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())
