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# Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.
# Revisions copyright 2009 by Peter Cock.
# 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.
"""This module provides code to work with the standalone version of AlignACE,
for motif search in DNA sequences.
AlignACE homepage:
http://arep.med.harvard.edu/mrnadata/mrnasoft.html
AlignACE Citations:
Computational identification of cis-regulatory elements associated with
groups of functionally related genes in Saccharomyces cerevisiae,
Hughes, JD, Estep, PW, Tavazoie S, & GM Church, Journal of Molecular
Biology 2000 Mar 10;296(5):1205-14.
Finding DNA Regulatory Motifs within Unaligned Non-Coding Sequences
Clustered by Whole-Genome mRNA Quantitation,
Roth, FR, Hughes, JD, Estep, PE & GM Church, Nature Biotechnology
1998 Oct;16(10):939-45.
"""
from __future__ import print_function
from Bio.Application import AbstractCommandline, _Option, _Argument
import warnings
from Bio import BiopythonDeprecationWarning
class AlignAceCommandline(AbstractCommandline):
"""Create a commandline for the AlignAce program (DEPRECATED).
Example:
>>> from Bio.motifs.applications import AlignAceCommandline
>>> in_file = "sequences.fasta"
>>> alignace_cline = AlignAceCommandline(infile=in_file, gcback=0.55)
>>> print(alignace_cline)
AlignACE -i sequences.fasta -gcback 0.55
You would typically run the command line with alignace_cline() or via
the Python subprocess module, as described in the Biopython tutorial.
"""
def __init__(self, cmd="AlignACE", **kwargs):
warnings.warn("""The AlignACE application wrapper is deprecated and
is likely to be removed in a future release of Biopython,
since an up to date version of the AlignACE software
cannot be obtained anymore. If you have a copy of
AlignACE 4, please consider contacting the Biopython
developers.""", BiopythonDeprecationWarning)
self.parameters = \
[
_Option(["-i", "infile"],
"Input Sequence file in FASTA format.",
checker_function=lambda x: isinstance(x, str),
equate=False,
filename=True),
_Option(["-numcols", "numcols"],
"Number of columns to align",
equate=False,
checker_function=lambda x: isinstance(x, int)),
_Option(["-expect", "expect"],
"number of sites expected in model",
equate=False,
checker_function=lambda x: isinstance(x, int)),
_Option(["-gcback", "gcback"],
"background fractional GC content of input sequence",
equate=False,
checker_function=lambda x: isinstance(x, float)),
_Option(["-minpass", "minpass"],
"minimum number of non-improved passes in phase 1",
equate=False,
checker_function=lambda x: isinstance(x, int)),
_Option(["-seed", "seed"],
"set seed for random number generator (time)",
equate=False,
checker_function=lambda x: isinstance(x, int)),
_Option(["-undersample", "undersample"],
"possible sites / (expect * numcols * seedings)",
equate=False,
checker_function=lambda x: isinstance(x, int)),
_Option(["-oversample", "oversample"],
"1/undersample",
equate=False,
checker_function=lambda x: isinstance(x, int)),
]
AbstractCommandline.__init__(self, cmd, **kwargs)
class CompareAceCommandline(AbstractCommandline):
"""Create a commandline for the CompareAce program.
Example:
>>> from Bio.motifs.applications import CompareAceCommandline
>>> m1_file = "sequences1.fasta"
>>> m2_file = "sequences2.fasta"
>>> compareace_cline = CompareAceCommandline(motif1=m1_file, motif2=m2_file)
>>> print(compareace_cline)
CompareACE sequences1.fasta sequences2.fasta
You would typically run the command line with compareace_cline() or via
the Python subprocess module, as described in the Biopython tutorial.
"""
def __init__(self, cmd="CompareACE", **kwargs):
warnings.warn("""The CompareACE application wrapper is deprecated and
is likely to be removed in a future release of Biopython,
since an up to date version of the AlignACE software
cannot be obtained anymore. If you have a copy of
AlignACE 4, please consider contacting the Biopython
developers.""", BiopythonDeprecationWarning)
self.parameters = \
[
_Argument(["motif1"],
"name of file containing motif 1",
checker_function=lambda x: isinstance(x, str),
filename=True),
_Argument(["motif2"],
"name of file containing motif 2",
checker_function=lambda x: isinstance(x, str),
filename=True),
]
AbstractCommandline.__init__(self, cmd, **kwargs)
def _test():
"""Run the module's doctests (PRIVATE)."""
print("Running alignace doctests...")
import doctest
doctest.testmod()
print("Done")
if __name__ == "__main__":
_test()
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