def run(self): logger.info('CycleStep2 object running, %s' % self.thisDir) lsc.verifyDirExists(self.thisDir) lsc.createTimestamp(os.path.join(self.thisDir, 'xml', 'cycle.step2.start.xml')) lsc.verifyDirExists(os.path.join(self.thisDir, 'inter')) lsc.verifyFileExists(os.path.join(self.thisDir, 'inter', 'inter.chrnames.txt')) f = open(os.path.join(self.thisDir, 'inter', 'inter.chrnames.txt'), 'r') for chrom in f: chrom = chrom.strip() self.addChildTarget(CycleStep2Chromosome(self.thisNewickStr, self.thisParentDir, self.thisStepLength, chrom, self.options)) f.close() self.setFollowOnTarget(CycleStep2FollowOn(self.thisNewickStr, self.thisParentDir, self.thisStepLength, self.options))
def checkForFiles(options): """ If files are missing, complains and dies. """ lsc.verifyDirExists(os.path.join(options.rootInputDir, 'stats')) for f in [os.path.join(options.rootInputDir, 'seq.rev'), os.path.join(options.rootInputDir, 'annots.gff'), os.path.join(options.paramsDir, 'model.txt'), os.path.join(options.rootInputDir, 'stats', 'merged_root.stats.txt'), os.path.join(options.rootInputDir, 'stats', 'cds_annots.gff'), os.path.join(options.rootInputDir, 'stats', 'exons.gff'), os.path.join(options.rootInputDir, 'stats', 'introns.gff'), os.path.join(options.rootInputDir, 'stats', 'expanded_annots.gff'), os.path.join(options.rootInputDir, 'stats', 'annotstats.txt')]: lsc.verifyFileExists(f) if not options.noMEs: lsc.verifyDirExists(os.path.join(options.rootInputDir, 'mobiles')) for f in [os.path.join(options.paramsDir, 'model.mes.txt'), os.path.join(options.paramsDir, 'mes.cfg'), os.path.join(options.rootInputDir, 'mobiles', 'LTR.fa'), os.path.join(options.rootInputDir, 'mobiles', 'ME.fa'), os.path.join(options.rootInputDir, 'mobiles', 'ME.gff')]: lsc.verifyFileExists(f)