argv = docopt(__doc__)
if argv['seq']:
source_genome = argv['<reference>']
avg_quality = int(argv['--quality'])
if avg_quality < Sequencer.quality_min or avg_quality > Sequencer.quality_max:
raise ValueError(
"Average quality of nucleotides must be from {} to {}. Try again..."
.format(Sequencer.quality_min, Sequencer.quality_max))
coverage = float(argv['--coverage'])
if coverage < 0 or coverage > 2:
raise ValueError("Coverage must be real value from 0 to 2.")
print(
"Started sequencing with the average nucleotide quality of {} and the coverage of {}."
.format(avg_quality, coverage))
my_sequencer = Sequencer(source_genome, avg_quality, coverage)
my_sequencer.simulate()
print("The reads are ready! Check your folder...")
elif argv['cmp']:
my_comparator = Comparator(
argv['--aln_src'],
argv['<aln_trgt>'],
)
my_comparator.compare()
