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_AlignAce.py
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_AlignAce.py
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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 Bio.Application import AbstractCommandline, _Option, _Argument
class AlignAceCommandline(AbstractCommandline):
"""Create a commandline for the AlignAce program.
XXX This could use more checking for valid paramters to the program.
"""
def __init__(self, cmd="AlignACE", **kwargs):
self.parameters = \
[
_Option(["-i","input"],["input"],lambda x : isinstance(x, str),1,
"Input Sequence file in FASTA format."),
_Option(["-numcols","numcols"],["input"],lambda x : isinstance(x, int),0,
"Number of columns to align"),
_Option(["-expect","expect"],["input"],lambda x : isinstance(x, int),0,
"number of sites expected in model "),
_Option(["-gcback","gcback"],["input"],lambda x : isinstance(x, float),0,
"background fractional GC content of input sequence"),
_Option(["-minpass","minpass"],["input"],lambda x : isinstance(x, int),0,
"minimum number of non-improved passes in phase 1"),
_Option(["-seed","seed"],["input"],lambda x : isinstance(x, int),0,
"set seed for random number generator (time)"),
_Option(["-undersample","undersample"],["input"],lambda x : isinstance(x, int),0,
"possible sites / (expect * numcols * seedings)"),
_Option(["-oversample","oversample"],["input"],lambda x : isinstance(x, int),0,
"1/undersample"),
]
AbstractCommandline.__init__(self, cmd, **kwargs)
class CompareAceCommandline(AbstractCommandline):
"""Create a commandline for the CompareAce program.
XXX This could use more checking for valid paramters to the program.
"""
def __init__(self, cmd="CompareACE", **kwargs):
import os.path
self.parameters = \
[
_Argument(["motif1"],["input","file"], os.path.exists,1,"name of file containing motif 1"),
_Argument(["motif2"],["input","file"], os.path.exists,1,"name of file containing motif 2"),
]
AbstractCommandline.__init__(self, cmd, **kwargs)