[Biopython] AssertionError

[Pierre-Yves]

Hi,

I am running into a problem which I can't figure why.

I parse a fasta file using biopython:
for seq_record in SeqIO.parse(fastafile, "fasta"):
     if seq_record.id == name:
            print seq_record.id
            return seq_record

This seq_record becomes seq and I try to extract only a subpart of the
sequence:
s = Seq(seq.seq[start:stop], generic_dna)
seq_out = SeqRecord(s, id = row[col_name])

Print of start and stop shows me:
251944 253441
which is what I expect.

But the creation of the sequence object fails with the following error:
Traceback (most recent call last):
  File "FastaExtractor.py", line 91, in <module>
    s = Seq(seq.seq[start:stop], generic_dna)
  File "/usr/lib64/python2.6/site-packages/Bio/Seq.py", line 87, in
__init__
    type(data) == type(u""))  # but can be a unicode string
AssertionError

When I try to create an object by hand using the python consol, it works
perfectly well.
Any idea what could be wrong ?

Thanks,

Pierre