN\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB""", 1
self.assertEqual(illumina_data_to_fastq(in2), expected)
def test_illumina_data_to_fastq_no_pass_filter_field(self):
"""illumina_data_to_fastq functions as expected with no pass filter field"""
in1 = (
"M10",
"68",
"1",
"1",
"28680",
"29475",
"0",
"1",
"AACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACG.",
"BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB")
expected = """@M10_68:1:1:28680:29475#0/1\nAACGAAAGGCAGTTTTGGAAGTAGGCGAATTAGGGTAACGCATATAGGATGCTAATACAACGTGAATGAAGTACTGCATCTATGTCACCAGCTTATTACAGCAGCTTGTCATACATGGCCGTACAGGAAACACACATCATAGCATCACACGN\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB""", 2
self.assertEqual(illumina_data_to_fastq(in1), expected)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_dir = opts.input_dir
output_dir = opts.output_dir
create_dir(output_dir)
lanes = opts.lanes.split(",")
bases = opts.bases
read = opts.read
ignore_pass_filter = opts.ignore_pass_filter
for lane in lanes:
read1_fps = sorted(glob("%s/s_%s_%d_*qseq.txt" % (input_dir, lane.replace(",", ""), read)))
# sort so results will be consistent across different runs (important
# so amplicon and barcodes read headers will match)
output_fp = "%s/s_%s_%s_sequences.fastq" % (output_dir, lane, read)
output_f = open(output_fp, "w")
for read1_fp in read1_fps:
for record in iter_split_lines(open(read1_fp, "U")):
fastq_s, pass_filter = illumina_data_to_fastq(record, number_of_bases=bases)
if ignore_pass_filter or pass_filter != 0:
output_f.write("%s\n" % fastq_s)
output_f.close()
