[Biopython] Passing sequence to local BLAST

[Peter Cock]

On Wednesday, July 20, 2011, Sheila the angel <from.d.putto at gmail.com> wrote:
> This method do not  work with Bio.Emboss.Applications!!!I am trying to do the same with 'Bio.Emboss.Applications' as
> seq_record = SeqIO.read(open("alpha.fasta"), "fasta")  #or a sequence object
> water_cline = WaterCommandline(asequence="-", bsequence="beta.fasta", gapopen=10, gapextend=0.5, outfile="water.txt")
> stdout, stderr =water_cline(stdin=seq_record.format("fasta"))
> but it is displaying error.How can I specify file handle or sequence only in  Emboss Applications???
>

What is the error message?

I think you need asequence="stdin" not "-" (although the later is a
widely used convention in command line tools). See:

http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html#stdin

Also try including auto=True in the command line, this tells EMBOSS
not to try and ask for user input (by default it will try and prompt
the user for any missing arguments, with the auto setting it uses it's
defaults).

Peter