mirror of
https://github.com/biopython/biopython.git
synced 2025-10-20 13:43:47 +08:00
de0bb21fb3
$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
64 lines
2.4 KiB
Python
64 lines
2.4 KiB
Python
# Copyright 2009 by Osvaldo Zagordi. All rights reserved.
|
|
#
|
|
# This file is part of the Biopython distribution and governed by your
|
|
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
|
|
# Please see the LICENSE file that should have been included as part of this
|
|
# package.
|
|
|
|
"""Sequencing related command line application wrappers (OBSOLETE).
|
|
|
|
We have decided to remove this module in future, and instead recommend
|
|
building your command and invoking it via the subprocess module directly.
|
|
"""
|
|
|
|
from ._bwa import BwaAlignCommandline
|
|
from ._bwa import BwaBwaswCommandline
|
|
from ._bwa import BwaIndexCommandline
|
|
from ._bwa import BwaMemCommandline
|
|
from ._bwa import BwaSampeCommandline
|
|
from ._bwa import BwaSamseCommandline
|
|
from ._Novoalign import NovoalignCommandline
|
|
from ._samtools import SamtoolsCalmdCommandline
|
|
from ._samtools import SamtoolsCatCommandline
|
|
from ._samtools import SamtoolsFaidxCommandline
|
|
from ._samtools import SamtoolsFixmateCommandline
|
|
from ._samtools import SamtoolsIdxstatsCommandline
|
|
from ._samtools import SamtoolsIndexCommandline
|
|
from ._samtools import SamtoolsMergeCommandline
|
|
from ._samtools import SamtoolsMpileupCommandline
|
|
from ._samtools import SamtoolsPhaseCommandline
|
|
from ._samtools import SamtoolsReheaderCommandline
|
|
from ._samtools import SamtoolsRmdupCommandline
|
|
from ._samtools import SamtoolsTargetcutCommandline
|
|
from ._samtools import SamtoolsVersion0xSortCommandline
|
|
from ._samtools import SamtoolsVersion0xSortCommandline as SamtoolsSortCommandline
|
|
from ._samtools import SamtoolsVersion1xSortCommandline
|
|
from ._samtools import SamtoolsViewCommandline
|
|
|
|
# Make this explicit, then they show up in the API docs
|
|
__all__ = (
|
|
"BwaIndexCommandline",
|
|
"BwaAlignCommandline",
|
|
"BwaSamseCommandline",
|
|
"BwaSampeCommandline",
|
|
"BwaBwaswCommandline",
|
|
"BwaMemCommandline",
|
|
"NovoalignCommandline",
|
|
"SamtoolsViewCommandline",
|
|
"SamtoolsCalmdCommandline",
|
|
"SamtoolsCatCommandline",
|
|
"SamtoolsFaidxCommandline",
|
|
"SamtoolsFixmateCommandline",
|
|
"SamtoolsIdxstatsCommandline",
|
|
"SamtoolsIndexCommandline",
|
|
"SamtoolsMergeCommandline",
|
|
"SamtoolsMpileupCommandline",
|
|
"SamtoolsPhaseCommandline",
|
|
"SamtoolsReheaderCommandline",
|
|
"SamtoolsRmdupCommandline",
|
|
"SamtoolsSortCommandline",
|
|
"SamtoolsVersion0xSortCommandline",
|
|
"SamtoolsVersion1xSortCommandline",
|
|
"SamtoolsTargetcutCommandline",
|
|
)
|