def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
exclude_otus_fp = opts.exclude_otus_fp
if not opts.taxonomy_fname:
otu_to_taxonomy = None
else:
infile = open(opts.taxonomy_fname, 'U')
otu_to_taxonomy = parse_taxonomy(infile)
ids_to_exclude = []
if exclude_otus_fp:
if splitext(exclude_otus_fp)[1] in ('.fasta', '.fna'):
ids_to_exclude = \
get_seq_ids_from_fasta_file(open(exclude_otus_fp, 'U'))
else:
ids_to_exclude = \
get_seq_ids_from_seq_id_file(open(exclude_otus_fp, 'U'))
sample_metadata = None
if opts.mapping_fp is not None:
with open(opts.mapping_fp, 'U') as map_f:
mapping_data, mapping_header, mapping_comments = \
parse_mapping_file(map_f)
sample_metadata = mapping_file_to_dict(mapping_data, mapping_header)
with open(opts.otu_map_fp, 'U') as otu_map_f:
biom_otu_table = make_otu_table(otu_map_f,
otu_to_taxonomy=otu_to_taxonomy,
otu_ids_to_exclude=ids_to_exclude,
sample_metadata=sample_metadata)
write_biom_table(biom_otu_table, opts.output_biom_fp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
exclude_otus_fp = opts.exclude_otus_fp
outfile = open(opts.output_biom_fp, 'w')
if not opts.taxonomy_fname:
otu_to_taxonomy = None
else:
infile = open(opts.taxonomy_fname,'U')
otu_to_taxonomy = parse_taxonomy(infile)
ids_to_exclude = []
if exclude_otus_fp:
if splitext(exclude_otus_fp)[1] in ('.fasta','.fna'):
ids_to_exclude = \
get_seq_ids_from_fasta_file(open(exclude_otus_fp,'U'))
else:
ids_to_exclude = \
get_seq_ids_from_seq_id_file(open(exclude_otus_fp,'U'))
biom_otu_table = make_otu_table(open(opts.otu_map_fp, 'U'),
otu_to_taxonomy,
ids_to_exclude)
outfile.write(biom_otu_table)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
exclude_otus_fp = opts.exclude_otus_fp
if not opts.taxonomy_fname:
otu_to_taxonomy = None
else:
infile = open(opts.taxonomy_fname, 'U')
otu_to_taxonomy = parse_taxonomy(infile)
ids_to_exclude = []
if exclude_otus_fp:
if splitext(exclude_otus_fp)[1] in ('.fasta', '.fna'):
ids_to_exclude = \
get_seq_ids_from_fasta_file(open(exclude_otus_fp, 'U'))
else:
ids_to_exclude = \
get_seq_ids_from_seq_id_file(open(exclude_otus_fp, 'U'))
sample_metadata = None
if opts.mapping_fp is not None:
mapping_data, mapping_header, mapping_comments = parse_mapping_file(open(opts.mapping_fp, 'U'))
sample_metadata = assemble_sample_metadata(mapping_data, mapping_header, mapping_comments)
biom_otu_table = make_otu_table(open(opts.otu_map_fp, 'U'),
otu_to_taxonomy=otu_to_taxonomy,
otu_ids_to_exclude=ids_to_exclude,
sample_metadata=sample_metadata)
write_biom_table(biom_otu_table, opts.output_biom_fp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
exclude_otus_fp = opts.exclude_otus_fp
if not opts.taxonomy_fname:
otu_to_taxonomy = None
else:
infile = open(opts.taxonomy_fname, 'U')
otu_to_taxonomy = parse_taxonomy(infile)
if not opts.counts_fname:
seq_counts = None
else:
seq_counts = {}
with open(opts.counts_fname, 'U') as infile:
for line in infile:
(key, val) = line.split()
seq_counts[key] = val
ids_to_exclude = []
if exclude_otus_fp:
if splitext(exclude_otus_fp)[1] in ('.fasta', '.fna'):
ids_to_exclude = \
get_seq_ids_from_fasta_file(open(exclude_otus_fp, 'U'))
else:
ids_to_exclude = \
get_seq_ids_from_seq_id_file(open(exclude_otus_fp, 'U'))
sample_metadata = None
if opts.mapping_fp is not None:
with open(opts.mapping_fp, 'U') as map_f:
mapping_data, mapping_header, mapping_comments = \
parse_mapping_file(map_f)
sample_metadata = mapping_file_to_dict(mapping_data,
mapping_header)
with open(opts.otu_map_fp, 'U') as otu_map_f:
biom_otu_table = make_otu_table(otu_map_f,
otu_to_taxonomy=otu_to_taxonomy,
otu_ids_to_exclude=ids_to_exclude,
sample_metadata=sample_metadata,seq_counts=seq_counts)
write_biom_table(biom_otu_table, opts.output_biom_fp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
exclude_otus_fp = opts.exclude_otus_fp
outfile = open(opts.output_biom_fp, 'w')
if not opts.taxonomy_fname:
otu_to_taxonomy = None
else:
infile = open(opts.taxonomy_fname, 'U')
otu_to_taxonomy = parse_taxonomy(infile)
ids_to_exclude = []
if exclude_otus_fp:
if splitext(exclude_otus_fp)[1] in ('.fasta', '.fna'):
ids_to_exclude = \
get_seq_ids_from_fasta_file(open(exclude_otus_fp, 'U'))
else:
ids_to_exclude = \
get_seq_ids_from_seq_id_file(open(exclude_otus_fp, 'U'))
biom_otu_table = make_otu_table(open(opts.otu_map_fp, 'U'),
otu_to_taxonomy, ids_to_exclude)
outfile.write(biom_otu_table)
