def __call__(self, seq_path=None, result_path=None, log_path=None):
"""Returns a dict mapping {seq_id:(taxonomy, confidence)} for each seq
Keep in mind, "confidence" is only done for consistency and in fact
all assignments will have a score of 0 because a method for determining
confidence is not currently implemented.
Parameters:
seq_path: path to file of sequences. The sequences themselves are
never actually used, but they are needed for their ids.
result_path: path to file of results. If specified, dumps the
result to the desired path instead of returning it.
log_path: path to log, which should include dump of params.
"""
# initialize the logger
logger = self._get_logger(log_path)
logger.info(str(self))
with open(seq_path, 'U') as f:
seqs = dict(MinimalFastaParser(f))
consensus_map = tax2tree.prep_consensus(
open(self.Params['id_to_taxonomy_fp']),
seqs.keys())
seed_con = consensus_map[0].strip().split('\t')[1]
determine_rank_order(seed_con)
tipnames_map = load_consensus_map(consensus_map, False)
tree = load_tree(open(self.Params['tree_fp']), tipnames_map)
results = tax2tree.generate_constrings(tree, tipnames_map)
results = tax2tree.clean_output(results, seqs.keys())
if result_path:
# if the user provided a result_path, write the
# results to file
with open(result_path, 'w') as f:
for seq_id, (lineage, confidence) in results.iteritems():
f.write('%s\t%s\t%s\n' % (seq_id, lineage, confidence))
logger.info('Result path: %s' % result_path)
return results
def __call__(self, seq_path=None, result_path=None, log_path=None):
"""Returns a dict mapping {seq_id:(taxonomy, confidence)} for each seq
Keep in mind, "confidence" is only done for consistency and in fact
all assignments will have a score of 0 because a method for determining
confidence is not currently implemented.
Parameters:
seq_path: path to file of sequences. The sequences themselves are
never actually used, but they are needed for their ids.
result_path: path to file of results. If specified, dumps the
result to the desired path instead of returning it.
log_path: path to log, which should include dump of params.
"""
# initialize the logger
logger = self._get_logger(log_path)
logger.info(str(self))
with open(seq_path, 'U') as f:
seqs = dict(parse_fasta(f))
consensus_map = tax2tree.prep_consensus(
open(self.Params['id_to_taxonomy_fp']),
seqs.keys())
seed_con = consensus_map[0].strip().split('\t')[1]
determine_rank_order(seed_con)
tipnames_map = load_consensus_map(consensus_map, False)
tree = load_tree(open(self.Params['tree_fp']), tipnames_map)
results = tax2tree.generate_constrings(tree, tipnames_map)
results = tax2tree.clean_output(results, seqs.keys())
if result_path:
# if the user provided a result_path, write the
# results to file
with open(result_path, 'w') as f:
for seq_id, (lineage, confidence) in results.iteritems():
f.write('%s\t%s\t%s\n' % (seq_id, lineage, confidence))
logger.info('Result path: %s' % result_path)
return results