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

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

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

           Summary: AlignInfo.py fails a test
           Product: Biopython
           Version: 1.46
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: sbassi at gmail.com


When I run:

$ python2.5 /mnt/hda2/bio/biopython-1.47/Bio/Align/AlignInfo.py

I get the first 2 test OK but then:

Traceback (most recent call last):
  File "/mnt/hda2/bio/biopython-1.47/Bio/Align/AlignInfo.py", line 723, in
<module>
    print summary.information_content()
  File "/mnt/hda2/bio/biopython-1.47/Bio/Align/AlignInfo.py", line 508, in
information_content
    raise ValueError, errstr
ValueError: Error in alphabet: not Nucleotide or Protein, supply expected
frequencies

I've also tried without the AlignIO:

from Bio import Alphabet
from Bio.Align.Generic import Alignment
from Bio.Seq import Seq
from Bio.Align.AlignInfo import SummaryInfo
seq1 = 'MHQAIFIYQIGYPLKSGYIQSIRSPEYDNW'
seq2 = 'MH--IFIYQIGYALKSGYIQSIRSPEY-NW'
a = Alignment(Alphabet.ProteinAlphabet)
a.add_sequence("asp",seq1)
a.add_sequence("unk",seq2)
summary = SummaryInfo(a)
summary.information_content()

Traceback (most recent call last):
  File "/mnt/hda2/py252/bin/align.py", line 16, in <module>
    summary.information_content()
  File "/mnt/hda2/py252/lib/python2.5/site-packages/Bio/Align/AlignInfo.py",
line 508, in information_content
    raise ValueError, errstr
ValueError: Error in alphabet: not Nucleotide or Protein, supply expected
frequencies


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