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: