[Biopython] Displaying pairwise2 output fails.

[Ivan Gregoretti]

Hello Biopythonians,

Are you able to display pairwise alignments? It fails in my system:

from Bio import pairwise2
for a in pairwise2.align.globalxx("ACCGT", "ACG"):
    print format_alignment(*a)

Traceback (most recent call last):
  File "<stdin>", line 2, in <module>
NameError: name 'format_alignment' is not defined

Notice that the commands above are just a copy/paste of its docstring.
It should have produced something like this

ACCGT
|||||
AC-G-
  Score=3
<BLANKLINE>
ACCGT
|||||
A-CG-
  Score=3
<BLANKLINE>

My system information (Fedora 18):
Python 2.7.3 (default, Aug  9 2012, 17:23:57)
[GCC 4.7.1 20120720 (Red Hat 4.7.1-5)] on linux2
and Biopython 1.61.

Any help would be appreciated.

Ivan



Ivan Gregoretti, PhD
Bioinformatics