index_table[n] = index inverse_table[index] = n index += 1 ### Retreiving sequence seq_dict = {} if BIOPY_AVAIL : for record in SeqIO.parse(cocntig_file, "fasta"): ID = record.seq seq = str(record.seq) seq_dict[ID] = seq else: parser = FAParser(args.contig_file) parser.open() for id , seq in parser.parse() : seq_dict[id] = seq ### Then k-mersize and insert into differenct list using indexes num_contigs = len(seq_dict.keys()) seq_ids = seq_dict[keys] index_set = [ [None] for _ in xrange(len(seq_ids)) ] for i , val in enumerate(seq_ids) : seq = seq_dict[val] for j in xrange(len(seq)-ksize): kmer = seq[j:j+ksize] idx = index_table[kmer]
# -*- coding: utf-8 -*- from __future__ import unicode_literals from argparse import ArgumentParser, SUPPRESS from parser import Parser version = '0.0.1' description = """\ Simple Calculator. """ if __name__ == '__main__': parser = ArgumentParser(description='Calculate result of simple mathematical operations', argument_default=SUPPRESS) parser.add_argument('--question', help='String with operations to calculate. Note that ' 'numbers like -7 will be -7 but numbers like +7 ' 'will be 7. Use spaces to separate numbers from' ' signs.') args = parser.parse_args() parser = Parser() parser.open(args.question) parser.read() print(parser.compute())