allpy: b556c96c6719 utils/flush

allpy

blocks3d/www Makefile: never check certificates of github, they are too confusing for wget

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Mon, 26 May 2014 17:20:29 +0400
parents	efca47965dc3
children

line source

1 #!/usr/bin/python

2 """Flush all monomers in given range to the left, all gaps to the right.

4 All position indexes are counting from 1.

6 import optparse

7 import sys

8 import os

9 from allpy import protein

11 def main():

12 alignment = protein.Alignment().append_file(open(options.in_file))

13 if not options.begin:

14 options.begin = 1

15 if not options.end:

16 options.end = len(alignment.columns)

17 columns = alignment.columns[options.begin-1:options.end]

18 block = protein.Block.from_alignment(alignment, columns=columns)

19 block.flush("left")

20 alignment.to_file(open(options.out_file, "w"))

21 if options.msf:

22 os.system("seqret " + options.out_file + " msf::" + options.out_file.split(".")[0] + ".msf")

23 os.system("rm " + options.out_file)

25 if __name__ == "__main__":

26 usage = "Usage: %s [options]\n\n%s" % (sys.argv[0], __doc__.strip())

27 parser = optparse.OptionParser(usage=usage)

28 parser.add_option("-i", "--in-file",

29 help="Input alignment file (in FASTA format)")

30 parser.add_option("-o", "--out-file",

31 help="Output file")

32 parser.add_option("-b", "--begin", type=int,

33 help="Position in alignment to start from")

34 parser.add_option("-e", "--end", type=int,

35 help="Position in alignment to end with")

36 parser.add_option("-m", "--msf", action='store_true',

37 help="Output in MSF format (FASTA by default)")

39 options, args = parser.parse_args()

41 if args:

42 parser.error("We take no positional arguments.")

43 if not options.in_file or not options.out_file:

44 parser.error("Both -i and -o parameters must be given.")

46 main()

48 # vim: set et ts=4 sts=4 sw=4: