1.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     1.2 +++ b/utils/mass_realign_blocks.py	Tue Feb 15 21:03:19 2011 +0300
     1.3 @@ -0,0 +1,48 @@
     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 read_task(file):
    1.16 +    task = {}
    1.17 +    for line in file:
    1.18 +        line = line.rstrip("\n\r")
    1.19 +        filename, begin, end = line.split("\t")
    1.20 +        task[filename] = task.get(filename, [])
    1.21 +        task[filename].append((begin, end))
    1.22 +    return task
    1.23 +
    1.24 +def main():
    1.25 +    taks = read_task(open(options.task_file))
    1.26 +    for filename in task:
    1.27 +        with open(filename) as in_file:
    1.28 +            alignment = protein.Alignment().append_file(in_file)
    1.29 +        columns = []
    1.30 +        for begin, end in task[filename]:
    1.31 +            columns += alignment.columns[begin-1:end]
    1.32 +        block = protein.Block.from_alignment(alignment, columns=columns)
    1.33 +        block.process(Muscle)
    1.34 +        with open(filename, "w") as out_file:
    1.35 +            alignment.to_file(out_file)
    1.36 +
    1.37 +if __name__ == "__main__":
    1.38 +    usage = "Usage: %s [options]\n\n%s" % (sys.argv[0], __doc__.strip())
    1.39 +    parser = optparse.OptionParser(usage=usage)
    1.40 +    parser.add_option("-t", "--task-file",
    1.41 +        help="Task description file. Each line has filename, start position, end position, separated with tabs.")
    1.42 +    options, args = parser.parse_args()
    1.43 +
    1.44 +    if args:
    1.45 +        parser.error("We take no positional arguments.")
    1.46 +    if not options.task_file:
    1.47 +        parser.error("-t option is mandatory; see -h for help")
    1.48 +
    1.49 +    main()
    1.50 +
    1.51 +# vim: set et ts=4 sts=4 sw=4: