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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
271 lines
9.8 KiB
Python
271 lines
9.8 KiB
Python
# Copyright 2011 by Andreas Wilm. All rights reserved.
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# Based on ClustalW wrapper copyright 2009 by Cymon J. Cox.
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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 Omega."""
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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 ClustalOmegaCommandline(AbstractCommandline):
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"""Command line wrapper for clustal omega.
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http://www.clustal.org/omega
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Notes
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-----
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Last checked against version: 1.2.0
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References
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----------
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Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R,
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McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011).
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Fast, scalable generation of high-quality protein multiple
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sequence alignments using Clustal Omega.
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Molecular Systems Biology 7:539 https://doi.org/10.1038/msb.2011.75
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Examples
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--------
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>>> from Bio.Align.Applications import ClustalOmegaCommandline
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>>> in_file = "unaligned.fasta"
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>>> out_file = "aligned.fasta"
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>>> clustalomega_cline = ClustalOmegaCommandline(infile=in_file, outfile=out_file, verbose=True, auto=True)
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>>> print(clustalomega_cline)
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clustalo -i unaligned.fasta -o aligned.fasta --auto -v
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You would typically run the command line with clustalomega_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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def __init__(self, cmd="clustalo", **kwargs):
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"""Initialize the class."""
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# order parameters in the same order as clustalo --help
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self.parameters = [
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# Sequence Input
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_Option(
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["-i", "--in", "--infile", "infile"],
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"Multiple sequence input file",
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filename=True,
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equate=False,
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),
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_Option(
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["--hmm-in", "HMM input", "hmm_input"],
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"HMM input files",
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filename=True,
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equate=False,
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),
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_Switch(["--dealign", "dealign"], "Dealign input sequences"),
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_Option(
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["--profile1", "--p1", "profile1"],
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"Pre-aligned multiple sequence file (aligned columns will be kept fix).",
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filename=True,
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equate=False,
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),
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_Option(
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["--profile2", "--p2", "profile2"],
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"Pre-aligned multiple sequence file (aligned columns will be kept fix).",
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filename=True,
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equate=False,
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),
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_Option(
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["-t", "--seqtype", "seqtype"],
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"{Protein, RNA, DNA} Force a sequence type (default: auto).",
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equate=False,
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checker_function=lambda x: x
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in ["protein", "rna", "dna", "Protein", "RNA", "DNA", "PROTEIN"],
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),
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_Switch(
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["--is-profile", "isprofile"],
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"disable check if profile, force profile (default no)",
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),
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_Option(
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["--infmt", "infmt"],
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"""Forced sequence input file format (default: auto)
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Allowed values: a2m, fa[sta], clu[stal], msf, phy[lip], selex, st[ockholm], vie[nna]
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""",
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equate=False,
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checker_function=lambda x: x
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in [
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"a2m",
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"fa",
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"fasta",
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"clu",
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"clustal",
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"msf",
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"phy",
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"phylip",
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"selex",
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"st",
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"stockholm",
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"vie",
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"vienna",
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],
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),
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# Clustering
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_Option(
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["--distmat-in", "distmat_in"],
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"Pairwise distance matrix input file (skips distance computation).",
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filename=True,
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equate=False,
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),
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_Option(
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["--distmat-out", "distmat_out"],
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"Pairwise distance matrix output file.",
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filename=True,
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equate=False,
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),
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_Option(
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["--guidetree-in", "guidetree_in"],
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"Guide tree input file (skips distance computation and guide-tree clustering step).",
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filename=True,
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equate=False,
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),
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_Option(
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["--guidetree-out", "guidetree_out"],
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"Guide tree output file.",
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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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["--full", "distmat_full"],
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"Use full distance matrix for guide-tree calculation (slow; mBed is default)",
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),
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_Switch(
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["--full-iter", "distmat_full_iter"],
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"Use full distance matrix for guide-tree calculation during iteration (mBed is default)",
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),
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_Option(
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["--cluster-size", "clustersize"],
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"soft maximum of sequences in sub-clusters",
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checker_function=lambda x: isinstance(x, int),
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),
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_Option(
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["--clustering-out", "clusteringout"],
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"Clustering output file",
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filename=True,
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),
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_Switch(
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["--use-kimura", "usekimura"],
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"use Kimura distance correction for aligned sequences (default no)",
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),
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_Switch(
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["--percent-id", "percentid"],
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"convert distances into percent identities (default no)",
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),
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# Alignment Output
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_Option(
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["-o", "--out", "--outfile", "outfile"],
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"Multiple sequence alignment output file (default: stdout).",
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filename=True,
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equate=False,
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),
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_Option(
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["--outfmt", "outfmt"],
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"MSA output file format:"
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" a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]"
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" (default: fasta).",
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equate=False,
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checker_function=lambda x: x
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in [
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"a2m",
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"fa",
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"fasta",
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"clu",
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"clustal",
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"msf",
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"phy",
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"phylip",
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"selex",
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"st",
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"stockholm",
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"vie",
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"vienna",
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],
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),
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_Switch(
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["--residuenumber", "--resno", "residuenumber"],
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"in Clustal format print residue numbers (default no)",
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),
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_Option(
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["--wrap", "wrap"],
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"number of residues before line-wrap in output",
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checker_function=lambda x: isinstance(x, int),
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),
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_Option(
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["--output-order", "outputorder"],
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"MSA output order like in input/guide-tree",
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checker_function=lambda x: x in ["input-order", "tree-order"],
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),
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# Iteration
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_Option(
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["--iterations", "--iter", "iterations"],
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"Number of (combined guide-tree/HMM) iterations",
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equate=False,
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checker_function=lambda x: isinstance(x, int),
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),
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_Option(
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["--max-guidetree-iterations", "max_guidetree_iterations"],
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"Maximum number of guidetree iterations",
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equate=False,
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checker_function=lambda x: isinstance(x, int),
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),
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_Option(
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["--max-hmm-iterations", "max_hmm_iterations"],
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"Maximum number of HMM iterations",
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equate=False,
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checker_function=lambda x: isinstance(x, int),
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),
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# Limits (will exit early, if exceeded):
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_Option(
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["--maxnumseq", "maxnumseq"],
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"Maximum allowed number of sequences",
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equate=False,
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checker_function=lambda x: isinstance(x, int),
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),
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_Option(
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["--maxseqlen", "maxseqlen"],
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"Maximum allowed sequence length",
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equate=False,
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checker_function=lambda x: isinstance(x, int),
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),
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# Miscellaneous:
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_Switch(
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["--auto", "auto"],
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"Set options automatically (might overwrite some of your options)",
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),
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_Option(
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["--threads", "threads"],
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"Number of processors to use",
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equate=False,
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checker_function=lambda x: isinstance(x, int),
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),
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_Option(
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["-l", "--log", "log"],
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"Log all non-essential output to this file.",
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filename=True,
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equate=False,
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),
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_Switch(["-h", "--help", "help"], "Print help and exit."),
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_Switch(["-v", "--verbose", "verbose"], "Verbose output"),
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_Switch(["--version", "version"], "Print version information and exit"),
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_Switch(
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["--long-version", "long_version"],
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"Print long version information and exit",
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),
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_Switch(["--force", "force"], "Force file overwriting."),
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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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