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