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)