def get_sam_ids(map_data, map_header, colorby, cat, primary_state,
secondary_state):
""" returns all sample ids matching the state strings and colorby:cat
colorby: eg: 'Country', or pass None to not filter only colorby:cat samples
cat: e.g.: 'USA'
primary_state: e.g.: 'AgeCategory:Child'
secondary state can be None, or like primary state
returns uniquified lists in randomized order
"""
if colorby is None:
sample_ids = [sam[0] for sam in map_data]
else:
sample_ids = get_sample_ids(map_data, map_header, {colorby: [cat]})
# primary key is the category label, e.g. AgeCategory
# value is the val for that category, e.g. Adult
# go through age1/age2
primary_states = parse_metadata_state_descriptions(primary_state)
if colorby is not None:
primary_states[colorby] = [cat]
state1_samids = get_sample_ids(map_data, map_header, primary_states)
if secondary_state is None:
state2_samids = set(sample_ids).difference(set(state1_samids))
else:
secondary_states =\
parse_metadata_state_descriptions(secondary_state)
if colorby is not None:
secondary_states[colorby] = [cat]
state2_samids = get_sample_ids(map_data, map_header, secondary_states)
return list(set(state1_samids)), list(set(state2_samids))
def get_sam_ids(map_data, map_header, colorby, cat, primary_state, secondary_state):
""" returns all sample ids matching the state strings and colorby:cat
colorby: eg: 'Country', or pass None to not filter only colorby:cat samples
cat: e.g.: 'USA'
primary_state: e.g.: 'AgeCategory:Child'
secondary state can be None, or like primary state
returns uniquified lists in randomized order
"""
if colorby == None:
sample_ids = [sam[0] for sam in map_data]
else:
sample_ids = get_sample_ids(map_data, map_header, {colorby: [cat]})
# primary key is the category label, e.g. AgeCategory
# value is the val for that category, e.g. Adult
# go through age1/age2
primary_states = parse_metadata_state_descriptions(primary_state)
if colorby != None:
primary_states[colorby] = [cat]
state1_samids = get_sample_ids(map_data, map_header, primary_states)
if secondary_state == None:
state2_samids = set(sample_ids).difference(set(state1_samids))
else:
secondary_states = parse_metadata_state_descriptions(secondary_state)
if colorby != None:
secondary_states[colorby] = [cat]
state2_samids = get_sample_ids(map_data, map_header, secondary_states)
return list(set(state1_samids)), list(set(state2_samids))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
negate = opts.negate
sample_ids = opts.sample_ids
mapping_fp = opts.mapping_fp
input_fasta_fp = opts.input_fasta_fp
output_fasta_fp = opts.output_fasta_fp
if not mapping_fp:
sample_ids = sample_ids.split(',')
else:
map_data, map_header, map_comments = parse_mapping_file(mapping_fp)
sample_ids = get_sample_ids(
map_data,
map_header,
parse_metadata_state_descriptions(sample_ids))
if len(sample_ids) == 0:
raise ValueError(
"No samples match the search criteria: %s" %
valid_states)
if opts.verbose:
# This is useful when using the --valid_states feature so you can
# find out if a search query didn't work as you expected before a
# lot of time is spent
print "Extracting samples: %s" % ', '.join(sample_ids)
try:
seqs = parse_fasta(open(input_fasta_fp))
except IOError:
option_parser.error(
'Cannot open %s. Does it exist? Do you have read access?' %
input_fasta_fp)
exit(1)
try:
output_fasta_f = open(output_fasta_fp, 'w')
except IOError:
option_parser.error(
"Cannot open %s. Does path exist? Do you have write access?" %
output_fasta_fp)
exit(1)
for r in extract_seqs_by_sample_id(seqs, sample_ids, negate):
output_fasta_f.write('>%s\n%s\n' % r)
output_fasta_f.close()
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
negate = opts.negate
sample_ids = opts.sample_ids
mapping_fp = opts.mapping_fp
input_fasta_fp = opts.input_fasta_fp
output_fasta_fp = opts.output_fasta_fp
if not mapping_fp:
sample_ids = sample_ids.split(',')
else:
map_data, map_header, map_comments = parse_mapping_file(mapping_fp)
sample_ids = get_sample_ids(
map_data,
map_header,
parse_metadata_state_descriptions(sample_ids))
if len(sample_ids) == 0:
raise ValueError(
"No samples match the search criteria: %s" %
valid_states)
if opts.verbose:
# This is useful when using the --valid_states feature so you can
# find out if a search query didn't work as you expected before a
# lot of time is spent
print "Extracting samples: %s" % ', '.join(sample_ids)
try:
seqs = parse_fasta(open(input_fasta_fp))
except IOError:
option_parser.error(
'Cannot open %s. Does it exist? Do you have read access?' %
input_fasta_fp)
exit(1)
try:
output_fasta_f = open(output_fasta_fp, 'w')
except IOError:
option_parser.error(
"Cannot open %s. Does path exist? Do you have write access?" %
output_fasta_fp)
exit(1)
for r in extract_seqs_by_sample_id(seqs, sample_ids, negate):
output_fasta_f.write('>%s\n%s\n' % r)
output_fasta_f.close()
