... help . ... 1.6 + 1.7 +All position indexes are counting from 1. 1.8 + 1.9 + import optparse 1.10 + import sys 1.11 + import os 1.12 +from allpy import protein 1.13 + 1.14 +def main(): 1.15 + alignment = protein. Alignment .from_fasta(open(options.in_file)) 1.16 + if not options.begin: 1.17 + options.begin = 1 1.18 + if not options. end : 1.19 + options. end = len( alignment .columns) 1.20 + columns = ...