def test_handle_error_codes(self):
"""handle_error_codes raises the right error."""
self.assertRaises(OSError, handle_error_codes, "test", False,1)
self.assertEqual(handle_error_codes("test", True, 1), 1)
self.assertEqual(handle_error_codes("test", False, 0), 0)
self.assertEqual(handle_error_codes("test"), 0)
def test_handle_error_codes(self):
"""handle_error_codes raises the right error."""
self.assertRaises(OSError, handle_error_codes, "test", False, 1)
self.assertEqual(handle_error_codes("test", True, 1), 1)
self.assertEqual(handle_error_codes("test", False, 0), 0)
self.assertEqual(handle_error_codes("test"), 0)
def main():
"""run denoiser on input flowgrams"""
option_parser, opts, args = parse_command_line_parameters(**script_info)
sff_files = opts.sff_fps
for f in sff_files:
if (not exists(f)):
option_parser.error(('Flowgram file path does not exist:\n %s \n'+\
'Pass a valid one via -i.')% f)
outdir = opts.output_dir
ret_val = create_dir(outdir, handle_errors_externally=True)
if ret_val == 1: #dir exists
if opts.force:
#do nothing, just overwrite content
pass
else:
# Since the analysis can take quite a while, I put this check
# in to help users avoid overwriting previous output.
option_parser.error("Output directory already exists. Please choose"+\
" a different directory, or force overwrite with -f.")
else:
handle_error_codes(outdir, error_code=ret_val)
log_fh = None
if (not (opts.primer or opts.map_fname)):
raise ApplicationError, "Either mapping file or primer required"
#Read primer from Meta data file if not set on command line
if not opts.primer:
mapping_data, header, comments = \
parse_mapping_file(open(opts.map_fname,"U"))
index = header.index("LinkerPrimerSequence")
all_primers = set(array(mapping_data)[:, index])
if len(all_primers) != 1:
raise ValueError,"Currently only data sets with one primer are allowed.\n"+\
"Make separate mapping files with only one primer, re-run split_libraries and\n"\
+"denoise with each split_library output separately."
primer = list(all_primers)[0]
last_char = primer[-1]
if (last_char not in "ACGT"):
raise ValueError,"We currently do not support primer with "+\
"degenerate bases at it's 3' end."
else:
primer = opts.primer
centroids, cluster_mapping = fast_denoiser(opts.sff_fps,
opts.fasta_fp,
outdir,
opts.num_cpus,
primer,
titanium=opts.titanium)
# store mapping file and centroids
result_otu_path = '%s/denoised_clusters.txt' % outdir
of = open(result_otu_path, 'w')
for i, cluster in cluster_mapping.iteritems():
of.write('%s\t%s\n' % (str(i), '\t'.join(cluster)))
of.close()
result_fasta_path = '%s/denoised_seqs.fasta' % outdir
oh = open(result_fasta_path, 'w')
write_Fasta_from_name_seq_pairs(centroids, oh)
def main():
"""run denoiser on input flowgrams"""
option_parser, opts, args = parse_command_line_parameters(**script_info)
sff_files = opts.sff_fps
for f in sff_files:
if (not exists(f)):
option_parser.error(('Flowgram file path does not exist:\n %s \n'+\
'Pass a valid one via -i.')% f)
outdir = opts.output_dir
ret_val = create_dir(outdir, handle_errors_externally=True)
if ret_val==1: #dir exists
if opts.force:
#do nothing, just overwrite content
pass
else:
# Since the analysis can take quite a while, I put this check
# in to help users avoid overwriting previous output.
option_parser.error("Output directory already exists. Please choose"+\
" a different directory, or force overwrite with -f.")
else:
handle_error_codes(outdir, error_code=ret_val)
log_fh=None
if (not (opts.primer or opts.map_fname)):
raise ApplicationError, "Either mapping file or primer required"
#Read primer from Meta data file if not set on command line
if not opts.primer:
mapping_data, header, comments = \
parse_mapping_file(open(opts.map_fname,"U"))
index = header.index("LinkerPrimerSequence")
all_primers = set(array(mapping_data)[:,index])
if len(all_primers)!= 1:
raise ValueError,"Currently only data sets with one primer are allowed.\n"+\
"Make separate mapping files with only one primer, re-run split_libraries and\n"\
+"denoise with each split_library output separately."
primer = list(all_primers)[0]
last_char = primer[-1]
if(last_char not in "ACGT"):
raise ValueError,"We currently do not support primer with "+\
"degenerate bases at it's 3' end."
else:
primer=opts.primer
centroids, cluster_mapping = fast_denoiser(opts.sff_fps,opts.fasta_fp,
outdir, opts.num_cpus, primer,
titanium=opts.titanium)
# store mapping file and centroids
result_otu_path = '%s/denoised_clusters.txt' % outdir
of = open(result_otu_path,'w')
for i,cluster in cluster_mapping.iteritems():
of.write('%s\t%s\n' % (str(i),'\t'.join(cluster)))
of.close()
result_fasta_path = '%s/denoised_seqs.fasta' % outdir
oh = open(result_fasta_path,'w')
write_Fasta_from_name_seq_pairs(centroids, oh)