1.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     1.2 +++ b/utils/realign_block.py	Tue Feb 15 20:29:48 2011 +0300
     1.3 @@ -0,0 +1,49 @@
     1.4 +#!/usr/bin/python
     1.5 +"""Realign given part of alignment.
     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 +from allpy.processors import Muscle
    1.14 +
    1.15 +def main():
    1.16 +    alignment = protein.Alignment().append_file(open(options.in_file))
    1.17 +    if not options.begin:
    1.18 +        options.begin = 1
    1.19 +    if not options.end:
    1.20 +        options.end = len(alignment.columns)
    1.21 +    columns = alignment.columns[options.begin-1:options.end]
    1.22 +    block = protein.Block.from_alignment(alignment, columns=columns)
    1.23 +    block.process(Muscle)
    1.24 +    alignment.to_file(open(options.out_file, "w"))
    1.25 +    if options.msf:
    1.26 +        os.system("seqret " + options.out_file + " msf::" + options.out_file.split(".")[0] + ".msf")
    1.27 +        os.system("rm " + options.out_file)
    1.28 +
    1.29 +if __name__ == "__main__":
    1.30 +    usage = "Usage: %s [options]\n\n%s" % (sys.argv[0], __doc__.strip())
    1.31 +    parser = optparse.OptionParser(usage=usage)
    1.32 +    parser.add_option("-i", "--in-file",
    1.33 +        help="Input alignment file (in FASTA format)")
    1.34 +    parser.add_option("-o", "--out-file",
    1.35 +        help="Output file")
    1.36 +    parser.add_option("-b", "--begin", type=int,
    1.37 +        help="Position in alignment to start from")
    1.38 +    parser.add_option("-e", "--end", type=int,
    1.39 +        help="Position in alignment to end with")
    1.40 +    parser.add_option("-m", "--msf", action='store_true',
    1.41 +        help="Output in MSF format (FASTA by default)")
    1.42 +
    1.43 +    options, args = parser.parse_args()
    1.44 +
    1.45 +    if args:
    1.46 +        parser.error("We take no positional arguments.")
    1.47 +    if not options.in_file or not options.out_file:
    1.48 +        parser.error("Both -i and -o parameters must be given.")
    1.49 +
    1.50 +    main()
    1.51 +
    1.52 +# vim: set et ts=4 sts=4 sw=4: