[Biopython-dev] Alignment problem. bug?

[Sebastian Bassi]

I would like to confirm that this is a bug ot not. If I get
confirmation, I would fill it in bugzilla.

With this code:

from Bio import Clustalw
from Bio.Clustalw import MultipleAlignCL

cline = MultipleAlignCL('foralig.txt')
cline.set_output("alig.aln")
alignment = Clustalw.do_alignment(cline)

I get:

Traceback (most recent call last):
  File "/mnt/hda2/py252/bin/ii.py", line 112, in <module>
    alignment = Clustalw.do_alignment(cline)
  File "/mnt/hda2/py252/lib/python2.5/site-packages/Bio/Clustalw/__init__.py",
line 125, in do_alignment
    return parse_file(out_file, alphabet)
  File "/mnt/hda2/py252/lib/python2.5/site-packages/Bio/Clustalw/__init__.py",
line 47, in parse_file
    generic_alignment = AlignIO.read(handle, "clustal")
  File "/mnt/hda2/py252/lib/python2.5/site-packages/Bio/AlignIO/__init__.py",
line 299, in read
    first = iterator.next()
  File "/mnt/hda2/py252/lib/python2.5/site-packages/Bio/AlignIO/ClustalIO.py",
line 169, in next
    raise ValueError("Could not parse line:\n%s" % line)
ValueError: Could not parse line:


I tested with Biopython 1.47 and 1.46 with the input file:
http://www.pastecode.com.ar/f44f28b41 (download at
http://www.pastecode.com.ar/pastebin.php?dl=f44f28b41)
The clustal program is running because I see in the disk its output
(posted here: http://www.pastecode.com.ar/f275a5475). It seems it
fails to parse it.

I also tested in an older version (I guess it is 1.44) and it works
OK. So I think the problem was introduced in 1.46.


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