1.1 --- a/pair_cores/compare_aln_3d.py	Wed Nov 02 19:44:22 2011 +0300
     1.2 +++ b/pair_cores/compare_aln_3d.py	Thu Nov 03 14:27:53 2011 +0300
     1.3 @@ -3,6 +3,7 @@
     1.4  import warnings
     1.5  import argparse
     1.6  from tempfile import NamedTemporaryFile
     1.7 +import sys
     1.8  
     1.9  from pair_cores import homology_from_3d
    1.10  from allpy.homology import MonomerHomology as MH
    1.11 @@ -47,15 +48,13 @@
    1.12              required=True, help='Second input alignment')
    1.13      p.add_argument('-f', '--format', default='fasta',
    1.14              help='Format of input alignments')
    1.15 -    p.add_argument('-o', '--out', type=argparse.FileType('w'), required=True,
    1.16 -            help='Output file with scores')
    1.17      p.add_argument('-d', '--delta', type=float, default=2.0,
    1.18              help='Distance spreading')
    1.19      p.add_argument('-c', '--cache', default='pdb_cache',
    1.20              help='Pdb cache directory')
    1.21      a = p.parse_args()
    1.22 -    compare_aln_3d(a=a.a_alignment, b=a.b_alignment, format=a.format, out=a.out,
    1.23 -            delta=a.delta, cache=a.cache)
    1.24 +    compare_aln_3d(a=a.a_alignment, b=a.b_alignment, format=a.format,
    1.25 +            out=sys.stdout, delta=a.delta, cache=a.cache)
    1.26  
    1.27  if __name__ == '__main__':
    1.28      try: