# Copyright 2011 by Andreas Wilm. All rights reserved. # Based on ClustalW wrapper copyright 2009 by Cymon J. Cox. # # This file is part of the Biopython distribution and governed by your # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". # Please see the LICENSE file that should have been included as part of this # package. """Command line wrapper for the multiple alignment program Clustal Omega.""" from Bio.Application import _Option from Bio.Application import _Switch from Bio.Application import AbstractCommandline class ClustalOmegaCommandline(AbstractCommandline): """Command line wrapper for clustal omega. http://www.clustal.org/omega Notes ----- Last checked against version: 1.2.0 References ---------- Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7:539 https://doi.org/10.1038/msb.2011.75 Examples -------- >>> from Bio.Align.Applications import ClustalOmegaCommandline >>> in_file = "unaligned.fasta" >>> out_file = "aligned.fasta" >>> clustalomega_cline = ClustalOmegaCommandline(infile=in_file, outfile=out_file, verbose=True, auto=True) >>> print(clustalomega_cline) clustalo -i unaligned.fasta -o aligned.fasta --auto -v You would typically run the command line with clustalomega_cline() or via the Python subprocess module, as described in the Biopython tutorial. """ def __init__(self, cmd="clustalo", **kwargs): """Initialize the class.""" # order parameters in the same order as clustalo --help self.parameters = [ # Sequence Input _Option( ["-i", "--in", "--infile", "infile"], "Multiple sequence input file", filename=True, equate=False, ), _Option( ["--hmm-in", "HMM input", "hmm_input"], "HMM input files", filename=True, equate=False, ), _Switch(["--dealign", "dealign"], "Dealign input sequences"), _Option( ["--profile1", "--p1", "profile1"], "Pre-aligned multiple sequence file (aligned columns will be kept fix).", filename=True, equate=False, ), _Option( ["--profile2", "--p2", "profile2"], "Pre-aligned multiple sequence file (aligned columns will be kept fix).", filename=True, equate=False, ), _Option( ["-t", "--seqtype", "seqtype"], "{Protein, RNA, DNA} Force a sequence type (default: auto).", equate=False, checker_function=lambda x: x in ["protein", "rna", "dna", "Protein", "RNA", "DNA", "PROTEIN"], ), _Switch( ["--is-profile", "isprofile"], "disable check if profile, force profile (default no)", ), _Option( ["--infmt", "infmt"], """Forced sequence input file format (default: auto) Allowed values: a2m, fa[sta], clu[stal], msf, phy[lip], selex, st[ockholm], vie[nna] """, equate=False, checker_function=lambda x: x in [ "a2m", "fa", "fasta", "clu", "clustal", "msf", "phy", "phylip", "selex", "st", "stockholm", "vie", "vienna", ], ), # Clustering _Option( ["--distmat-in", "distmat_in"], "Pairwise distance matrix input file (skips distance computation).", filename=True, equate=False, ), _Option( ["--distmat-out", "distmat_out"], "Pairwise distance matrix output file.", filename=True, equate=False, ), _Option( ["--guidetree-in", "guidetree_in"], "Guide tree input file (skips distance computation and guide-tree clustering step).", filename=True, equate=False, ), _Option( ["--guidetree-out", "guidetree_out"], "Guide tree output file.", filename=True, equate=False, ), _Switch( ["--full", "distmat_full"], "Use full distance matrix for guide-tree calculation (slow; mBed is default)", ), _Switch( ["--full-iter", "distmat_full_iter"], "Use full distance matrix for guide-tree calculation during iteration (mBed is default)", ), _Option( ["--cluster-size", "clustersize"], "soft maximum of sequences in sub-clusters", checker_function=lambda x: isinstance(x, int), ), _Option( ["--clustering-out", "clusteringout"], "Clustering output file", filename=True, ), _Switch( ["--use-kimura", "usekimura"], "use Kimura distance correction for aligned sequences (default no)", ), _Switch( ["--percent-id", "percentid"], "convert distances into percent identities (default no)", ), # Alignment Output _Option( ["-o", "--out", "--outfile", "outfile"], "Multiple sequence alignment output file (default: stdout).", filename=True, equate=False, ), _Option( ["--outfmt", "outfmt"], "MSA output file format:" " a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]" " (default: fasta).", equate=False, checker_function=lambda x: x in [ "a2m", "fa", "fasta", "clu", "clustal", "msf", "phy", "phylip", "selex", "st", "stockholm", "vie", "vienna", ], ), _Switch( ["--residuenumber", "--resno", "residuenumber"], "in Clustal format print residue numbers (default no)", ), _Option( ["--wrap", "wrap"], "number of residues before line-wrap in output", checker_function=lambda x: isinstance(x, int), ), _Option( ["--output-order", "outputorder"], "MSA output order like in input/guide-tree", checker_function=lambda x: x in ["input-order", "tree-order"], ), # Iteration _Option( ["--iterations", "--iter", "iterations"], "Number of (combined guide-tree/HMM) iterations", equate=False, checker_function=lambda x: isinstance(x, int), ), _Option( ["--max-guidetree-iterations", "max_guidetree_iterations"], "Maximum number of guidetree iterations", equate=False, checker_function=lambda x: isinstance(x, int), ), _Option( ["--max-hmm-iterations", "max_hmm_iterations"], "Maximum number of HMM iterations", equate=False, checker_function=lambda x: isinstance(x, int), ), # Limits (will exit early, if exceeded): _Option( ["--maxnumseq", "maxnumseq"], "Maximum allowed number of sequences", equate=False, checker_function=lambda x: isinstance(x, int), ), _Option( ["--maxseqlen", "maxseqlen"], "Maximum allowed sequence length", equate=False, checker_function=lambda x: isinstance(x, int), ), # Miscellaneous: _Switch( ["--auto", "auto"], "Set options automatically (might overwrite some of your options)", ), _Option( ["--threads", "threads"], "Number of processors to use", equate=False, checker_function=lambda x: isinstance(x, int), ), _Option( ["-l", "--log", "log"], "Log all non-essential output to this file.", filename=True, equate=False, ), _Switch(["-h", "--help", "help"], "Print help and exit."), _Switch(["-v", "--verbose", "verbose"], "Verbose output"), _Switch(["--version", "version"], "Print version information and exit"), _Switch( ["--long-version", "long_version"], "Print long version information and exit", ), _Switch(["--force", "force"], "Force file overwriting."), ] AbstractCommandline.__init__(self, cmd, **kwargs) if __name__ == "__main__": from Bio._utils import run_doctest run_doctest()