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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
127 lines
4.5 KiB
Python
127 lines
4.5 KiB
Python
# Copyright 2009 by Cymon J. Cox and Brad Chapman. 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 TCOFFEE."""
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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 TCoffeeCommandline(AbstractCommandline):
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"""Commandline object for the TCoffee alignment program.
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http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
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The T-Coffee command line tool has a lot of switches and options.
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This wrapper implements a VERY limited number of options - if you
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would like to help improve it please get in touch.
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Notes
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-----
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Last checked against: Version_6.92
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References
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----------
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T-Coffee: A novel method for multiple sequence alignments.
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Notredame, Higgins, Heringa, JMB,302(205-217) 2000
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Examples
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--------
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To align a FASTA file (unaligned.fasta) with the output in ClustalW
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format (file aligned.aln), and otherwise default settings, use:
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>>> from Bio.Align.Applications import TCoffeeCommandline
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>>> tcoffee_cline = TCoffeeCommandline(infile="unaligned.fasta",
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... output="clustalw",
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... outfile="aligned.aln")
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>>> print(tcoffee_cline)
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t_coffee -output clustalw -infile unaligned.fasta -outfile aligned.aln
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You would typically run the command line with tcoffee_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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SEQ_TYPES = ["dna", "protein", "dna_protein"]
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def __init__(self, cmd="t_coffee", **kwargs):
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"""Initialize the class."""
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self.parameters = [
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_Option(
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["-output", "output"],
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"""Specify the output type.
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One (or more separated by a comma) of:
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'clustalw_aln', 'clustalw', 'gcg', 'msf_aln',
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'pir_aln', 'fasta_aln', 'phylip', 'pir_seq', 'fasta_seq'
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""",
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equate=False,
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),
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_Option(
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["-infile", "infile"],
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"Specify the input file.",
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filename=True,
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is_required=True,
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equate=False,
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),
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# Indicates the name of the alignment output by t_coffee. If the
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# default is used, the alignment is named <your sequences>.aln
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_Option(
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["-outfile", "outfile"],
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"Specify the output file. Default: <your sequences>.aln",
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filename=True,
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equate=False,
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),
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_Switch(
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["-convert", "convert"], "Specify you want to perform a file conversion"
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),
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_Option(
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["-type", "type"],
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"Specify the type of sequence being aligned",
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checker_function=lambda x: x in self.SEQ_TYPES,
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equate=False,
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),
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_Option(
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["-outorder", "outorder"],
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"Specify the order of sequence to output"
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"Either 'input', 'aligned' or <filename> of "
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"Fasta file with sequence order",
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equate=False,
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),
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_Option(
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["-matrix", "matrix"],
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"Specify the filename of the substitution matrix to use. "
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"Default: blosum62mt",
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equate=False,
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),
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_Option(
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["-gapopen", "gapopen"],
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"Indicates the penalty applied for opening a gap (negative integer)",
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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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_Option(
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["-gapext", "gapext"],
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"Indicates the penalty applied for extending a gap (negative integer)",
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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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_Switch(["-quiet", "quiet"], "Turn off log output"),
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_Option(
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["-mode", "mode"],
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"Specifies a special mode: genome, quickaln, dali, 3dcoffee",
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equate=False,
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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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