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Updated to reflect changes in Engine 0.10.*

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This commit is contained in:
Harrison Deng 2025-02-12 21:54:34 +00:00
parent 4eca35a556
commit 32dcfd99f8
4 changed files with 7 additions and 16 deletions
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2
pyproject.toml
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@ -8,7 +8,7 @@ dynamic = ["version"]
readme = "README.md" readme = "README.md"
license = {file = "LICENSE"} license = {file = "LICENSE"}
dependencies = [ dependencies = [
"autoBIGS-engine" "autoBIGS-engine==0.10.*"
] ]
requires-python = ">=3.12" requires-python = ">=3.12"
description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases." description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."

2
requirements.txt
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@ -4,4 +4,4 @@ pytest-cov
build build
twine twine
setuptools_scm setuptools_scm
autoBIGS.engine autoBIGS.engine==0.10.*

2
src/autobigs/cli/info.py
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@ -1,6 +1,6 @@
from argparse import ArgumentParser, Namespace from argparse import ArgumentParser, Namespace
import asyncio import asyncio
from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex from autobigs.engine.analysis.bigsdb import BIGSdbIndex
def setup_parser(parser: ArgumentParser): def setup_parser(parser: ArgumentParser):
parser.description = "Fetches the latest BIGSdb MLST database definitions." parser.description = "Fetches the latest BIGSdb MLST database definitions."

17
src/autobigs/cli/st.py
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@ -2,9 +2,9 @@
from argparse import ArgumentParser, Namespace from argparse import ArgumentParser, Namespace
import asyncio import asyncio
import datetime import datetime
from autobigs.engine.data.local.csv import write_mlst_profiles_as_csv from autobigs.engine.writing import write_mlst_profiles_as_csv
from autobigs.engine.data.local.fasta import read_multiple_fastas from autobigs.engine.reading import read_multiple_fastas
from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex from autobigs.engine.analysis.bigsdb import BIGSdbIndex
def setup_parser(parser: ArgumentParser): def setup_parser(parser: ArgumentParser):
@ -35,15 +35,6 @@ def setup_parser(parser: ArgumentParser):
help="The output CSV name (.csv will be appended)." help="The output CSV name (.csv will be appended)."
) )
parser.add_argument(
"--exact", "-ex",
action="store_true",
dest="exact",
required=False,
default=False,
help="Should run exact matching rather than returning all similar ones"
)
parser.add_argument( parser.add_argument(
"--stop-on-fail", "-sof", "--stop-on-fail", "-sof",
action="store_true", action="store_true",
@ -58,7 +49,7 @@ def setup_parser(parser: ArgumentParser):
async def run(args: Namespace): async def run(args: Namespace):
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(False, args.seqdefdb, args.schema) as mlst_profiler:
mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings, exact=args.exact) 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: