if makeRandomTestData.checkForFasta(randomTrans + '.fa'):
x = os.remove(randomTrans + '.fa')
for i in range(0, numTranscripts):
isoform = random.randint(1, 100)
if isoform <= isoformProb and len(genes) > 2:
geneSelected = random.choice(genes.keys())
geneSelectedParts = geneSelected.split(' ')
geneSelectedId = ''
for part in geneSelectedParts:
geneSelectedId += part
identifier = 'testgene_' + str(i) + ' Isoform_' + geneSelectedId
thisGeneName, seq = makeRandomTestData.generateIsoforms(identifier, genes[geneSelected], 'random', 0, 0, 0, min, max)
genes[thisGeneName] = seq
else:
thisGeneName = 'testgene_' + str(i) + ' ' + randomTrans
genes[thisGeneName] = makeRandomTestData.makeKmerCountData(random.randint(101, 4999), 'default')
complete = makeRandomTestData.outputFastaSeq(randomTrans + '.fa', thisGeneName, genes[thisGeneName])
infileName = randomTrans + '.fa'
filename = 'DataSet' + name
genes = makeRandomTestData.inputFastaSeq(infileName)
errors = 1
if makeRandomTestData.checkForFasta(filename + 'E1R100G100.fa'):
x = os.remove(filename + 'E1R100G100.fa')
if makeRandomTestData.checkForFasta(filename + 'E1R100G100RandomReads.fa'):
x = os.remove(filename + 'E1R100G100RandomReads.fa')
if makeRandomTestData.checkForFasta(filename + 'E1R100G100RandomReads.txt'):
x = os.remove(filename + 'E1R100G100RandomReads.txt')
if makeRandomTestData.checkForFasta(filename + 'E1R90G100.fa'):
x = os.remove(filename + 'E1R90G100.fa')
import makeRandomTestData, os, random
genes = {}
name = '241rep2'
filename = 'DataSet' + name
numGenesMake = 5000
for i in range(0, numGenesMake):
key = 'testgene_' + str(i) + ' '
genes[key] = makeRandomTestData.makeKmerCountData(random.randint(101,4999), 'default')
errors = 1
if makeRandomTestData.checkForFasta(filename + 'E1R100G100.fa'):
x = os.remove(filename + 'E1R100G100.fa')
if makeRandomTestData.checkForFasta(filename + 'E1R100G100RandomReadsPair1.fa'):
x = os.remove(filename + 'E1R100G100RandomReadsPair1.fa')
if makeRandomTestData.checkForFasta(filename + 'E1R100G100RandomReadsPair2.fa'):
x = os.remove(filename + 'E1R100G100RandomReadsPair2.fa')
if makeRandomTestData.checkForFasta(filename + 'E1R100G100RandomReads.txt'):
x = os.remove(filename + 'E1R100G100RandomReads.txt')
count = 0
count2 = 0
readLength = 100
insertSize = 50
coverage = 20
numGenes = len(genes)
for key in genes:
thisGeneName = key
if len(genes[thisGeneName]) > readLength:
