ydeng/autoBIGS.engine
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Added untested partial matching

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This commit is contained in:
Harrison Deng 2025-01-10 16:12:56 +00:00
parent f20a656f45
commit e634647774
2 changed files with 13 additions and 3 deletions
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4
src/automlst/cli/program.py
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@ -4,7 +4,7 @@ import datetime
from os import path from os import path
import os import os
from automlst.cli import info, type from automlst.cli import info, st
from automlst.cli.meta import get_module_base_name from automlst.cli.meta import get_module_base_name
from automlst.engine.data.genomics import NamedString from automlst.engine.data.genomics import NamedString
from automlst.engine.local.abif import read_abif from automlst.engine.local.abif import read_abif
@ -16,7 +16,7 @@ root_parser = argparse.ArgumentParser()
subparsers = root_parser.add_subparsers(required=True) subparsers = root_parser.add_subparsers(required=True)
info.setup_parser(subparsers.add_parser(get_module_base_name(info.__name__))) info.setup_parser(subparsers.add_parser(get_module_base_name(info.__name__)))
type.setup_parser(subparsers.add_parser(get_module_base_name(type.__name__))) st.setup_parser(subparsers.add_parser(get_module_base_name(st.__name__)))
def run(): def run():

12
src/automlst/cli/type.py → src/automlst/cli/st.py
View File

@ -38,17 +38,27 @@ def setup_parser(parser: ArgumentParser):
parser.add_argument( parser.add_argument(
"--exact", "-ex", "--exact", "-ex",
action="store_true", action="store_true",
dest="exact",
required=False, required=False,
default=False, default=False,
help="Should run exact matching rather than returning all similar ones" help="Should run exact matching rather than returning all similar ones"
) )
parser.add_argument(
"--stop-on-fail", "-sof",
action="store_true",
dest="stop_on_fail",
required=False,
default=False,
help="Should the algorithm stop in the case there are no matches (or partial matches when expecting exact matches)."
)
parser.set_defaults(func=run_asynchronously) parser.set_defaults(func=run_asynchronously)
async def run(args): async def run(args):
async with BIGSdbIndex() as bigsdb_index: async with BIGSdbIndex() as bigsdb_index:
gen_strings = read_multiple_fastas(args.fastas) gen_strings = read_multiple_fastas(args.fastas)
async with await bigsdb_index.build_profiler_from_seqdefdb(args.seqdefdb, args.schema) as mlst_profiler: async with await bigsdb_index.build_profiler_from_seqdefdb(args.seqdefdb, args.schema) as mlst_profiler:
mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings) mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings, exact=args.exact)
failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out) failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out)
if len(failed) > 0: if len(failed) > 0:
print(f"A total of {len(failed)} IDs failed:\n{"\n".join(failed)}") print(f"A total of {len(failed)} IDs failed:\n{"\n".join(failed)}")