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###--------------------------------------------------------------###
### ###
### This file is part of the BiBench package for biclustering ###
### analysis. ###
### ###
### Copyright (c) 2011 by: ###
### * Kemal Eren, ###
### * Mehmet Deveci, ###
### * Umit V. Catalyurek ###
### ###
###--------------------------------------------------------------###
### ###
### For license info, please see the README and LICENSE files ###
### in the main directory. ###
### ###
###--------------------------------------------------------------###
"""
Ordered Preserved SubMatrix wrapper.
"""
from bibench.algorithms.wrapper import wrapper_helper
from bibench.bicluster import \
Bicluster, BiclusterList, bicluster_algorithm
import os, subprocess
from bibench import util
BINARY = 'opsm.sh'
RESULTFILE = 'opsm_results.txt'
@bicluster_algorithm
[docs]def opsm(data, lValue = 10):
"""
OPSM biclustering algorithm. Finds biclusters that have non-decreasing rows.
Args:
* data: 2 dimensional numpy.array format to represent the data matrix.
* lValue: the number of passed models for each iteration. Default is 10.
Returns:
A list of biclusters.
"""
kwargs = locals()
return wrapper_helper(BINARY,
_write_dataset_,
_read_results_,
_do_call_,
**kwargs)
def _do_call_(data, datafile, results_dir, **kwargs):
"""Executes the OPSM.jar executable with given parameters"""
outpath = os.path.join(results_dir, RESULTFILE)
cmd = [BINARY, datafile, str(data.shape[0]),
str(data.shape[1]), outpath, str(kwargs["lValue"])]
subprocess.check_call(cmd)
def _read_results_(dirname, data):
"""Read OPSM result file and return list of Bicluster instances."""
infile = file(os.path.join(dirname, RESULTFILE), 'r')
geneLine = ""
conditionLine = ""
biclusters = []
for geneLine, conditionLine, seperator in util.grouper(infile, 3):
bic = _createBicluster_(geneLine, conditionLine, data)
biclusters.append(bic)
infile.close()
return biclusters
def _createBicluster_(geneLine, conditionLine, data):
"""
Extracts the rows and columns of the bicluster from the given gene
and condition lines.
"""
genes = map(int, geneLine.split(" "))
conditions = map(int, conditionLine.split(" "))
return Bicluster(genes, conditions, data)
def _write_dataset_(data, filename):
"""
Writes a dataset in the format for OPSM.
Separates with tab.
"""
f = file(filename, 'w')
for row in data:
f.write('\t'.join(map(str, row)))
f.write('\n')
f.close()