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### This file is part of the BiBench package for biclustering ###
### analysis. ###
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### Copyright (c) 2011 by: ###
### * Kemal Eren, ###
### * Mehmet Deveci, ###
### * Umit V. Catalyurek ###
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###--------------------------------------------------------------###
### ###
### For license info, please see the README and LICENSE files ###
### in the main directory. ###
### ###
###--------------------------------------------------------------###
"""
Wrapper architecture for tasks common to many biclustering
wrappers. Contains utility functions for writing datasets,
reading back results, etc.
This module is only useful for wrapping binaries that expect data
input as a file, and/or write their results out to a file.
To easily write an interface for such binaries, simply implement
write_dataset(), read_results, and do_call(). Then you can call
wrapper_helper(), passing those functions
To see how this works, try looking at qubic.py, cpb.py, or any other
module that uses this function.
"""
import os
import os.path
import shutil
import tempfile
import subprocess
import logging
import bibench.util as util
[docs]def wrapper_helper(binary,
write_dataset,
read_results,
do_call,
data,
*args,
**kwargs):
"""
Perform biclustering. Convenience function for wrappers.
Takes care of creating a temporary directory, exporting the
dataset, running, and reading back the results.
Many biclustering implementations require specific data formats
and produce results in specialized formats. Call function for such
algorithms, implementing write_dataset(), read_results(), and
do_call().
Args:
* binary: the name of the binary to call.
* do_call: This function formats the command and runs it. It
must have the following arguments::
(data, datafile, results_dir, **kwargs)
It must call ``binary``, passing it the data in ``datafile``
and storing results in the ``resultsdir`` directory. Any
other arguments specific to each algorithm are passed in
kwargs.
* write_dataset: The function that writes the dataset out to
``filename`` in the necessary format. It must have the
following arguments::
(data, filename)
* read_results: The function that reads the results back and
returns them as a list of Biclusters. It must have the
following arguments::
(results_dir, data)
Returns:
* A BiclusterList of Biclusters.
"""
if util.which(binary) is None:
raise WrapperException(
"executable '{0}' not found on $PATH".format(binary))
#get a temporary directory to hold dataset and results
directory = tempfile.mkdtemp()
#write the dataset in the appropriate format
datafile = os.path.join(directory, "data.txt")
write_dataset(data, datafile)
#prepare location to hold results
results_dir = os.path.join(directory, "results")
os.mkdir(results_dir)
do_call(data, datafile, results_dir, *args, **kwargs)
#read back the results
biclusters = read_results(results_dir, data)
#cleanup the temporary directory
shutil.rmtree(directory)
return biclusters