[Biopython] error writing fasta file using SeqIO

[A M Torres, Hugo]

Hi folks.

Thanks once again for helping me out. That problem is solved. I took a look
at the glob module. It is really just neat!

A new problem has arised when I try to call the process that should run the
sequence alignment. I try to use the 'needle' subprocess but it fails with
this error: http://paste.pound-python.org/show/9395/.

Here is how the code looks now: http://paste.pound-python.org/show/9394/.

The weird thing is needle executes ok when I use needle_cline as it is in a
bash shell. I took care to write full paths when pointing to individual
files and the needle binary but that hasn't solved the error.

Any clues?

On Fri, Jul 8, 2011 at 1:46 AM, Wibowo Arindrarto <w.arindrarto at gmail.com>wrote:

> Hi Hugo,
>
> I think the problem is you tried to concatenate a SeqRecord object and a
> string object. Do this in 'salva_fasta' instead:
>
> SeqIO.write([obj_SeqRecord], obj_SeqRecord.id + '.fasta', 'fasta')
>
> And just as an additional input, in the 'processar_lote' method, you can
> use this to generate a list of absolute file name paths (import the os and
> glob module beforehand).
>
> files = [os.path.abspath(x) for x in glob.glob('*.ab1')]
>
> os.path.abspath() returns the absolute file path for a given file, and
> glob.glob() returns a list of names that matches the given pattern.
>
> Hope that helps!
> ---
> Wibowo Arindrarto (bow)
> http://bow.web.id
>
>
>
>