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bioioTest.py
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#!/usr/bin/env python
#Copyright (C) 2006-2012 by Benedict Paten ([email protected])
#
#Released under the MIT license, see LICENSE.txt
import unittest
import os
import sys
import random
import math
from bioio import getTempFile
from bioio import getTempDirectory
from bioio import TempFileTree
from bioio import getRandomAlphaNumericString
from bioio import fastaRead
from bioio import fastaWrite
from bioio import fastqRead
from bioio import fastqWrite
from bioio import getRandomSequence
from bioio import pWMRead
from bioio import pWMWrite
from bioio import newickTreeParser
from bioio import printBinaryTree
from bioio import cigarRead
from bioio import cigarWrite
from bioio import PairwiseAlignment
from bioio import getRandomPairwiseAlignment
from sonLib.bioio import TestStatus
from bioio import system
from bioio import logger
class TestCase(unittest.TestCase):
def setUp(self):
self.testNo = TestStatus.getTestSetup()
unittest.TestCase.setUp(self)
self.tempDir = getTempDirectory(os.getcwd())
self.tempFiles = []
def tearDown(self):
unittest.TestCase.tearDown(self)
system("rm -rf %s" % self.tempDir)
for tempFile in self.tempFiles:
os.remove(tempFile)
#########################################################
#########################################################
#########################################################
#temp file functions
#########################################################
#########################################################
#########################################################
def testTempFileTree(self):
for test in xrange(100): #self.testNo):
levels = random.choice(xrange(1, 4))
fileNo = random.choice(xrange(1, 6))
maxTempFiles = int(math.pow(fileNo, levels))
print "Got %s levels, %s fileNo and %s maxTempFiles" % (levels, fileNo, maxTempFiles)
tempFileTreeRootDir = os.path.join(self.tempDir, getRandomAlphaNumericString())
tempFileTree = TempFileTree(tempFileTreeRootDir, fileNo, levels)
tempFiles = []
tempDirs = []
#Check we can mac number of temp files.
for i in xrange(maxTempFiles):
if random.random() > 0.5:
tempFile = tempFileTree.getTempFile()
assert os.path.isfile(tempFile)
tempFiles.append(tempFile)
else:
tempFile = tempFileTree.getTempDirectory()
assert os.path.isdir(tempFile)
tempDirs.append(tempFile)
#Check assertion is created
try:
tempFileTree.getTempFile()
assert False
except RuntimeError:
logger.debug("Got expected error message")
#Now remove a few temp files
while random.random() > 0.1 and len(tempFiles) > 0:
tempFile = tempFiles.pop()
assert os.path.isfile(tempFile)
tempFileTree.destroyTempFile(tempFile)
assert not os.path.isfile(tempFile)
#Now remove a few temp dirs
while random.random() > 0.1 and len(tempDirs) > 0:
tempDir = tempDirs.pop()
assert os.path.isdir(tempDir)
tempFileTree.destroyTempDir(tempDir)
assert not os.path.isdir(tempDir)
#Check temp files is okay
set(tempFileTree.listFiles()) == set(tempFiles + tempDirs)
#Either remove all the temp files or just destroy the whole thing
if random.random() > 0.5:
#Remove all temp files and check thing is empty.
for tempFile in tempFiles:
tempFileTree.destroyTempFile(tempFile)
for tempDir in tempDirs:
tempFileTree.destroyTempDir(tempDir)
os.remove(os.path.join(tempFileTreeRootDir, "lock"))
os.rmdir(tempFileTreeRootDir)
else:
tempFileTree.destroyTempFiles()
assert not os.path.isdir(tempFileTreeRootDir)
#########################################################
#########################################################
#########################################################
#fasta functions
#########################################################
#########################################################
#########################################################
def testFastaReadWrite(self):
tempFile = getTempFile()
self.tempFiles.append(tempFile)
for test in xrange(0, self.testNo):
fastaNumber = random.choice(xrange(10))
l = [ getRandomSequence() for i in xrange(fastaNumber) ]
fileHandle = open(tempFile, 'w')
for name, seq in l:
fastaWrite(fileHandle, name, seq)
fileHandle.close()
fileHandle = open(tempFile, 'r')
l.reverse()
for i in fastaRead(fileHandle):
assert i == l.pop()
name, seq = i
fastaWrite(sys.stdout, name, seq)
fileHandle.close()
def testFastqReadWrite(self):
tempFile = getTempFile()
self.tempFiles.append(tempFile)
for test in xrange(0, self.testNo):
fastaNumber = random.choice(xrange(10))
fastqs = [ (name, seq, [ random.randint(33, 126) for i in range(len(seq)) ]) for name, seq in [ getRandomSequence() for i in xrange(fastaNumber) ]]
fH = open(tempFile, 'w')
for name, seq, quals in fastqs:
fastqWrite(fH, name, seq, quals)
fH.close()
fastqs.reverse()
for i in fastqRead(tempFile):
assert i == fastqs.pop()
name, seq, quals = i
fastqWrite(sys.stdout, name, seq, quals)
def testFastaReadWriteC(self):
"""Tests consistency with C version of this function.
"""
tempFile = getTempFile()
self.tempFiles.append(tempFile)
tempFile2 = getTempFile()
self.tempFiles.append(tempFile2)
for test in xrange(0, self.testNo):
fastaNumber = random.choice(xrange(10))
l = [ getRandomSequence() for i in xrange(fastaNumber) ]
fileHandle = open(tempFile, 'w')
for name, seq in l:
fastaWrite(fileHandle, name, seq)
fileHandle.close()
command = "sonLib_fastaCTest %s %s" % (tempFile, tempFile2)
print command
system(command)
fileHandle = open(tempFile2, 'r')
l.reverse()
for i in fastaRead(fileHandle):
name, seq = i
assert i == l.pop()
fastaWrite(sys.stdout, name, seq)
fileHandle.close()
#########################################################
#########################################################
#########################################################
#newick tree functions
#########################################################
#########################################################
#########################################################
def testNewickTreeParser(self):
if self.testNo > 0:
d = '((human,baboon),chimp);'
e = newickTreeParser(d)
f = printBinaryTree(e, False)
print d, f
assert d == f
def testNewickTreeParser_UnaryNodes(self):
#tests with unary nodes
for test in xrange(0, self.testNo):
tree = getRandomTreeString()
logger.debug("tree to try\t", tree)
tree2 = newickTreeParser(tree, reportUnaryNodes=True)
tree3 = printBinaryTree(tree2, True)
logger.debug("tree found\t", tree3)
assert tree == tree3
#########################################################
#########################################################
#########################################################
#functions for position weight matrices
#########################################################
#########################################################
#########################################################
def testPWMParser(self):
tempFile = getTempFile()
self.tempFiles.append(tempFile)
for test in xrange(0, self.testNo):
pWM = getRandomPWM()
fileHandle = open(tempFile, 'w')
pWMWrite(fileHandle, pWM)
fileHandle.close()
fileHandle = open(tempFile, 'r')
pWM2 = pWMRead(fileHandle)
fileHandle.close()
for i in xrange(0, len(pWM)):
pWM[i] == pWM2[i]
#########################################################
#########################################################
#########################################################
#Cigar functions
#########################################################
#########################################################
#########################################################
def testCigarReadWrite(self):
tempFile = getTempFile()
self.tempFiles.append(tempFile)
for test in xrange(0, self.testNo):
cigarNumber = random.choice(xrange(10))
l = [ getRandomPairwiseAlignment() for i in xrange(cigarNumber) ]
fileHandle = open(tempFile, 'w')
for cigar in l:
cigarWrite(fileHandle, cigar)
fileHandle.close()
fileHandle = open(tempFile, 'r')
l.reverse()
for cigar in cigarRead(fileHandle):
cigarWrite(sys.stdout, l[-1])
cigarWrite(sys.stdout, cigar)
assert cigar == l.pop()
assert len(l) == 0
fileHandle.close()
def getRandomTreeString():
def iDFn():
return random.choice([ "one", "1", "", "he44"])
def dFn():
#if random.random() > 0.5:
return ":%.6f" % random.random()
#return ''
def fn3():
if random.random() > 0.5:
if random.random() > 0.5:
#is unary
return '(' + fn3() + ')' + iDFn() + dFn()
else:
return '(' + fn3() + "," + fn3() + ')' + iDFn() + dFn()
else:
return iDFn() + dFn()
return fn3() + ';'
def getRandomPWM(length=-1):
if length == -1:
length = 1 + int(random.random()*10)
def fn():
l = [ random.random()*100 for i in xrange(0, 4) ]
i = sum(l)
return [ j/i for j in l ]
return [ fn() for i in xrange(0, length) ]
if __name__ == '__main__':
unittest.main()