def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
negate = opts.negate
error_msg = "Must pass exactly one of -a, -b, -s, -p, -m, or --valid_states and --mapping_fp."
if 1 != sum(
map(bool, [
opts.otu_map, opts.seq_id_fp, opts.subject_fasta_fp,
opts.seq_id_prefix, opts.biom_fp, opts.sample_id_fp,
opts.mapping_fp and opts.valid_states
])):
option_parser.error(error_msg)
seqid_f = None
if opts.otu_map:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_otu_map(
open(opts.otu_map, 'U'))
elif opts.seq_id_fp:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_seq_id_file(
open(opts.seq_id_fp, 'U'))
elif opts.subject_fasta_fp:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_fasta_file(
open(opts.subject_fasta_fp, 'U'))
elif opts.seq_id_prefix:
seqs_to_keep_lookup = None
seqid_f = lambda x: x.startswith(opts.seq_id_prefix)
elif opts.mapping_fp and opts.valid_states:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_mapping_file(
open(opts.mapping_fp, 'U'),
opts.valid_states)
seqid_f = lambda x: x.split()[0].rsplit('_')[0] in seqs_to_keep_lookup
elif opts.biom_fp:
seqs_to_keep_lookup = \
get_seqs_to_keep_lookup_from_biom(opts.biom_fp)
elif opts.sample_id_fp:
sample_ids = set(
[e.strip().split()[0] for e in open(opts.sample_id_fp, 'U')])
seqs_to_keep_lookup = \
get_seqs_to_keep_lookup_from_sample_ids(sample_ids)
seqid_f = lambda x: x.split()[0].rsplit('_')[0] in seqs_to_keep_lookup
else:
option_parser.error(error_msg)
if opts.input_fasta_fp.endswith('.fastq'):
filter_fp_f = filter_fastq
else:
filter_fp_f = filter_fasta
input_fasta_f = open(opts.input_fasta_fp, 'U')
output_fasta_f = open(opts.output_fasta_fp, 'w')
filter_fp_f(input_fasta_f,
output_fasta_f,
seqs_to_keep_lookup,
negate,
seqid_f=seqid_f)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
negate = opts.negate
if 1 != sum(map(bool,[opts.otu_map,
opts.seq_id_fp,
opts.subject_fasta_fp,
opts.seq_id_prefix])):
option_parser.error("Must pass exactly one of -a, -s, -p, or -m.")
if opts.otu_map:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_otu_map(
open(opts.otu_map,'U'))
elif opts.seq_id_fp:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_seq_id_file(
open(opts.seq_id_fp,'U'))
elif opts.subject_fasta_fp:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_fasta_file(
open(opts.subject_fasta_fp,'U'))
elif opts.seq_id_prefix:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_prefix(
open(opts.input_fasta_fp),opts.seq_id_prefix)
else:
option_parser.error("Must pass exactly one of -a, -s, or -m.")
filter_fasta_fp(opts.input_fasta_fp,
opts.output_fasta_fp,
seqs_to_keep_lookup,
negate)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
negate = opts.negate
error_msg = "Must pass exactly one of -a, -b, -s, -p, -m, or --valid_states and --mapping_fp."
if 1 != sum(map(bool, [opts.otu_map,
opts.seq_id_fp,
opts.subject_fasta_fp,
opts.seq_id_prefix,
opts.biom_fp,
opts.sample_id_fp,
opts.mapping_fp and opts.valid_states])):
option_parser.error(error_msg)
if opts.otu_map:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_otu_map(
open(opts.otu_map, 'U'))
elif opts.seq_id_fp:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_seq_id_file(
open(opts.seq_id_fp, 'U'))
elif opts.subject_fasta_fp:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_fasta_file(
open(opts.subject_fasta_fp, 'U'))
elif opts.seq_id_prefix:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_prefix(
open(opts.input_fasta_fp), opts.seq_id_prefix)
elif opts.mapping_fp and opts.valid_states:
seqs_to_keep_lookup =\
get_seqs_to_keep_lookup_from_mapping_file(
open(opts.input_fasta_fp, 'U'),
open(opts.mapping_fp, 'U'),
opts.valid_states)
elif opts.biom_fp:
seqs_to_keep_lookup = \
get_seqs_to_keep_lookup_from_biom(opts.biom_fp)
elif opts.sample_id_fp:
sample_ids = set([e.strip().split()[0]
for e in open(opts.sample_id_fp, 'U')])
seqs_to_keep_lookup = get_seqs_to_keep_lookup_from_sample_ids(
open(opts.input_fasta_fp), sample_ids)
else:
option_parser.error(error_msg)
if opts.input_fasta_fp.endswith('.fastq'):
filter_fp_f = filter_fastq
else:
filter_fp_f = filter_fasta
input_fasta_f = open(opts.input_fasta_fp, 'U')
output_fasta_f = open(opts.output_fasta_fp, 'w')
filter_fp_f(input_fasta_f,
output_fasta_f,
seqs_to_keep_lookup,
negate)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
negate = opts.negate
error_msg = "Must pass exactly one of -a, -b, -s, -p, -m, or --valid_states and --mapping_fp."
if 1 != sum(
map(
bool,
[
opts.otu_map,
opts.seq_id_fp,
opts.subject_fasta_fp,
opts.seq_id_prefix,
opts.biom_fp,
opts.sample_id_fp,
opts.mapping_fp and opts.valid_states,
],
)
):
option_parser.error(error_msg)
seqid_f = None
if opts.otu_map:
seqs_to_keep_lookup = get_seqs_to_keep_lookup_from_otu_map(open(opts.otu_map, "U"))
elif opts.seq_id_fp:
seqs_to_keep_lookup = get_seqs_to_keep_lookup_from_seq_id_file(open(opts.seq_id_fp, "U"))
elif opts.subject_fasta_fp:
seqs_to_keep_lookup = get_seqs_to_keep_lookup_from_fasta_file(open(opts.subject_fasta_fp, "U"))
elif opts.seq_id_prefix:
seqs_to_keep_lookup = None
seqid_f = lambda x: x.startswith(opts.seq_id_prefix)
elif opts.mapping_fp and opts.valid_states:
seqs_to_keep_lookup = get_seqs_to_keep_lookup_from_mapping_file(open(opts.mapping_fp, "U"), opts.valid_states)
seqid_f = lambda x: x.split()[0].rsplit("_")[0] in seqs_to_keep_lookup
elif opts.biom_fp:
seqs_to_keep_lookup = get_seqs_to_keep_lookup_from_biom(opts.biom_fp)
elif opts.sample_id_fp:
sample_ids = set([e.strip().split()[0] for e in open(opts.sample_id_fp, "U")])
seqs_to_keep_lookup = get_seqs_to_keep_lookup_from_sample_ids(sample_ids)
seqid_f = lambda x: x.split()[0].rsplit("_")[0] in seqs_to_keep_lookup
else:
option_parser.error(error_msg)
if opts.input_fasta_fp.endswith(".fastq"):
filter_fp_f = filter_fastq
else:
filter_fp_f = filter_fasta
input_fasta_f = open(opts.input_fasta_fp, "U")
output_fasta_f = open(opts.output_fasta_fp, "w")
filter_fp_f(input_fasta_f, output_fasta_f, seqs_to_keep_lookup, negate, seqid_f=seqid_f)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_tree_fp = opts.input_tree_fp
tips_fp = opts.tips_fp
fasta_fp = opts.fasta_fp
output_tree_fp = opts.output_tree_fp
if tips_fp != None:
tips_to_keep = get_seqs_to_keep_lookup_from_seq_id_file(open(tips_fp,'U'))
elif fasta_fp != None:
tips_to_keep = get_seqs_to_keep_lookup_from_fasta_file(open(fasta_fp,'U'))
else:
option_parser.error("Must provide either -t or -f.")
tree = DndParser(open(input_tree_fp,'U'))
if opts.negate:
tips_to_keep = negate_tips_to_keep(tips_to_keep, tree)
filtered_tree = filter_tree(tree,tips_to_keep)
filtered_tree.writeToFile(output_tree_fp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_tree_fp = opts.input_tree_fp
tips_fp = opts.tips_fp
fasta_fp = opts.fasta_fp
output_tree_fp = opts.output_tree_fp
if tips_fp != None:
tips_to_keep = get_seqs_to_keep_lookup_from_seq_id_file(
open(tips_fp, 'U'))
elif fasta_fp != None:
tips_to_keep = get_seqs_to_keep_lookup_from_fasta_file(
open(fasta_fp, 'U'))
else:
option_parser.error("Must provide either -t or -f.")
tree = DndParser(open(input_tree_fp, 'U'))
if opts.negate:
tips_to_keep = negate_tips_to_keep(tips_to_keep, tree)
filtered_tree = filter_tree(tree, tips_to_keep)
filtered_tree.writeToFile(output_tree_fp)
