def main(args):
dataDir = args[0]
outDir = args[1]
DEFAULT_COUNT = 300
dataCount = DEFAULT_COUNT
if (len(args) >= 2):
dataCount = int(args[2])
print 'Processing ' + dataDir
print 'Progress: '
for i in xrange(1, dataCount+1):
print '\t' + str(i) + '/' + str(dataCount)
filenamePrefix = 's' + '{:03d}'.format(i)
filename = filenamePrefix + '.align.1.msl'
filePath = os.path.join(dataDir, filename)
treeNoisyName = filenamePrefix + 'Noisy.tree'
treeNoisyPath = os.path.join(outDir, treeNoisyName)
treeNoisyOut = open(treeNoisyPath, 'w')
treeDenoisedName = filenamePrefix + 'Denoised.tree'
treeDenoisedPath = os.path.join(outDir, treeDenoisedName)
treeDenoisedOut = open(treeDenoisedPath, 'w')
try:
treeCalc.calcTrees(filePath, treeNoisyOut, treeDenoisedOut)
except RuntimeError:
treeNoisyOut.close()
subprocess.call(['rm', treeNoisyPath])
treeDenoisedOut.close()
subprocess.call(['rm', treeDenoisedPath])
continue
treeNoisyOut.close()
treeDenoisedOut.close()
'''
import os
import sys
#path = os.path.abspath(os.path.join(os.path.dirname(__file__), '../src'))
path = os.path.abspath('src')
if not path in sys.path:
sys.path.append(path)
del path
import treeCalc
treeNoisyOut = open('./results/2012-12-23/treecalc_control/indelTreeNoisy', 'w')
treeDenoisedOut = open('./results/2012-12-23/treecalc_control/indelTreeDenoised', 'w')
treeCalc.calcTrees('data/2012-12-23/treecalc_control/indels.fa', treeNoisyOut, treeDenoisedOut)
treeNoisyOut.close()
treeDenoisedOut.close()
treeNoisyOut = open('results/2012-12-23/treecalc_control/s001TreeNoisy', 'w')
treeDenoisedOut = open('results/2012-12-23/treecalc_control/s001TreeDenoised', 'w')
treeCalc.calcTrees('data/2012-12-23/treecalc_control/s001.align.1.msl', treeNoisyOut, treeDenoisedOut)
treeNoisyOut.close()
treeDenoisedOut.close()
treeNoisyOut = open('results/2012-12-23/treecalc_control/onlynoiseTreeNoisy', 'w')
treeDenoisedOut = open('results/2012-12-23/treecalc_control/onlynoiseTreeDenoised', 'w')
try:
treeCalc.calcTrees('data/2012-12-23/treecalc_control/only_noise.fa', treeNoisyOut, treeDenoisedOut)
except RuntimeError as e:
print >> sys.stderr, e.message
