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| author | Arun Isaac | 2023-01-18 16:58:07 +0000 |
|---|---|---|
| committer | Arun Isaac | 2023-01-18 16:58:07 +0000 |
| commit | 411526a3d6fb3f52e9f2aca0eb394fefc6f53ead (patch) | |
| tree | da12c70e9e613690f94568bdfd099ccd5d322841 | |
| parent | 4cc328ef78c7b8108d7623fdd4fcae5294317f2e (diff) | |
| download | genenetwork3-411526a3d6fb3f52e9f2aca0eb394fefc6f53ead.tar.gz | |
Pass species and species prefix as a single query argument.
* gn3/api/search.py (parse_location_field): Accept a single species query
argument instead of separate species and species prefix arguments.
(parse_query): Pass parse_location_field a single species query argument.
| -rw-r--r-- | gn3/api/search.py | 15 |
1 files changed, 6 insertions, 9 deletions
diff --git a/gn3/api/search.py b/gn3/api/search.py index 3cdee67..7f7a4ff 100644 --- a/gn3/api/search.py +++ b/gn3/api/search.py @@ -153,7 +153,7 @@ def apply_si_suffix(location: str) -> int: return int(float(location[:-1])*10**suffixes.get(location[-1].lower(), 0)) -def parse_location_field(lifted_species: str, species_prefix: str, # pylint: disable=[too-many-arguments] +def parse_location_field(species_query: xapian.Query, chromosome_prefix: str, location_slot: int, liftover_function: IntervalLiftoverFunction, query: bytes) -> xapian.Query: @@ -171,11 +171,11 @@ def parse_location_field(lifted_species: str, species_prefix: str, # pylint: dis *[location.map(apply_si_suffix) for location in parse_range(location)]) - def make_query(species: str, interval: ChromosomalInterval) -> xapian.Query: + def make_query(interval: ChromosomalInterval) -> xapian.Query: # TODO: Convert the xapian index to use bases instead of megabases. to_megabases = lambda x: str(float(x)/1e6) return combine_queries(xapian.Query.OP_AND, - xapian.Query(species_prefix + species), + species_query, xapian.Query(chromosome_prefix + interval.chromosome), xapian.NumberRangeProcessor(location_slot) (interval.start.maybe("", to_megabases), @@ -186,8 +186,7 @@ def parse_location_field(lifted_species: str, species_prefix: str, # pylint: dis except ValueError: return xapian.Query(xapian.Query.OP_INVALID) return (liftover_function(interval) - .maybe(xapian.Query.MatchNothing, - partial(make_query, lifted_species))) + .maybe(xapian.Query.MatchNothing, make_query)) def parse_synteny_field(synteny_prefix: str, query: bytes) -> xapian.Query: @@ -265,8 +264,7 @@ def parse_query(synteny_files_directory: Path, query: str): "Mm": "mouse"} for shorthand, species in species_shorthands.items(): field_processors = [partial(parse_location_field, - species, - species_prefix, + xapian.Query(species_prefix + species), chromosome_prefix, range_prefixes.index("mb"), Just)] @@ -280,8 +278,7 @@ def parse_query(synteny_files_directory: Path, query: str): for lifted_species, chain_file in chain_files.items(): field_processors.append( partial(parse_location_field, - lifted_species, - species_prefix, + xapian.Query(species_prefix + lifted_species), chromosome_prefix, range_prefixes.index("mb"), partial(liftover_interval, |