import makeRandomTestData, os, random genes = {} name = '245rep3' infileName = 'Gallus_gallus.WASHUC2.63.cdna.all.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 + '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') if makeRandomTestData.checkForFasta(filename + 'E1R90G100.fa'): x = os.remove(filename + 'E1R90G100.fa') if makeRandomTestData.checkForFasta(filename + 'E1R80G100.fa'): x = os.remove(filename + 'E1R80G100.fa') if makeRandomTestData.checkForFasta(filename + 'E1R70G100.fa'): x = os.remove(filename + 'E1R70G100.fa') if makeRandomTestData.checkForFasta(filename + 'E1R60G100.fa'): x = os.remove(filename + 'E1R60G100.fa') if makeRandomTestData.checkForFasta(filename + 'E1R50G100.fa'): x = os.remove(filename + 'E1R50G100.fa') if makeRandomTestData.checkForFasta(filename + 'E1R40G100.fa'): x = os.remove(filename + 'E1R40G100.fa') if makeRandomTestData.checkForFasta(filename + 'E1R30G100.fa'): x = os.remove(filename + 'E1R30G100.fa')
import makeRandomTestData, os, random genes = {} name = '278rep2' infileName = 'Mus_musculus.NCBIM37.65.cdna.all.fa' filename = 'DataSet' + name genes = makeRandomTestData.inputFastaSeq(infileName) errors = 0 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 readLength = 100 insertSize = 400 totalReadLength = readLength * 2 + insertSize numGenes = len(genes) for key in genes: thisGeneName = key if len(genes[thisGeneName]) > totalReadLength: complete = makeRandomTestData.outputFastaSeq(filename + 'E1R100G100.fa', thisGeneName, genes[thisGeneName]) level = 20 complete = makeRandomTestData.makeRandomlyPlacedPairedEndReads(genes[thisGeneName], thisGeneName, readLength, insertSize, level, filename + 'E1R100G100RandomReadsPair1.fa', filename + 'E1R100G100RandomReadsPair2.fa', filename + 'E1R100G100RandomReads.txt', errors, 0)
import makeRandomTestData, os, random genes = {} name = '183rep3' numTranscripts = 5000 randomTrans = 'Random.' + str(numTranscripts) + '.' + name isoformProb = 10 min = 100 max = 5000 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)
import makeRandomTestData, os, random genes = {} name = "201rep3" infileName = "Mus_musculus.NCBIM37.65.cdna.all.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") if makeRandomTestData.checkForFasta(filename + "E1R80G100.fa"): x = os.remove(filename + "E1R80G100.fa") if makeRandomTestData.checkForFasta(filename + "E1R70G100.fa"): x = os.remove(filename + "E1R70G100.fa") if makeRandomTestData.checkForFasta(filename + "E1R60G100.fa"): x = os.remove(filename + "E1R60G100.fa") if makeRandomTestData.checkForFasta(filename + "E1R50G100.fa"): x = os.remove(filename + "E1R50G100.fa") count = 0 readLength = 100 numGenes = len(genes) r90 = int(numGenes * 0.9) r80 = int(numGenes * 0.8)