init.init(args, version) # logging import log args.logfilename = 'for_debug.log' if os.path.exists(os.path.join(args.outdir, args.logfilename)) is True: os.remove(os.path.join(args.outdir, args.logfilename)) log.start_log(args) log.logger.debug('Logging started.') # initial check import initial_check print() log.logger.info('You are using version "%s"' % version) log.logger.info('Initial check started.') initial_check.check(args, sys.argv, init.base) # set up import setup setup.setup(args, init.base) params = setup.params # output file names import utils filenames = utils.empclass() filenames.discordant_bam = os.path.join(args.outdir, 'discordant.bam') filenames.discordant_sort_bam = os.path.join(args.outdir, 'discordant_sorted.bam') filenames.unmapped_1 = os.path.join(args.outdir, 'unmapped_1.fq') filenames.unmapped_2 = os.path.join(args.outdir, 'unmapped_2.fq')
init.init(args, version) # logging import log args.logfilename = 'for_debug.log' if os.path.exists(os.path.join(args.outdir, args.logfilename)) is True: os.remove(os.path.join(args.outdir, args.logfilename)) log.start_log(args) log.logger.debug('Logging started.') # initial check import initial_check log.logger.debug('This is version %s' % version) print() log.logger.info('Initial check started.') initial_check.check(args, sys.argv) # set up import setup setup.setup(args, init.base) params = setup.params # output file names import utils filenames = utils.empclass() filenames.summary = os.path.join(args.outdir, 'kmer_counts.txt') # 1. K-mer count import kmer_count_rel_ref_hervk_norm log.logger.info('K-mer counting started.') kmer_count_rel_ref_hervk_norm.calc_depth_coeff(args, params)