[Biopython] error writing fasta file using SeqIO

[Wibowo Arindrarto]

Hi Hugo,

I think you should pass 'alinhar' as the argument for subprocess.call()
instead of 'needle_cline'. You can use the 'needle_cline' for the argument,
but you should also set shell to true, so the command
is subprocess.call(needle_cline, shell=True).

Hope that helps.
---
Wibowo Arindrarto (bow)
http://bow.web.id



On Mon, Jul 11, 2011 at 08:22, A M Torres, Hugo <
mnemonico at posthocergopropterhoc.net> wrote:

> 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
>>
>>
>>
>>
>