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# Copyright 2009 by Cymon J. Cox. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# 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 W.
"""
from __future__ import print_function
import os
from Bio.Application import _Option, _Switch, AbstractCommandline
class ClustalwCommandline(AbstractCommandline):
"""Command line wrapper for clustalw (version one or two).
http://www.clustal.org/
Example:
--------
>>> from Bio.Align.Applications import ClustalwCommandline
>>> in_file = "unaligned.fasta"
>>> clustalw_cline = ClustalwCommandline("clustalw2", infile=in_file)
>>> print(clustalw_cline)
clustalw2 -infile=unaligned.fasta
You would typically run the command line with clustalw_cline() or via
the Python subprocess module, as described in the Biopython tutorial.
Citation:
---------
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA,
McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD,
Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0.
Bioinformatics, 23, 2947-2948.
Last checked against versions: 1.83 and 2.1
"""
# TODO - Should we default to cmd="clustalw2" now?
def __init__(self, cmd="clustalw", **kwargs):
self.parameters = \
[
_Option(["-infile", "-INFILE", "INFILE", "infile"],
"Input sequences.",
filename=True),
_Option(["-profile1", "-PROFILE1", "PROFILE1", "profile1"],
"Profiles (old alignment).",
filename=True),
_Option(["-profile2", "-PROFILE2", "PROFILE2", "profile2"],
"Profiles (old alignment).",
filename=True),
# ################# VERBS (do things) #############################
_Switch(["-options", "-OPTIONS", "OPTIONS", "options"],
"List the command line parameters"),
_Switch(["-help", "-HELP", "HELP", "help"],
"Outline the command line params."),
_Switch(["-check", "-CHECK", "CHECK", "check"],
"Outline the command line params."),
_Switch(["-fullhelp", "-FULLHELP", "FULLHELP", "fullhelp"],
"Output full help content."),
_Switch(["-align", "-ALIGN", "ALIGN", "align"],
"Do full multiple alignment."),
_Switch(["-tree", "-TREE", "TREE", "tree"],
"Calculate NJ tree."),
_Switch(["-pim", "-PIM", "PIM", "pim"],
"Output percent identity matrix (while calculating the tree)."),
_Option(["-bootstrap", "-BOOTSTRAP", "BOOTSTRAP", "bootstrap"],
"Bootstrap a NJ tree (n= number of bootstraps; def. = 1000).",
checker_function=lambda x: isinstance(x, int)),
_Switch(["-convert", "-CONVERT", "CONVERT", "convert"],
"Output the input sequences in a different file format."),
# #################### PARAMETERS (set things) #########################
# ***General settings:****
# Makes no sense in biopython
# _Option(["-interactive", "-INTERACTIVE", "INTERACTIVE", "interactive"],
# [],
# lambda x: 0, # Does not take value
# False,
# "read command line, then enter normal interactive menus",
# False),
_Switch(["-quicktree", "-QUICKTREE", "QUICKTREE", "quicktree"],
"Use FAST algorithm for the alignment guide tree"),
_Option(["-type", "-TYPE", "TYPE", "type"],
"PROTEIN or DNA sequences",
checker_function=lambda x: x in ["PROTEIN", "DNA",
"protein", "dna"]),
_Switch(["-negative", "-NEGATIVE", "NEGATIVE", "negative"],
"Protein alignment with negative values in matrix"),
_Option(["-outfile", "-OUTFILE", "OUTFILE", "outfile"],
"Output sequence alignment file name",
filename=True),
_Option(["-output", "-OUTPUT", "OUTPUT", "output"],
"Output format: CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA",
checker_function=lambda x: x in ["CLUSTAL", "GCG", "GDE", "PHYLIP",
"PIR", "NEXUS", "FASTA",
"clustal", "gcg", "gde", "phylip",
"pir", "nexus", "fasta"]),
_Option(["-outorder", "-OUTORDER", "OUTORDER", "outorder"],
"Output taxon order: INPUT or ALIGNED",
checker_function=lambda x: x in ["INPUT", "input",
"ALIGNED", "aligned"]),
_Option(["-case", "-CASE", "CASE", "case"],
"LOWER or UPPER (for GDE output only)",
checker_function=lambda x: x in ["UPPER", "upper",
"LOWER", "lower"]),
_Option(["-seqnos", "-SEQNOS", "SEQNOS", "seqnos"],
"OFF or ON (for Clustal output only)",
checker_function=lambda x: x in ["ON", "on",
"OFF", "off"]),
_Option(["-seqno_range", "-SEQNO_RANGE", "SEQNO_RANGE", "seqno_range"],
"OFF or ON (NEW- for all output formats)",
checker_function=lambda x: x in ["ON", "on",
"OFF", "off"]),
_Option(["-range", "-RANGE", "RANGE", "range"],
"Sequence range to write starting m to m+n. "
"Input as string eg. '24,200'"),
_Option(["-maxseqlen", "-MAXSEQLEN", "MAXSEQLEN", "maxseqlen"],
"Maximum allowed input sequence length",
checker_function=lambda x: isinstance(x, int)),
_Switch(["-quiet", "-QUIET", "QUIET", "quiet"],
"Reduce console output to minimum"),
_Option(["-stats", "-STATS", "STATS", "stats"],
"Log some alignment statistics to file",
filename=True),
# ***Fast Pairwise Alignments:***
_Option(["-ktuple", "-KTUPLE", "KTUPLE", "ktuple"],
"Word size",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Option(["-topdiags", "-TOPDIAGS", "TOPDIAGS", "topdiags"],
"Number of best diags.",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Option(["-window", "-WINDOW", "WINDOW", "window"],
"Window around best diags.",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Option(["-pairgap", "-PAIRGAP", "PAIRGAP", "pairgap"],
"Gap penalty",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Option(["-score", "-SCORE", "SCORE", "score"],
"Either: PERCENT or ABSOLUTE",
checker_function=lambda x: x in ["percent", "PERCENT",
"absolute", "ABSOLUTE"]),
# ***Slow Pairwise Alignments:***
_Option(["-pwmatrix", "-PWMATRIX", "PWMATRIX", "pwmatrix"],
"Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename",
checker_function=lambda x: x in ["BLOSUM", "PAM",
"GONNET", "ID",
"blosum", "pam",
"gonnet", "id"] or
os.path.exists(x),
filename=True),
_Option(["-pwdnamatrix", "-PWDNAMATRIX", "PWDNAMATRIX", "pwdnamatrix"],
"DNA weight matrix=IUB, CLUSTALW or filename",
checker_function=lambda x: x in ["IUB", "CLUSTALW",
"iub", "clustalw"] or
os.path.exists(x),
filename=True),
_Option(["-pwgapopen", "-PWGAPOPEN", "PWGAPOPEN", "pwgapopen"],
"Gap opening penalty",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Option(["-pwgapext", "-PWGAPEXT", "PWGAPEXT", "pwgapext"],
"Gap extension penalty",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
# ***Multiple Alignments:***
_Option(["-newtree", "-NEWTREE", "NEWTREE", "newtree"],
"Output file name for newly created guide tree",
filename=True),
_Option(["-usetree", "-USETREE", "USETREE", "usetree"],
"File name of guide tree",
checker_function=lambda x: os.path.exists,
filename=True),
_Option(["-matrix", "-MATRIX", "MATRIX", "matrix"],
"Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename",
checker_function=lambda x: x in ["BLOSUM", "PAM",
"GONNET", "ID",
"blosum", "pam",
"gonnet", "id"] or
os.path.exists(x),
filename=True),
_Option(["-dnamatrix", "-DNAMATRIX", "DNAMATRIX", "dnamatrix"],
"DNA weight matrix=IUB, CLUSTALW or filename",
checker_function=lambda x: x in ["IUB", "CLUSTALW",
"iub", "clustalw"] or
os.path.exists(x),
filename=True),
_Option(["-gapopen", "-GAPOPEN", "GAPOPEN", "gapopen"],
"Gap opening penalty",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Option(["-gapext", "-GAPEXT", "GAPEXT", "gapext"],
"Gap extension penalty",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Switch(["-endgaps", "-ENDGAPS", "ENDGAPS", "endgaps"],
"No end gap separation pen."),
_Option(["-gapdist", "-GAPDIST", "GAPDIST", "gapdist"],
"Gap separation pen. range",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Switch(["-nopgap", "-NOPGAP", "NOPGAP", "nopgap"],
"Residue-specific gaps off"),
_Switch(["-nohgap", "-NOHGAP", "NOHGAP", "nohgap"],
"Hydrophilic gaps off"),
_Switch(["-hgapresidues", "-HGAPRESIDUES", "HGAPRESIDUES", "hgapresidues"],
"List hydrophilic res."),
_Option(["-maxdiv", "-MAXDIV", "MAXDIV", "maxdiv"],
"% ident. for delay",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
# Already handled in General Settings section, but appears a second
# time under Multiple Alignments in the help
# _Option(["-type", "-TYPE", "TYPE", "type"],
# "PROTEIN or DNA",
# checker_function=lambda x: x in ["PROTEIN", "DNA",
# "protein", "dna"]),
_Option(["-transweight", "-TRANSWEIGHT", "TRANSWEIGHT", "transweight"],
"Transitions weighting",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Option(["-iteration", "-ITERATION", "ITERATION", "iteration"],
"NONE or TREE or ALIGNMENT",
checker_function=lambda x: x in ["NONE", "TREE",
"ALIGNMENT",
"none", "tree",
"alignment"]),
_Option(["-numiter", "-NUMITER", "NUMITER", "numiter"],
"maximum number of iterations to perform",
checker_function=lambda x: isinstance(x, int)),
_Switch(["-noweights", "-NOWEIGHTS", "NOWEIGHTS", "noweights"],
"Disable sequence weighting"),
# ***Profile Alignments:***
_Switch(["-profile", "-PROFILE", "PROFILE", "profile"],
"Merge two alignments by profile alignment"),
_Option(["-newtree1", "-NEWTREE1", "NEWTREE1", "newtree1"],
"Output file name for new guide tree of profile1",
filename=True),
_Option(["-newtree2", "-NEWTREE2", "NEWTREE2", "newtree2"],
"Output file for new guide tree of profile2",
filename=True),
_Option(["-usetree1", "-USETREE1", "USETREE1", "usetree1"],
"File name of guide tree for profile1",
checker_function=lambda x: os.path.exists,
filename=True),
_Option(["-usetree2", "-USETREE2", "USETREE2", "usetree2"],
"File name of guide tree for profile2",
checker_function=lambda x: os.path.exists,
filename=True),
# ***Sequence to Profile Alignments:***
_Switch(["-sequences", "-SEQUENCES", "SEQUENCES", "sequences"],
"Sequentially add profile2 sequences to profile1 alignment"),
# These are already handled in the Multiple Alignments section,
# but appear a second time here in the help.
# _Option(["-newtree", "-NEWTREE", "NEWTREE", "newtree"],
# "File for new guide tree",
# filename=True),
# _Option(["-usetree", "-USETREE", "USETREE", "usetree"],
# "File for old guide tree",
# checker_function=lambda x: os.path.exists,
# filename=True),
# ***Structure Alignments:***
_Switch(["-nosecstr1", "-NOSECSTR1", "NOSECSTR1", "nosecstr1"],
"Do not use secondary structure-gap penalty mask for profile 1"),
_Switch(["-nosecstr2", "-NOSECSTR2", "NOSECSTR2", "nosecstr2"],
"Do not use secondary structure-gap penalty mask for profile 2"),
_Option(["-secstrout", "-SECSTROUT", "SECSTROUT", "secstrout"],
"STRUCTURE or MASK or BOTH or NONE output in alignment file",
checker_function=lambda x: x in ["STRUCTURE", "MASK",
"BOTH", "NONE",
"structure", "mask",
"both", "none"]),
_Option(["-helixgap", "-HELIXGAP", "HELIXGAP", "helixgap"],
"Gap penalty for helix core residues",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Option(["-strandgap", "-STRANDGAP", "STRANDGAP", "strandgap"],
"gap penalty for strand core residues",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Option(["-loopgap", "-LOOPGAP", "LOOPGAP", "loopgap"],
"Gap penalty for loop regions",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Option(["-terminalgap", "-TERMINALGAP", "TERMINALGAP", "terminalgap"],
"Gap penalty for structure termini",
checker_function=lambda x: isinstance(x, int) or
isinstance(x, float)),
_Option(["-helixendin", "-HELIXENDIN", "HELIXENDIN", "helixendin"],
"Number of residues inside helix to be treated as terminal",
checker_function=lambda x: isinstance(x, int)),
_Option(["-helixendout", "-HELIXENDOUT", "HELIXENDOUT", "helixendout"],
"Number of residues outside helix to be treated as terminal",
checker_function=lambda x: isinstance(x, int)),
_Option(["-strandendin", "-STRANDENDIN", "STRANDENDIN", "strandendin"],
"Number of residues inside strand to be treated as terminal",
checker_function=lambda x: isinstance(x, int)),
_Option(["-strandendout", "-STRANDENDOUT", "STRANDENDOUT", "strandendout"],
"Number of residues outside strand to be treated as terminal",
checker_function=lambda x: isinstance(x, int)),
# ***Trees:***
_Option(["-outputtree", "-OUTPUTTREE", "OUTPUTTREE", "outputtree"],
"nj OR phylip OR dist OR nexus",
checker_function=lambda x: x in ["NJ", "PHYLIP",
"DIST", "NEXUS",
"nj", "phylip",
"dist", "nexus"]),
_Option(["-seed", "-SEED", "SEED", "seed"],
"Seed number for bootstraps.",
checker_function=lambda x: isinstance(x, int)),
_Switch(["-kimura", "-KIMURA", "KIMURA", "kimura"],
"Use Kimura's correction."),
_Switch(["-tossgaps", "-TOSSGAPS", "TOSSGAPS", "tossgaps"],
"Ignore positions with gaps."),
_Option(["-bootlabels", "-BOOTLABELS", "BOOTLABELS", "bootlabels"],
"Node OR branch position of bootstrap values in tree display",
checker_function=lambda x: x in ["NODE", "BRANCH",
"node", "branch"]),
_Option(["-clustering", "-CLUSTERING", "CLUSTERING", "clustering"],
"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()
|
