[Biopython] Piping in and out of clustal

[Ivan Gregoretti]

I'll take a look at the examples. Thank you.

Ivan



Ivan Gregoretti, PhD


On Thu, Mar 28, 2013 at 12:28 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Thu, Mar 28, 2013 at 4:13 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
>> Indeed, from the command line I pipe in and out of clustal regularly.
>> I do it like this:
>>
>> zcat input_big.fa.gz | clustalo -i /dev/stdin -o /dev/stdout | pigz -9
>>> output_big.fa.gz
>>
>> This suggestion of yours "stdout,stderr = clustalo_cline(stdin)" is
>> what I am looking for.
>>
>> Would some good-hearted Biopythonian around the world share a code
>> snippet using this strategy? I'm curious to see how people pass one by
>> one their SeqRecords to properly formatted strings in memory. I'm
>> guessing that it is a very common task.
>>
>> Anyone?
>
> You will probably want/need the StringIO module for preparing input
> or using the output (i.e. going between strings and handles).
>
> There are some more complicated examples using alignment tools
> via the subprocess module in the Tutorial - trying to avoid temp
> files and large strings in memory.
>
> Peter