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()