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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
489 lines
20 KiB
Python
489 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 program Clustal W."""
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import os
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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 ClustalwCommandline(AbstractCommandline):
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"""Command line wrapper for clustalw (version one or two).
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http://www.clustal.org/
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Notes
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-----
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Last checked against versions: 1.83 and 2.1
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References
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----------
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Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA,
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McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD,
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Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0.
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Bioinformatics, 23, 2947-2948.
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Examples
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--------
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>>> from Bio.Align.Applications import ClustalwCommandline
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>>> in_file = "unaligned.fasta"
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>>> clustalw_cline = ClustalwCommandline("clustalw2", infile=in_file)
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>>> print(clustalw_cline)
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clustalw2 -infile=unaligned.fasta
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You would typically run the command line with clustalw_cline() or via
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the Python subprocess module, as described in the Biopython tutorial.
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"""
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# TODO - Should we default to cmd="clustalw2" now?
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def __init__(self, cmd="clustalw", **kwargs):
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"""Initialize the class."""
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self.parameters = [
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_Option(
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["-infile", "-INFILE", "INFILE", "infile"],
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"Input sequences.",
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filename=True,
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),
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_Option(
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["-profile1", "-PROFILE1", "PROFILE1", "profile1"],
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"Profiles (old alignment).",
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filename=True,
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),
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_Option(
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["-profile2", "-PROFILE2", "PROFILE2", "profile2"],
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"Profiles (old alignment).",
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filename=True,
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),
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# ################# VERBS (do things) #############################
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_Switch(
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["-options", "-OPTIONS", "OPTIONS", "options"],
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"List the command line parameters",
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),
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_Switch(
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["-help", "-HELP", "HELP", "help"], "Outline the command line params."
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),
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_Switch(
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["-check", "-CHECK", "CHECK", "check"],
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"Outline the command line params.",
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),
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_Switch(
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["-fullhelp", "-FULLHELP", "FULLHELP", "fullhelp"],
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"Output full help content.",
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),
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_Switch(
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["-align", "-ALIGN", "ALIGN", "align"], "Do full multiple alignment."
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),
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_Switch(["-tree", "-TREE", "TREE", "tree"], "Calculate NJ tree."),
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_Switch(
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["-pim", "-PIM", "PIM", "pim"],
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"Output percent identity matrix (while calculating the tree).",
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),
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_Option(
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["-bootstrap", "-BOOTSTRAP", "BOOTSTRAP", "bootstrap"],
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"Bootstrap a NJ tree (n= number of bootstraps; def. = 1000).",
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checker_function=lambda x: isinstance(x, int),
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),
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_Switch(
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["-convert", "-CONVERT", "CONVERT", "convert"],
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"Output the input sequences in a different file format.",
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),
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# #################### PARAMETERS (set things) #########################
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# ***General settings:****
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# Makes no sense in biopython
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# _Option(["-interactive", "-INTERACTIVE", "INTERACTIVE", "interactive"],
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# [],
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# lambda x: 0, # Does not take value
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# False,
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# "read command line, then enter normal interactive menus",
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# False),
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_Switch(
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["-quicktree", "-QUICKTREE", "QUICKTREE", "quicktree"],
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"Use FAST algorithm for the alignment guide tree",
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),
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_Option(
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["-type", "-TYPE", "TYPE", "type"],
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"PROTEIN or DNA sequences",
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checker_function=lambda x: x in ["PROTEIN", "DNA", "protein", "dna"],
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),
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_Switch(
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["-negative", "-NEGATIVE", "NEGATIVE", "negative"],
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"Protein alignment with negative values in matrix",
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),
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_Option(
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["-outfile", "-OUTFILE", "OUTFILE", "outfile"],
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"Output sequence alignment file name",
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filename=True,
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),
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_Option(
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["-output", "-OUTPUT", "OUTPUT", "output"],
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"Output format: CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA",
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checker_function=lambda x: x
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in [
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"CLUSTAL",
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"GCG",
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"GDE",
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"PHYLIP",
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"PIR",
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"NEXUS",
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"FASTA",
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"clustal",
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"gcg",
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"gde",
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"phylip",
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"pir",
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"nexus",
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"fasta",
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],
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),
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_Option(
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["-outorder", "-OUTORDER", "OUTORDER", "outorder"],
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"Output taxon order: INPUT or ALIGNED",
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checker_function=lambda x: x
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in ["INPUT", "input", "ALIGNED", "aligned"],
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),
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_Option(
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["-case", "-CASE", "CASE", "case"],
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"LOWER or UPPER (for GDE output only)",
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checker_function=lambda x: x in ["UPPER", "upper", "LOWER", "lower"],
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),
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_Option(
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["-seqnos", "-SEQNOS", "SEQNOS", "seqnos"],
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"OFF or ON (for Clustal output only)",
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checker_function=lambda x: x in ["ON", "on", "OFF", "off"],
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),
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_Option(
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["-seqno_range", "-SEQNO_RANGE", "SEQNO_RANGE", "seqno_range"],
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"OFF or ON (NEW- for all output formats)",
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checker_function=lambda x: x in ["ON", "on", "OFF", "off"],
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),
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_Option(
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["-range", "-RANGE", "RANGE", "range"],
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"Sequence range to write starting m to m+n. "
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"Input as string eg. '24,200'",
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),
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_Option(
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["-maxseqlen", "-MAXSEQLEN", "MAXSEQLEN", "maxseqlen"],
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"Maximum allowed input sequence length",
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checker_function=lambda x: isinstance(x, int),
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),
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_Switch(
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["-quiet", "-QUIET", "QUIET", "quiet"],
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"Reduce console output to minimum",
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),
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_Option(
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["-stats", "-STATS", "STATS", "stats"],
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"Log some alignment statistics to file",
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filename=True,
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),
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# ***Fast Pairwise Alignments:***
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_Option(
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["-ktuple", "-KTUPLE", "KTUPLE", "ktuple"],
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"Word size",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Option(
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["-topdiags", "-TOPDIAGS", "TOPDIAGS", "topdiags"],
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"Number of best diags.",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Option(
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["-window", "-WINDOW", "WINDOW", "window"],
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"Window around best diags.",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Option(
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["-pairgap", "-PAIRGAP", "PAIRGAP", "pairgap"],
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"Gap penalty",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Option(
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["-score", "-SCORE", "SCORE", "score"],
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"Either: PERCENT or ABSOLUTE",
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checker_function=lambda x: x
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in ["percent", "PERCENT", "absolute", "ABSOLUTE"],
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),
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# ***Slow Pairwise Alignments:***
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_Option(
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["-pwmatrix", "-PWMATRIX", "PWMATRIX", "pwmatrix"],
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"Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename",
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checker_function=lambda x: (
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x
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in [
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"BLOSUM",
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"PAM",
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"GONNET",
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"ID",
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"blosum",
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"pam",
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"gonnet",
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"id",
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]
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or os.path.exists(x)
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),
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filename=True,
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),
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_Option(
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["-pwdnamatrix", "-PWDNAMATRIX", "PWDNAMATRIX", "pwdnamatrix"],
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"DNA weight matrix=IUB, CLUSTALW or filename",
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checker_function=lambda x: (
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x in ["IUB", "CLUSTALW", "iub", "clustalw"] or os.path.exists(x)
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),
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filename=True,
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),
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_Option(
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["-pwgapopen", "-PWGAPOPEN", "PWGAPOPEN", "pwgapopen"],
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"Gap opening penalty",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Option(
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["-pwgapext", "-PWGAPEXT", "PWGAPEXT", "pwgapext"],
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"Gap extension penalty",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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# ***Multiple Alignments:***
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_Option(
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["-newtree", "-NEWTREE", "NEWTREE", "newtree"],
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"Output file name for newly created guide tree",
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filename=True,
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),
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_Option(
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["-usetree", "-USETREE", "USETREE", "usetree"],
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"File name of guide tree",
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checker_function=lambda x: os.path.exists,
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filename=True,
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),
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_Option(
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["-matrix", "-MATRIX", "MATRIX", "matrix"],
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"Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename",
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checker_function=lambda x: (
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x
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in [
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"BLOSUM",
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"PAM",
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"GONNET",
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"ID",
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"blosum",
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"pam",
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"gonnet",
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"id",
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]
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or os.path.exists(x)
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),
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filename=True,
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),
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_Option(
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["-dnamatrix", "-DNAMATRIX", "DNAMATRIX", "dnamatrix"],
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"DNA weight matrix=IUB, CLUSTALW or filename",
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checker_function=lambda x: (
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x in ["IUB", "CLUSTALW", "iub", "clustalw"] or os.path.exists(x)
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),
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filename=True,
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),
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_Option(
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["-gapopen", "-GAPOPEN", "GAPOPEN", "gapopen"],
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"Gap opening penalty",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Option(
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["-gapext", "-GAPEXT", "GAPEXT", "gapext"],
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"Gap extension penalty",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Switch(
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["-endgaps", "-ENDGAPS", "ENDGAPS", "endgaps"],
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"No end gap separation pen.",
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),
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_Option(
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["-gapdist", "-GAPDIST", "GAPDIST", "gapdist"],
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"Gap separation pen. range",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Switch(
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["-nopgap", "-NOPGAP", "NOPGAP", "nopgap"], "Residue-specific gaps off"
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),
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_Switch(["-nohgap", "-NOHGAP", "NOHGAP", "nohgap"], "Hydrophilic gaps off"),
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_Switch(
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["-hgapresidues", "-HGAPRESIDUES", "HGAPRESIDUES", "hgapresidues"],
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"List hydrophilic res.",
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),
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_Option(
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["-maxdiv", "-MAXDIV", "MAXDIV", "maxdiv"],
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"% ident. for delay",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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# Already handled in General Settings section, but appears a second
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# time under Multiple Alignments in the help
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# _Option(["-type", "-TYPE", "TYPE", "type"],
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# "PROTEIN or DNA",
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# checker_function=lambda x: x in ["PROTEIN", "DNA",
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# "protein", "dna"]),
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_Option(
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["-transweight", "-TRANSWEIGHT", "TRANSWEIGHT", "transweight"],
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"Transitions weighting",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Option(
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["-iteration", "-ITERATION", "ITERATION", "iteration"],
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"NONE or TREE or ALIGNMENT",
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checker_function=lambda x: x
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in ["NONE", "TREE", "ALIGNMENT", "none", "tree", "alignment"],
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),
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_Option(
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["-numiter", "-NUMITER", "NUMITER", "numiter"],
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"maximum number of iterations to perform",
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checker_function=lambda x: isinstance(x, int),
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),
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_Switch(
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["-noweights", "-NOWEIGHTS", "NOWEIGHTS", "noweights"],
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"Disable sequence weighting",
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),
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# ***Profile Alignments:***
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_Switch(
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["-profile", "-PROFILE", "PROFILE", "profile"],
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"Merge two alignments by profile alignment",
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),
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_Option(
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["-newtree1", "-NEWTREE1", "NEWTREE1", "newtree1"],
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"Output file name for new guide tree of profile1",
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filename=True,
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),
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_Option(
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["-newtree2", "-NEWTREE2", "NEWTREE2", "newtree2"],
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"Output file for new guide tree of profile2",
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filename=True,
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),
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_Option(
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["-usetree1", "-USETREE1", "USETREE1", "usetree1"],
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"File name of guide tree for profile1",
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checker_function=lambda x: os.path.exists,
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filename=True,
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),
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_Option(
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["-usetree2", "-USETREE2", "USETREE2", "usetree2"],
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"File name of guide tree for profile2",
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checker_function=lambda x: os.path.exists,
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filename=True,
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),
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# ***Sequence to Profile Alignments:***
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_Switch(
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["-sequences", "-SEQUENCES", "SEQUENCES", "sequences"],
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"Sequentially add profile2 sequences to profile1 alignment",
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),
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# These are already handled in the Multiple Alignments section,
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# but appear a second time here in the help.
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# _Option(["-newtree", "-NEWTREE", "NEWTREE", "newtree"],
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# "File for new guide tree",
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# filename=True),
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# _Option(["-usetree", "-USETREE", "USETREE", "usetree"],
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# "File for old guide tree",
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# checker_function=lambda x: os.path.exists,
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# filename=True),
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# ***Structure Alignments:***
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_Switch(
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["-nosecstr1", "-NOSECSTR1", "NOSECSTR1", "nosecstr1"],
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"Do not use secondary structure-gap penalty mask for profile 1",
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),
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_Switch(
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["-nosecstr2", "-NOSECSTR2", "NOSECSTR2", "nosecstr2"],
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"Do not use secondary structure-gap penalty mask for profile 2",
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),
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_Option(
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["-secstrout", "-SECSTROUT", "SECSTROUT", "secstrout"],
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"STRUCTURE or MASK or BOTH or NONE output in alignment file",
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checker_function=lambda x: x
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in [
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"STRUCTURE",
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"MASK",
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"BOTH",
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"NONE",
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"structure",
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"mask",
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"both",
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"none",
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],
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),
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_Option(
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["-helixgap", "-HELIXGAP", "HELIXGAP", "helixgap"],
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"Gap penalty for helix core residues",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Option(
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["-strandgap", "-STRANDGAP", "STRANDGAP", "strandgap"],
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"gap penalty for strand core residues",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Option(
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["-loopgap", "-LOOPGAP", "LOOPGAP", "loopgap"],
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"Gap penalty for loop regions",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Option(
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["-terminalgap", "-TERMINALGAP", "TERMINALGAP", "terminalgap"],
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"Gap penalty for structure termini",
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checker_function=lambda x: (isinstance(x, (float, int))),
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),
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_Option(
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["-helixendin", "-HELIXENDIN", "HELIXENDIN", "helixendin"],
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"Number of residues inside helix to be treated as terminal",
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checker_function=lambda x: isinstance(x, int),
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),
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_Option(
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["-helixendout", "-HELIXENDOUT", "HELIXENDOUT", "helixendout"],
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"Number of residues outside helix to be treated as terminal",
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checker_function=lambda x: isinstance(x, int),
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),
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_Option(
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["-strandendin", "-STRANDENDIN", "STRANDENDIN", "strandendin"],
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"Number of residues inside strand to be treated as terminal",
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checker_function=lambda x: isinstance(x, int),
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),
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_Option(
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["-strandendout", "-STRANDENDOUT", "STRANDENDOUT", "strandendout"],
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"Number of residues outside strand to be treated as terminal",
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checker_function=lambda x: isinstance(x, int),
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),
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# ***Trees:***
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_Option(
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["-outputtree", "-OUTPUTTREE", "OUTPUTTREE", "outputtree"],
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"nj OR phylip OR dist OR nexus",
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checker_function=lambda x: x
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in ["NJ", "PHYLIP", "DIST", "NEXUS", "nj", "phylip", "dist", "nexus"],
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),
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_Option(
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["-seed", "-SEED", "SEED", "seed"],
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"Seed number for bootstraps.",
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checker_function=lambda x: isinstance(x, int),
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),
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_Switch(
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["-kimura", "-KIMURA", "KIMURA", "kimura"], "Use Kimura's correction."
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),
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_Switch(
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["-tossgaps", "-TOSSGAPS", "TOSSGAPS", "tossgaps"],
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"Ignore positions with gaps.",
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),
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_Option(
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["-bootlabels", "-BOOTLABELS", "BOOTLABELS", "bootlabels"],
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"Node OR branch position of bootstrap values in tree display",
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checker_function=lambda x: x in ["NODE", "BRANCH", "node", "branch"],
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),
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_Option(
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["-clustering", "-CLUSTERING", "CLUSTERING", "clustering"],
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"NJ or UPGMA",
|
|
checker_function=lambda x: x in ["NJ", "UPGMA", "nj", "upgma"],
|
|
),
|
|
]
|
|
AbstractCommandline.__init__(self, cmd, **kwargs)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
from Bio._utils import run_doctest
|
|
|
|
run_doctest()
|