# Copyright 2009 by Cymon J. Cox. All rights reserved.
#
# 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 W."""
import os
from Bio.Application import _Option
from Bio.Application import _Switch
from Bio.Application import AbstractCommandline
class ClustalwCommandline(AbstractCommandline):
"""Command line wrapper for clustalw (version one or two).
http://www.clustal.org/
Notes
-----
Last checked against versions: 1.83 and 2.1
References
----------
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.
Examples
--------
>>> 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.
"""
# TODO - Should we default to cmd="clustalw2" now?
def __init__(self, cmd="clustalw", **kwargs):
"""Initialize the class."""
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, (float, int))),
),
_Option(
["-topdiags", "-TOPDIAGS", "TOPDIAGS", "topdiags"],
"Number of best diags.",
checker_function=lambda x: (isinstance(x, (float, int))),
),
_Option(
["-window", "-WINDOW", "WINDOW", "window"],
"Window around best diags.",
checker_function=lambda x: (isinstance(x, (float, int))),
),
_Option(
["-pairgap", "-PAIRGAP", "PAIRGAP", "pairgap"],
"Gap penalty",
checker_function=lambda x: (isinstance(x, (float, int))),
),
_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, (float, int))),
),
_Option(
["-pwgapext", "-PWGAPEXT", "PWGAPEXT", "pwgapext"],
"Gap extension penalty",
checker_function=lambda x: (isinstance(x, (float, int))),
),
# ***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, (float, int))),
),
_Option(
["-gapext", "-GAPEXT", "GAPEXT", "gapext"],
"Gap extension penalty",
checker_function=lambda x: (isinstance(x, (float, int))),
),
_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, (float, int))),
),
_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, (float, int))),
),
# 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, (float, int))),
),
_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, (float, int))),
),
_Option(
["-strandgap", "-STRANDGAP", "STRANDGAP", "strandgap"],
"gap penalty for strand core residues",
checker_function=lambda x: (isinstance(x, (float, int))),
),
_Option(
["-loopgap", "-LOOPGAP", "LOOPGAP", "loopgap"],
"Gap penalty for loop regions",
checker_function=lambda x: (isinstance(x, (float, int))),
),
_Option(
["-terminalgap", "-TERMINALGAP", "TERMINALGAP", "terminalgap"],
"Gap penalty for structure termini",
checker_function=lambda x: (isinstance(x, (float, int))),
),
_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()