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"""Definitions for interacting with AlignAce.
"""
from Bio import Application
from Bio.Application import _Option,_Argument
class AlignAceCommandline(Application.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"):
Application.AbstractCommandline.__init__(self)
self.program_name = cmd
self.parameters = \
[
_Option(["-i","input","Sequence File"],["input"],lambda x : x.__class__== str,1,
"Input Sequence file in FASTA format."),
_Option(["-numcols","numcols","number of columns to align"],["input"],lambda x : x.__class__== int,0,
"Number of columns to align"),
_Option(["-expect","expect","number of sites expected in model "],["input"],lambda x : x.__class__== int,0,
"number of sites expected in model "),
_Option(["-gcback","gcback","background fractional GC content of input sequence"],["input"],lambda x : x.__class__== float,0,
"background fractional GC content of input sequence"),
_Option(["-minpass","minpass","minimum number of non-improved passes in phase 1"],["input"],lambda x : x.__class__== int,0,
"minimum number of non-improved passes in phase 1"),
_Option(["-seed","seed","set seed for random number generator (time)"],["input"],lambda x : x.__class__== int,0,
"set seed for random number generator (time)"),
_Option(["-undersample","undersample","possible sites / (expect * numcols * seedings)"],["input"],lambda x : x.__class__== int,0,
"possible sites / (expect * numcols * seedings)"),
_Option(["-oversample","oversample","1/undersample"],["input"],lambda x : x.__class__== int,0,
"1/undersample"),
]
def run(self):
return Application.generic_run(self)
class CompareAceCommandline(Application.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"):
Application.AbstractCommandline.__init__(self)
self.program_name = cmd
self.parameters = \
[
_Argument(["motif1"],["input","file"], _file_exists,1,"name of file containing motif 1"),
_Argument(["motif2"],["input","file"], _file_exists,1,"name of file containing motif 2"),
]
def run(self):
return Application.generic_run(self)
def _file_exists(file_name):
"""
Checks whether a given file exists
"""
import os
try:
os.stat(file_name)
return True
except OSError:
return False
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