def test_combine_mappings(self):
"""combine_mappings works as expected"""
self.tmp_dir = mkdtemp(dir="./", suffix="/")
combine_mappings(
fasta,
denoiser_mapping,
denoised_seqs,
otu_picker_map,
self.tmp_dir)
observed_otu_map = "".join(
list(open(self.tmp_dir + "/denoised_otu_map.txt")))
expected_otu_map = """1:\tS1_1\tS1_2\tS2_4\tS2_5
2:\tS2_3\tS1_6
"""
self.assertEqual(observed_otu_map, expected_otu_map)
observed_fasta = "".join(
list(open(self.tmp_dir + "/denoised_all.fasta")))
expected_fasta = """>S1_1 Read1
AAA
>S1_2 Read2
TTT
>S2_3 Read3
GGG
"""
self.assertEqual(observed_fasta, expected_fasta)
def test_combine_mappings(self):
"""combine_mappings works as expected"""
self.tmp_dir = mkdtemp(dir="./", suffix="/")
combine_mappings(fasta, denoiser_mapping, denoised_seqs,
otu_picker_map, self.tmp_dir)
observed_otu_map = "".join(
list(open(self.tmp_dir + "/denoised_otu_map.txt")))
expected_otu_map = """1:\tS1_1\tS1_2\tS2_4\tS2_5
2:\tS2_3\tS1_6
"""
self.assertEqual(observed_otu_map, expected_otu_map)
observed_fasta = "".join(
list(open(self.tmp_dir + "/denoised_all.fasta")))
expected_fasta = """>S1_1 Read1
AAA
>S1_2 Read2
TTT
>S2_3 Read3
GGG
"""
self.assertEqual(observed_fasta, expected_fasta)
def main(commandline_args=None):
option_parser, opts, args = parse_command_line_parameters(**script_info)
#check for missing files
required_files = [opts.denoiser_map_file, opts.otu_picker_map_file,
opts.fasta_fp, opts.denoised_fasta_fp]
if (not all(required_files) or not all(map(exists, required_files))):
option_parser.error('Missing input files.')
create_dir(opts.output_dir, fail_on_exist=False)
combine_mappings(open(opts.fasta_fp), open(opts.denoiser_map_file),
open(opts.denoised_fasta_fp),
open(opts.otu_picker_map_file), opts.output_dir)