def main():
parser = argparse.ArgumentParser(
description="Fetch Condel scores")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
parser.add_argument("muts_path", metavar="SNVS_PATH",
help="SNV's to check. Use - for standard input.")
parser.add_argument("out_path", metavar="OUTPUT_PATH",
help="The results path. Use - for standard output.")
cmd.add_selected_predictors_args()
cmd.add_selected_annotations_args()
cmd.add_selected_columns_args()
args, logger = cmd.parse_args("fetch")
db = cmd.open_db()
predictors = cmd.get_selected_predictors()
annotations = cmd.get_selected_annotations()
columns = cmd.get_selected_columns()
logger.info("Reading {} ...".format(args.muts_path if args.muts_path != "-" else "from standard input"))
try:
progress = RatedProgress(logger, name="SNVs")
with tsv.open(args.muts_path) as f:
with tsv.open(args.out_path, "w") as wf:
tsv.write_line(wf, "ID", *[c.upper() for c in columns] + [a.upper() for a in annotations] + predictors)
hit = fail = 0
mut = DnaAndProtMutationParser()
for line_num, line in enumerate(f, start=1):
line = line.rstrip(" \n\r")
if len(line) == 0 or line.startswith("#"):
continue
try:
mut.parse(line)
except PrematureEnd:
logger.error("Missing fields at line {}".format(line_num))
fail += 1
continue
except UnexpectedToken as ex:
logger.error("Unexpected field '{}' at line {}".format(ex.args[0], line_num))
fail += 1
continue
exists = False
for row in query_mutation(logger, db, mut, annotations, predictors):
exists = True
ann = row["annotations"]
scores = row["scores"]
tsv.write_line(wf, mut.identifier,
*[row[c] for c in columns]
+ [ann[a] for a in annotations]
+ [scores[p] for p in predictors])
"""
if logger.isEnabledFor(logging.DEBUG):
logger.debug(" --> {} {} {} {} {} {} {} {} {} {}".format(
row["chr"], row["start"], row["ref"], row["alt"], row["transcript"],
row["protein"], row["aa_pos"], row["aa_ref"], row["aa_alt"],
mut.identifier or "*"))
"""
progress.update()
if exists:
hit += 1
else:
fail += 1
progress.log_totals()
logger.info("Finished. total={}, hits={}, fails={}, elapsed={}".format(hit + fail, hit, fail, progress.elapsed_time))
except:
return cmd.handle_error()
finally:
db.close()
def fetch_iter(db, muts_path, maps=None, predictors=None, muts_header=False, state=None, logger=None):
"""
Iterator that fetches scores from the database from the mutations in a file.
:param db: FannsDb interface.
:param muts_path: The input path for mutations.
:param maps: Map transcript/protein ensembl identifiers with external identifiers (swissprot_id, ...)
:param predictors: Predictors for which to obtain the scores.
:param muts_header: Whether the muts_path has a header or not.
:param state: The state of the iteration: hits, fails.
:param logger: Logger to use. If not specified a new one is created.
"""
def query_mutation(logger, db, mut, maps, predictors):
if mut.coord == Mutation.GENOMIC:
if logger.isEnabledFor(logging.DEBUG):
logger.debug(" Querying {} {} {} {} {} {} {} ...".format(
mut.chr, mut.start, mut.end or "*", mut.ref or "*", mut.alt, mut.strand or "*", mut.identifier or "*"))
for row in db.query_scores(chr=mut.chr, start=mut.start,
ref=mut.ref, alt=mut.alt, strand=mut.strand,
predictors=predictors, maps=maps):
yield row
elif mut.coord == Mutation.PROTEIN:
if logger.isEnabledFor(logging.DEBUG):
logger.debug(" Querying {} {} {} {} {} ...".format(
mut.protein, mut.start, mut.ref or "*", mut.alt, mut.identifier or "*"))
for row in db.query_scores(protein=mut.protein, aa_pos=mut.start, aa_ref=mut.ref, aa_alt=mut.alt,
predictors=predictors, maps=maps):
yield row
else:
logger.warn("Unknown coordinates system: {}".format(mut.line))
if logger is None:
logger = logging.getLogger("fannsdb.fetch")
state = state if state is not None else {}
state[STATE_HITS] = state[STATE_FAILS] = 0
maps = maps if maps is not None else []
predictors = predictors if predictors is not None else []
logger.info("Reading {} ...".format(os.path.basename(muts_path) if muts_path != "-" else "from standard input"))
progress = RatedProgress(logger, name="SNVs")
with tsv.open(muts_path) as f:
if muts_header:
tsv.skip_comments_and_empty(f) # this returns the first non empty nor comment line (the header)
mutparser = DnaAndProtMutationParser()
for line_num, line in enumerate(f, start=1):
line = line.rstrip(" \n\r")
if len(line) == 0 or line.startswith("#"):
continue
try:
mut = mutparser.parse(line)
except PrematureEnd:
logger.error("Missing fields at line {}".format(line_num))
state[STATE_FAILS] += 1
continue
except UnexpectedToken as ex:
logger.error("Unexpected field '{}' at line {}".format(ex.args[0], line_num))
state[STATE_FAILS] += 1
continue
state.update({
STATE_LINE_NUM : line_num,
STATE_LINE : line,
STATE_MUTATION : mut})
exists = False
for row in query_mutation(logger, db, mut, maps, predictors):
exists = True
yield row
progress.update()
if exists:
state[STATE_HITS] += 1
else:
state[STATE_FAILS] += 1
progress.log_totals()
hits, fails = [state[k] for k in [STATE_HITS, STATE_FAILS]]
logger.info("Finished. total={}, hits={}, fails={}, elapsed={}".format(hits + fails, hits, fails, progress.elapsed_time))