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)