[Biopython-dev] BWA Wrapper

[Saket Choudhary]

I was thinking of adding one more parameter to the _call function, lets say
'stdout_to_filepath'.
If this is set then I add one more if condition
here<https://github.com/saketkc/biopython/blob/master/Bio/Application/__init__.py#L415>
to set the stdout as


stdout_arg = open(stdout_to_filepath, "w")

I tried it and it did work, but I am not sure if it  this standard can be
incorporated in the biopython codebase ?

Thanks

Saket

On 14 February 2013 21:49, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, Feb 14, 2013 at 4:02 PM, Saket Choudhary <saketkc at gmail.com>
> wrote:
> > Theres one more issue that I have run into . Consider the following
> command
> > , the outout generated is written by piping it to a file called
> aln_sa.sai,
> >
> > bwa aln database.fasta short_read.fastq > aln_sa.sai
> >
> > Now if we look into the _call method here , it takes as its inout a
> boolean
> > for stdout. So should I modify this so that it can take 'stdout' as on
> > opened file  instance which I can invoke while unvoking my
> BwaAlnCommandLine
> > functions as follwos:
> >
> > a=BwaAlnCommandLine()
> > b=a(stdout=open("aln_sa.sai","wb"))
>
> Is that possible?
>
> For complex use of subprocess and pipes, we've previously recommend
> the user handle this explicitly themselves, just use str() on the command
> line wrapper object to get 'bwa aln database.fasta short_read.fastq' in
> this
> case. There are some examples in the Tutorial with (multiple sequence)
> alignment tools.
>
> Peter
>