def main():
# parse command line parameters
option_parser, opts, args = parse_command_line_parameters(**script_info)
# Create local copy of options
forward_reads_fp = opts.forward_reads_fp
reverse_reads_fp = opts.reverse_reads_fp
pe_join_method = opts.pe_join_method
output_dir = opts.output_dir
# fastq-join only options:
perc_max_diff = opts.perc_max_diff
# SeqPrep only options:
max_ascii_score = opts.max_ascii_score
min_frac_match = opts.min_frac_match
max_good_mismatch = opts.max_good_mismatch
phred_64 = opts.phred_64
# both fastq-join & SeqPrep options
min_overlap = opts.min_overlap
create_dir(output_dir, fail_on_exist=False)
# send parameters to appropriate join method
# currently only two join methods exist:
# 'fastq-join' and 'SeqPrep'
if pe_join_method == "fastq-join":
join_func = join_method_names["fastq-join"]
paths = join_func(
forward_reads_fp,
reverse_reads_fp,
perc_max_diff=perc_max_diff,
min_overlap=min_overlap,
working_dir=output_dir,
)
if pe_join_method == "SeqPrep":
join_func = join_method_names["SeqPrep"]
paths = join_func(
forward_reads_fp,
reverse_reads_fp,
max_overlap_ascii_q_score=max_ascii_score,
min_overlap=min_overlap,
max_mismatch_good_frac=max_good_mismatch,
min_frac_matching=min_frac_match,
phred_64=phred_64,
working_dir=output_dir,
)
# If index / barcode file is supplied, filter unused barcode reads
# and write them to a new file. Name based on joined-pairs / assembled
# outfile
if opts.index_reads_fp:
index_reads = opts.index_reads_fp
assembly_fp = paths["Assembled"] # grab joined-pairs output path
write_synced_barcodes_fastq(assembly_fp, index_reads)
def main():
# parse command line parameters
option_parser, opts, args = parse_command_line_parameters(**script_info)
# Create local copy of options
forward_reads_fp = opts.forward_reads_fp
reverse_reads_fp = opts.reverse_reads_fp
pe_join_method = opts.pe_join_method
output_dir = opts.output_dir
# fastq-join only options:
perc_max_diff = opts.perc_max_diff
# SeqPrep only options:
max_ascii_score = opts.max_ascii_score
min_frac_match = opts.min_frac_match
max_good_mismatch = opts.max_good_mismatch
phred_64 = opts.phred_64
# both fastq-join & SeqPrep options
min_overlap = opts.min_overlap
create_dir(output_dir, fail_on_exist=False)
# send parameters to appropriate join method
# currently only two join methods exist:
# 'fastq-join' and 'SeqPrep'
if pe_join_method == "fastq-join":
join_func = join_method_names["fastq-join"]
paths = join_func(forward_reads_fp,
reverse_reads_fp,
perc_max_diff=perc_max_diff,
min_overlap=min_overlap,
working_dir=output_dir)
if pe_join_method == "SeqPrep":
join_func = join_method_names["SeqPrep"]
paths = join_func(forward_reads_fp,
reverse_reads_fp,
max_overlap_ascii_q_score=max_ascii_score,
min_overlap=min_overlap,
max_mismatch_good_frac=max_good_mismatch,
min_frac_matching=min_frac_match,
phred_64=phred_64,
working_dir=output_dir)
# If index / barcode file is supplied, filter unused barcode reads
# and write them to a new file. Name based on joined-pairs / assembled
# outfile
if opts.index_reads_fp:
index_reads = opts.index_reads_fp
assembly_fp = paths['Assembled'] # grab joined-pairs output path
write_synced_barcodes_fastq(assembly_fp, index_reads)
def test_write_synced_barcodes_fastq(self):
"""write_synced_barcodes_fastq: should work properly.
This function expects the barcodes.fastq and joined_pairs.fastq
files to be in the same order except for those missing data
that could not be joined. That is, not all paired-ends will
assemble.
"""
filtered_bc_path = write_synced_barcodes_fastq(self.jpe_fp, self.all_bc_fp)
observed_barcodes = open(filtered_bc_path, "U").read()
self.assertEqual(observed_barcodes, synced_barcodes)
os.remove(filtered_bc_path)
def test_write_synced_barcodes_fastq(self):
"""write_synced_barcodes_fastq: should work properly.
This function expects the barcodes.fastq and joined_pairs.fastq
files to be in the same order except for those missing data
that could not be joined. That is, not all paired-ends will
assemble.
"""
filtered_bc_path = write_synced_barcodes_fastq(self.jpe_fp,
self.all_bc_fp)
observed_barcodes = open(filtered_bc_path, 'U').read()
self.assertEqual(observed_barcodes, synced_barcodes)
os.remove(filtered_bc_path)