def test_get_template_alignment_column_mask(self):
# make sure the literal Lane mask matches the real file's MD5 (without
# the trailing newline)
exp = 'e3e5f2804e29694e03a01fd9cc157a53'
obs = safe_md5(
StringIO(get_template_alignment_column_mask())).hexdigest()
self.assertEqual(obs, exp)
def test_get_template_alignment_column_mask(self):
# make sure the literal Lane mask matches the real file's MD5 (without
# the trailing newline)
exp = 'e3e5f2804e29694e03a01fd9cc157a53'
obs = safe_md5(BytesIO(
get_template_alignment_column_mask())).hexdigest()
self.assertEqual(obs, exp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# build the output filepath and open it any problems can be caught
# before starting the work
try:
mkdir(opts.output_dir)
except OSError:
pass
input_dir, input_filename = split(opts.input_fasta_file)
input_basename, ext = splitext(input_filename)
if getsize(opts.input_fasta_file) == 0:
raise ValueError("An empty fasta file was provided. "
"Did the alignment complete sucessfully? "
"Did PyNAST discard all sequences due to too-stringent minimum length "
"or minimum percent ID settings?")
output_fp = '%s/%s_pfiltered.fasta' % (opts.output_dir, input_basename)
try:
outfile = open(output_fp, 'w')
except IOError:
raise IOError("Can't open output_filepath for writing: %s"
% output_filepath)
if not opts.suppress_lane_mask_filter and not opts.entropy_threshold:
if opts.lane_mask_fp is not None:
lane_mask = open(opts.lane_mask_fp, 'U').read().strip()
else:
lane_mask = get_template_alignment_column_mask()
else:
lane_mask = None
# open the input and output files
infile = open(opts.input_fasta_file, 'U')
if opts.remove_outliers:
# apply the lanemask/gap removal, then remove outliers
seq_gen = apply_lane_mask_and_gap_filter(infile, lane_mask,
opts.allowed_gap_frac,
entropy_threshold=opts.entropy_threshold)
filtered_aln = remove_outliers(seq_gen, opts.threshold)
for seq in filtered_aln:
outfile.write(seq.to_fasta())
outfile.write('\n')
else:
# just apply the lanemask/gap removal
for result in apply_lane_mask_and_gap_filter(infile, lane_mask,
opts.allowed_gap_frac,
entropy_threshold=opts.entropy_threshold):
outfile.write(result)
infile.close()
outfile.close()
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# build the output filepath and open it any problems can be caught
# before starting the work
try:
mkdir(opts.output_dir)
except OSError:
pass
input_dir, input_filename = split(opts.input_fasta_file)
input_basename, ext = splitext(input_filename)
if getsize(opts.input_fasta_file) == 0:
raise ValueError("An empty fasta file was provided. "
"Did the alignment complete sucessfully? "
"Did PyNAST discard all sequences due to too-stringent minimum length "
"or minimum percent ID settings?")
output_fp = '%s/%s_pfiltered.fasta' % (opts.output_dir, input_basename)
try:
outfile = open(output_fp, 'w')
except IOError:
raise IOError("Can't open output_filepath for writing: %s"
% output_filepath)
if not opts.suppress_lane_mask_filter and not opts.entropy_threshold:
if opts.lane_mask_fp is not None:
lane_mask = open(opts.lane_mask_fp, 'U').read().strip()
else:
lane_mask = get_template_alignment_column_mask()
else:
lane_mask = None
# open the input and output files
infile = open(opts.input_fasta_file, 'U')
if opts.remove_outliers:
# apply the lanemask/gap removal, then remove outliers
seq_gen = apply_lane_mask_and_gap_filter(infile, lane_mask,
opts.allowed_gap_frac, verbose=opts.verbose,
entropy_threshold=opts.entropy_threshold)
filtered_aln = remove_outliers(seq_gen, opts.threshold)
for seq in filtered_aln.Seqs:
outfile.write(seq.toFasta())
outfile.write('\n')
else:
# just apply the lanemask/gap removal
for result in apply_lane_mask_and_gap_filter(infile, lane_mask,
opts.allowed_gap_frac, verbose=opts.verbose,
entropy_threshold=opts.entropy_threshold):
outfile.write(result)
infile.close()
outfile.close()
