def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.qual_score_window and not opts.qual_fnames:
option_parser.error('To enable sliding window quality test (-w), '+\
'.qual files must be included.')
mapping_file = opts.map_fname
fasta_files = set(opts.fasta_fnames.split(','))
if opts.qual_fnames:
qual_files = set(opts.qual_fnames.split(','))
else:
qual_files = set()
for q in qual_files:
if not q.endswith('qual'):
stderr.write(
"Qual file does not end with .qual: is it really a qual file?\n%s\n"
% q)
for f in fasta_files:
if not (f.endswith('fasta') or f.endswith('fna')):
stderr.write(
"Fasta file does not end with .fna: is it really a seq file?\n%s\n"
% f)
preprocess(fasta_files, qual_files, mapping_file,
barcode_type=opts.barcode_type,
starting_ix = opts.start_index,
min_seq_len = opts.min_seq_len,
max_seq_len = opts.max_seq_len,
min_qual_score=opts.min_qual_score,
keep_barcode=opts.keep_barcode,
keep_primer=opts.keep_primer,
max_ambig=opts.max_ambig,
max_primer_mm=opts.max_primer_mm,
trim_seq_len=opts.trim_seq_len,
dir_prefix=opts.dir_prefix,
max_bc_errors = opts.max_bc_errors,
max_homopolymer = opts.max_homopolymer,
retain_unassigned_reads = opts.retain_unassigned_reads,
#remove_unassigned = opts.remove_unassigned,
attempt_bc_correction = not opts.disable_bc_correction,
qual_score_window = opts.qual_score_window,
disable_primer_check = opts.disable_primers,
reverse_primers = opts.reverse_primers,
record_qual_scores = opts.record_qual_scores,
discard_bad_windows = opts.discard_bad_windows,
median_length_filtering = opts.median_length_filtering,
added_demultiplex_field = opts.added_demultiplex_field)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.qual_score_window and not opts.qual_fnames:
option_parser.error('To enable sliding window quality test (-w), ' +
'.qual files must be included.')
if opts.record_qual_scores and not opts.qual_fnames:
option_parser.error('To enable recording of truncated quality ' +
'scores, one must supply quality score files.')
min_qual_score = opts.min_qual_score
if min_qual_score is None:
min_qual_score = min_qual_score_default
else:
if not opts.qual_fnames:
option_parser.error('To specify a minimum quality score for '
'reads, one must supply quality score files.')
mapping_file = opts.map_fname
try:
m = open(mapping_file, "U")
except IOError:
raise IOError('Unable to open mapping file %s ' % mapping_file +
'Please check filepath and read permissions.')
fasta_files = set(opts.fasta_fnames)
if opts.qual_fnames:
qual_files = set(opts.qual_fnames)
else:
qual_files = set()
for q in qual_files:
try:
test_qual_file = open(q, "U")
test_qual_file.close()
except IOError:
raise IOError('Unable to open file %s ' % q + ' please check ' +
'filepath and read permissions.')
for f in fasta_files:
try:
test_fasta_file = open(f, "U")
test_fasta_file.close()
except IOError:
raise IOError('Unable to open file %s ' % f + ' please check ' +
'filepath and read permissions.')
preprocess(
fasta_files,
qual_files,
mapping_file,
barcode_type=opts.barcode_type,
starting_ix=opts.start_index,
min_seq_len=opts.min_seq_len,
max_seq_len=opts.max_seq_len,
min_qual_score=min_qual_score,
keep_barcode=opts.keep_barcode,
keep_primer=opts.keep_primer,
max_ambig=opts.max_ambig,
max_primer_mm=opts.max_primer_mm,
trim_seq_len=opts.trim_seq_len,
dir_prefix=opts.dir_prefix,
max_bc_errors=opts.max_bc_errors,
max_homopolymer=opts.max_homopolymer,
retain_unassigned_reads=opts.retain_unassigned_reads,
#remove_unassigned = opts.remove_unassigned,
attempt_bc_correction=not opts.disable_bc_correction,
qual_score_window=opts.qual_score_window,
disable_primer_check=opts.disable_primers,
reverse_primers=opts.reverse_primers,
reverse_primer_mismatches=opts.reverse_primer_mismatches,
record_qual_scores=opts.record_qual_scores,
discard_bad_windows=opts.discard_bad_windows,
median_length_filtering=opts.median_length_filtering,
added_demultiplex_field=opts.added_demultiplex_field,
truncate_ambi_bases=opts.truncate_ambi_bases)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.qual_score_window and not opts.qual_fnames:
option_parser.error('To enable sliding window quality test (-w), '+\
'.qual files must be included.')
if opts.record_qual_scores and not opts.qual_fnames:
option_parser.error('To enable recording of truncated quality '+\
'scores, one must supply quality score files.')
mapping_file = opts.map_fname
try:
m = open(mapping_file, "U")
except IOError:
raise IOError,('Unable to open mapping file %s ' % mapping_file +\
'Please check filepath and read permissions.')
fasta_files = set(opts.fasta_fnames)
if opts.qual_fnames:
qual_files = set(opts.qual_fnames)
else:
qual_files = set()
for q in qual_files:
try:
test_qual_file = open(q, "U")
test_qual_file.close()
except IOError:
raise IOError,('Unable to open file %s ' % q +' please check '+\
'filepath and read permissions.')
if not q.endswith('qual'):
stderr.write(
"Qual file does not end with .qual: is it really a qual file?\n%s\n"
% q)
for f in fasta_files:
try:
test_fasta_file = open(f, "U")
test_fasta_file.close()
except IOError:
raise IOError,('Unable to open file %s ' % f +' please check '+\
'filepath and read permissions.')
if not (f.endswith('fasta') or f.endswith('fna')):
stderr.write(
"Fasta file does not end with .fna: is it really a seq file?\n%s\n"
% f)
preprocess(fasta_files, qual_files, mapping_file,
barcode_type=opts.barcode_type,
starting_ix = opts.start_index,
min_seq_len = opts.min_seq_len,
max_seq_len = opts.max_seq_len,
min_qual_score=opts.min_qual_score,
keep_barcode=opts.keep_barcode,
keep_primer=opts.keep_primer,
max_ambig=opts.max_ambig,
max_primer_mm=opts.max_primer_mm,
trim_seq_len=opts.trim_seq_len,
dir_prefix=opts.dir_prefix,
max_bc_errors = opts.max_bc_errors,
max_homopolymer = opts.max_homopolymer,
retain_unassigned_reads = opts.retain_unassigned_reads,
#remove_unassigned = opts.remove_unassigned,
attempt_bc_correction = not opts.disable_bc_correction,
qual_score_window = opts.qual_score_window,
disable_primer_check = opts.disable_primers,
reverse_primers = opts.reverse_primers,
reverse_primer_mismatches = opts.reverse_primer_mismatches,
record_qual_scores = opts.record_qual_scores,
discard_bad_windows = opts.discard_bad_windows,
median_length_filtering = opts.median_length_filtering,
added_demultiplex_field = opts.added_demultiplex_field,
truncate_ambi_bases = opts.truncate_ambi_bases)
