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$ 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
438 lines
20 KiB
Python
438 lines
20 KiB
Python
# Copyright 2009 by Cymon J. Cox. All rights reserved.
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#
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# This file is part of the Biopython distribution and governed by your
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# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
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# Please see the LICENSE file that should have been included as part of this
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# package.
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"""Command line wrapper for the multiple alignment programme MAFFT."""
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from Bio.Application import _Argument
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from Bio.Application import _Option
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from Bio.Application import _Switch
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from Bio.Application import AbstractCommandline
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class MafftCommandline(AbstractCommandline):
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"""Command line wrapper for the multiple alignment program MAFFT.
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http://align.bmr.kyushu-u.ac.jp/mafft/software/
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Notes
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-----
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Last checked against version: MAFFT v6.717b (2009/12/03)
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References
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----------
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Katoh, Toh (BMC Bioinformatics 9:212, 2008) Improved accuracy of
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multiple ncRNA alignment by incorporating structural information into
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a MAFFT-based framework (describes RNA structural alignment methods)
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Katoh, Toh (Briefings in Bioinformatics 9:286-298, 2008) Recent
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developments in the MAFFT multiple sequence alignment program
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(outlines version 6)
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Katoh, Toh (Bioinformatics 23:372-374, 2007) Errata PartTree: an
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algorithm to build an approximate tree from a large number of
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unaligned sequences (describes the PartTree algorithm)
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Katoh, Kuma, Toh, Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT
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version 5: improvement in accuracy of multiple sequence alignment
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(describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i
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strategies)
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Katoh, Misawa, Kuma, Miyata (Nucleic Acids Res. 30:3059-3066, 2002)
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Examples
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--------
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>>> from Bio.Align.Applications import MafftCommandline
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>>> mafft_exe = "/opt/local/mafft"
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>>> in_file = "../Doc/examples/opuntia.fasta"
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>>> mafft_cline = MafftCommandline(mafft_exe, input=in_file)
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>>> print(mafft_cline)
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/opt/local/mafft ../Doc/examples/opuntia.fasta
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If the mafft binary is on the path (typically the case on a Unix style
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operating system) then you don't need to supply the executable location:
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>>> from Bio.Align.Applications import MafftCommandline
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>>> in_file = "../Doc/examples/opuntia.fasta"
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>>> mafft_cline = MafftCommandline(input=in_file)
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>>> print(mafft_cline)
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mafft ../Doc/examples/opuntia.fasta
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You would typically run the command line with mafft_cline() or via
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the Python subprocess module, as described in the Biopython tutorial.
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Note that MAFFT will write the alignment to stdout, which you may
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want to save to a file and then parse, e.g.::
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stdout, stderr = mafft_cline()
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with open("aligned.fasta", "w") as handle:
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handle.write(stdout)
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from Bio import AlignIO
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align = AlignIO.read("aligned.fasta", "fasta")
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Alternatively, to parse the output with AlignIO directly you can
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use StringIO to turn the string into a handle::
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stdout, stderr = mafft_cline()
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from io import StringIO
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from Bio import AlignIO
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align = AlignIO.read(StringIO(stdout), "fasta")
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"""
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def __init__(self, cmd="mafft", **kwargs):
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"""Initialize the class."""
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BLOSUM_MATRICES = ["30", "45", "62", "80"]
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self.parameters = [
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# **** Algorithm ****
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# Automatically selects an appropriate strategy from L-INS-i, FFT-NS-
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# i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
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_Switch(["--auto", "auto"], "Automatically select strategy. Default off."),
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# Distance is calculated based on the number of shared 6mers. Default: on
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_Switch(
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["--6merpair", "6merpair", "sixmerpair"],
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"Distance is calculated based on the number of shared "
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"6mers. Default: on",
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),
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# All pairwise alignments are computed with the Needleman-Wunsch
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# algorithm. More accurate but slower than --6merpair. Suitable for a
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# set of globally alignable sequences. Applicable to up to ~200
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# sequences. A combination with --maxiterate 1000 is recommended (G-
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# INS-i). Default: off (6mer distance is used)
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_Switch(
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["--globalpair", "globalpair"],
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"All pairwise alignments are computed with the "
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"Needleman-Wunsch algorithm. Default: off",
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),
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# All pairwise alignments are computed with the Smith-Waterman
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# algorithm. More accurate but slower than --6merpair. Suitable for a
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# set of locally alignable sequences. Applicable to up to ~200
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# sequences. A combination with --maxiterate 1000 is recommended (L-
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# INS-i). Default: off (6mer distance is used)
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_Switch(
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["--localpair", "localpair"],
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"All pairwise alignments are computed with the "
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"Smith-Waterman algorithm. Default: off",
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),
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# All pairwise alignments are computed with a local algorithm with
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# the generalized affine gap cost (Altschul 1998). More accurate but
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# slower than --6merpair. Suitable when large internal gaps are
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# expected. Applicable to up to ~200 sequences. A combination with --
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# maxiterate 1000 is recommended (E-INS-i). Default: off (6mer
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# distance is used)
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_Switch(
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["--genafpair", "genafpair"],
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"All pairwise alignments are computed with a local "
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"algorithm with the generalized affine gap cost "
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"(Altschul 1998). Default: off",
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),
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# All pairwise alignments are computed with FASTA (Pearson and Lipman
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# 1988). FASTA is required. Default: off (6mer distance is used)
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_Switch(
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["--fastapair", "fastapair"],
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"All pairwise alignments are computed with FASTA "
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"(Pearson and Lipman 1988). Default: off",
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),
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# Weighting factor for the consistency term calculated from pairwise
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# alignments. Valid when either of --blobalpair, --localpair, --
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# genafpair, --fastapair or --blastpair is selected. Default: 2.7
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_Option(
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["--weighti", "weighti"],
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"Weighting factor for the consistency term calculated "
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"from pairwise alignments. Default: 2.7",
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checker_function=lambda x: isinstance(x, float),
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equate=False,
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),
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# Guide tree is built number times in the progressive stage. Valid
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# with 6mer distance. Default: 2
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_Option(
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["--retree", "retree"],
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"Guide tree is built number times in the progressive "
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"stage. Valid with 6mer distance. Default: 2",
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checker_function=lambda x: isinstance(x, int),
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equate=False,
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),
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# Number cycles of iterative refinement are performed. Default: 0
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_Option(
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["--maxiterate", "maxiterate"],
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"Number cycles of iterative refinement are performed. Default: 0",
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checker_function=lambda x: isinstance(x, int),
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equate=False,
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),
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# Number of threads to use. Default: 1
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_Option(
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["--thread", "thread"],
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"Number of threads to use. Default: 1",
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checker_function=lambda x: isinstance(x, int),
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equate=False,
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),
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# Use FFT approximation in group-to-group alignment. Default: on
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_Switch(
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["--fft", "fft"],
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"Use FFT approximation in group-to-group alignment. Default: on",
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),
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# Do not use FFT approximation in group-to-group alignment. Default:
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# off
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_Switch(
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["--nofft", "nofft"],
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"Do not use FFT approximation in group-to-group "
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"alignment. Default: off",
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),
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# Alignment score is not checked in the iterative refinement stage.
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# Default: off (score is checked)
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_Switch(
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["--noscore", "noscore"],
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"Alignment score is not checked in the iterative "
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"refinement stage. Default: off (score is checked)",
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),
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# Use the Myers-Miller (1988) algorithm. Default: automatically
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# turned on when the alignment length exceeds 10,000 (aa/nt).
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_Switch(
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["--memsave", "memsave"],
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"Use the Myers-Miller (1988) algorithm. Default: "
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"automatically turned on when the alignment length "
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"exceeds 10,000 (aa/nt).",
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),
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# Use a fast tree-building method (PartTree, Katoh and Toh 2007) with
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# the 6mer distance. Recommended for a large number (> ~10,000) of
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# sequences are input. Default: off
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_Switch(
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["--parttree", "parttree"],
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"Use a fast tree-building method with the 6mer "
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"distance. Default: off",
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),
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# The PartTree algorithm is used with distances based on DP. Slightly
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# more accurate and slower than --parttree. Recommended for a large
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# number (> ~10,000) of sequences are input. Default: off
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_Switch(
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["--dpparttree", "dpparttree"],
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"The PartTree algorithm is used with distances "
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"based on DP. Default: off",
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),
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# The PartTree algorithm is used with distances based on FASTA.
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# Slightly more accurate and slower than --parttree. Recommended for
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# a large number (> ~10,000) of sequences are input. FASTA is
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# required. Default: off
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_Switch(
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["--fastaparttree", "fastaparttree"],
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"The PartTree algorithm is used with distances based "
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"on FASTA. Default: off",
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),
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# The number of partitions in the PartTree algorithm. Default: 50
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_Option(
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["--partsize", "partsize"],
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"The number of partitions in the PartTree algorithm. Default: 50",
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checker_function=lambda x: isinstance(x, int),
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equate=False,
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),
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# Do not make alignment larger than number sequences. Valid only with
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# the --*parttree options. Default: the number of input sequences
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_Switch(
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["--groupsize", "groupsize"],
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"Do not make alignment larger than number sequences. "
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"Default: the number of input sequences",
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),
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# Adjust direction according to the first sequence
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# Mafft V6 beta function
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_Switch(
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["--adjustdirection", "adjustdirection"],
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"Adjust direction according to the first sequence. Default off.",
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),
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# Adjust direction according to the first sequence
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# for highly diverged data; very slow
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# Mafft V6 beta function
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_Switch(
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["--adjustdirectionaccurately", "adjustdirectionaccurately"],
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"Adjust direction according to the first sequence,"
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"for highly diverged data; very slow"
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"Default off.",
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),
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# **** Parameter ****
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# Gap opening penalty at group-to-group alignment. Default: 1.53
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_Option(
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["--op", "op"],
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"Gap opening penalty at group-to-group alignment. Default: 1.53",
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checker_function=lambda x: isinstance(x, float),
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equate=False,
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),
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# Offset value, which works like gap extension penalty, for group-to-
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# group alignment. Default: 0.123
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_Option(
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["--ep", "ep"],
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"Offset value, which works like gap extension penalty, "
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"for group-to- group alignment. Default: 0.123",
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checker_function=lambda x: isinstance(x, float),
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equate=False,
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),
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# Gap opening penalty at local pairwise alignment. Valid when the --
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# localpair or --genafpair option is selected. Default: -2.00
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_Option(
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["--lop", "lop"],
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"Gap opening penalty at local pairwise alignment. Default: 0.123",
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checker_function=lambda x: isinstance(x, float),
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equate=False,
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),
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# Offset value at local pairwise alignment. Valid when the --
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# localpair or --genafpair option is selected. Default: 0.1
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_Option(
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["--lep", "lep"],
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"Offset value at local pairwise alignment. Default: 0.1",
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checker_function=lambda x: isinstance(x, float),
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equate=False,
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),
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# Gap extension penalty at local pairwise alignment. Valid when the -
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# -localpair or --genafpair option is selected. Default: -0.1
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_Option(
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["--lexp", "lexp"],
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"Gap extension penalty at local pairwise alignment. Default: -0.1",
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checker_function=lambda x: isinstance(x, float),
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equate=False,
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),
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# Gap opening penalty to skip the alignment. Valid when the --
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# genafpair option is selected. Default: -6.00
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_Option(
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["--LOP", "LOP"],
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"Gap opening penalty to skip the alignment. Default: -6.00",
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checker_function=lambda x: isinstance(x, float),
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equate=False,
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),
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# Gap extension penalty to skip the alignment. Valid when the --
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# genafpair option is selected. Default: 0.00
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_Option(
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["--LEXP", "LEXP"],
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"Gap extension penalty to skip the alignment. Default: 0.00",
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checker_function=lambda x: isinstance(x, float),
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equate=False,
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),
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# BLOSUM number matrix (Henikoff and Henikoff 1992) is used.
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# number=30, 45, 62 or 80. Default: 62
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_Option(
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["--bl", "bl"],
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"BLOSUM number matrix is used. Default: 62",
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checker_function=lambda x: x in BLOSUM_MATRICES,
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equate=False,
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),
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# JTT PAM number (Jones et al. 1992) matrix is used. number>0.
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# Default: BLOSUM62
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_Option(
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["--jtt", "jtt"],
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"JTT PAM number (Jones et al. 1992) matrix is used. "
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"number>0. Default: BLOSUM62",
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equate=False,
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),
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# Transmembrane PAM number (Jones et al. 1994) matrix is used.
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# number>0. Default: BLOSUM62
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_Option(
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["--tm", "tm"],
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"Transmembrane PAM number (Jones et al. 1994) "
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"matrix is used. number>0. Default: BLOSUM62",
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filename=True, # to ensure spaced inputs are quoted
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equate=False,
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),
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# Use a user-defined AA scoring matrix. The format of matrixfile is
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# the same to that of BLAST. Ignored when nucleotide sequences are
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# input. Default: BLOSUM62
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_Option(
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["--aamatrix", "aamatrix"],
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"Use a user-defined AA scoring matrix. Default: BLOSUM62",
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filename=True, # to ensure spaced inputs are quoted
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equate=False,
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),
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# Incorporate the AA/nuc composition information into the scoring
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# matrix. Default: off
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_Switch(
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["--fmodel", "fmodel"],
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"Incorporate the AA/nuc composition information into "
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"the scoring matrix (True) or not (False, default)",
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),
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# **** Output ****
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# Name length for CLUSTAL and PHYLIP format output
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_Option(
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["--namelength", "namelength"],
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"""Name length in CLUSTAL and PHYLIP output.
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MAFFT v6.847 (2011) added --namelength for use with
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the --clustalout option for CLUSTAL output.
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MAFFT v7.024 (2013) added support for this with the
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--phylipout option for PHYLIP output (default 10).
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""",
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checker_function=lambda x: isinstance(x, int),
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equate=False,
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),
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# Output format: clustal format. Default: off (fasta format)
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_Switch(
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["--clustalout", "clustalout"],
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"Output format: clustal (True) or fasta (False, default)",
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),
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# Output format: phylip format.
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# Added in beta with v6.847, fixed in v6.850 (2011)
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_Switch(
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["--phylipout", "phylipout"],
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"Output format: phylip (True), or fasta (False, default)",
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),
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# Output order: same as input. Default: on
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_Switch(
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["--inputorder", "inputorder"],
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"Output order: same as input (True, default) or alignment "
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"based (False)",
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),
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# Output order: aligned. Default: off (inputorder)
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_Switch(
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["--reorder", "reorder"],
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"Output order: aligned (True) or in input order (False, default)",
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),
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# Guide tree is output to the input.tree file. Default: off
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_Switch(
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["--treeout", "treeout"],
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"Guide tree is output to the input.tree file (True) or "
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"not (False, default)",
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),
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# Do not report progress. Default: off
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_Switch(
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["--quiet", "quiet"],
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"Do not report progress (True) or not (False, default).",
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),
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# **** Input ****
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# Assume the sequences are nucleotide. Default: auto
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_Switch(
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["--nuc", "nuc"],
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"Assume the sequences are nucleotide (True/False). Default: auto",
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),
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# Assume the sequences are amino acid. Default: auto
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_Switch(
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["--amino", "amino"],
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"Assume the sequences are amino acid (True/False). Default: auto",
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),
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# MAFFT has multiple --seed commands where the unaligned input is
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# aligned to the seed alignment. There can be multiple seeds in the
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# form: "mafft --seed align1 --seed align2 [etc] input"
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# Effectively for n number of seed alignments.
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# TODO - Can we use class _ArgumentList here?
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_Option(
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["--seed", "seed"],
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"Seed alignments given in alignment_n (fasta format) "
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"are aligned with sequences in input.",
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filename=True,
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equate=False,
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),
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# The input (must be FASTA format)
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_Argument(["input"], "Input file name", filename=True, is_required=True),
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# mafft-profile takes a second alignment input as an argument:
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# mafft-profile align1 align2
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_Argument(
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["input1"],
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"Second input file name for the mafft-profile command",
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filename=True,
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),
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]
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AbstractCommandline.__init__(self, cmd, **kwargs)
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if __name__ == "__main__":
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from Bio._utils import run_doctest
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run_doctest()
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