allpy: b556c96c6719 utils/case_to

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
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1 #!/usr/bin/python

2 import os

3 import sys

4 from allpy import protein, markups

7 self, keyword = sys.argv

8 assert keyword == "-s"

9 except Exception:

10 self = os.path.basename(sys.argv[0])

11 print "Usage: %s -s < infile.markup > outfile.fasta" % self

12 print ""

13 print "Accept input alignment in markup format on stdin."

14 print "Print the alignment to stdout in fasta format with case preserved."

15 sys.exit(1)

17 infile = sys.stdin

18 outfile = sys.stdout

20 aln = protein.Alignment().append_file(infile, format='markup')

22 for seq in aln.sequences:

23 for monomer in seq:

24 if monomer.case == 'lower':

25 monomer.code1 = monomer.code1.lower()

26 else:

27 monomer.code1 = monomer.code1.upper()

29 aln.to_file(outfile)

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