[Biopython] AssertionError
Pierre-Yves
pingou at pingoured.fr
Wed Jul 21 09:22:12 UTC 2010
On Wed, 2010-07-21 at 10:17 +0100, Peter wrote:
> If seq is a SeqRecord (a variable name I avoid),
Changed.
> then seq.seq is
> a Seq object, and slicing a Seq object gives another Seq object.
> This means you shouldn't do this:
>
> Seq(seq.seq[start:stop], generic_dna)
>
> Just do this:
>
> seq.seq[start:stop]
Indeed:
seq_out = SeqRecord( seq_record.seq[start:stop],
id = row[col_name]
)
just works.
> >
> > 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
>
> That should be a clearer error message, the Seq object is not
> expecting you to give it a Seq object - but a string or unicode.
A clearer error message would indeed be nice.
Pierre
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