[Biopython-dev] [Bug 2542] AlignInfo.py fails a test

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2542





------- Comment #4 from sbassi at gmail.com  2008-07-11 17:00 EST -------
(In reply to comment #1)
> First problem, you gave the Alignment object an Alphabet class, rather than an
> instance of the class.  I guess we should an explicit check to the Alignment
> object...

Yes, that is my fault.

> You mentioned having a similar issue with Bio.AlignIO - could you attached the
> example file to this bug with some trivial code showing your problem?

Yes, this code with Bio.AlignIO also fails (I tried right now with AlignInfo.py
rev. 1.17):

from Bio.Align import AlignInfo
from Bio.Align.AlignInfo import SummaryInfo
from Bio import AlignIO
fn = open("secu3.aln")
alignment = AlignIO.read(fn, "clustal")
summary = SummaryInfo(alignment)
print summary.information_content()

And I got (and this time I am not supplying any alphabet, at least not
explicit):

Traceback (most recent call last):
  File "/mnt/hda2/py252/bin/2542.py", line 12, in <module>
    print summary.information_content()
  File "/mnt/hda2/py252/lib/python2.5/site-packages/Bio/Align/AlignInfo.py",
line 499, in information_content
    raise ValueError, errstr
ValueError: Error in alphabet: not Nucleotide or Protein, supply expected
frequencies

> P.S. Please update to Biopython 1.47 rather than using 1.46

I was using Biopython 1.47, but I reported as 1.46 just because 1.47 it is not
available from the drop-down menu in bugzilla form.


> 


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