[Biopython] Passing sequence to local BLAST

[Sheila the angel]

Thanks Peter,
Yes I understand that I can't use 'stdin' twice so this is not going to work

>>> water_cline = WaterCommandline(asequence="stdin",
bsequence="stdin",gapopen=10, gapextend=0.5, outfile="water.txt")
>>> stdout, stderr =water_cline(stdin=seq_record.format("fasta"),
stdin=seq_record2.format("fasta"))

>You have to use either two input files, or stdin and one file, (or one
>file and stdin).

But how can I specify two input files, or stdin


On Thu, Jul 21, 2011 at 11:40 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Thu, Jul 21, 2011 at 10:14 AM, Sheila the angel
> <from.d.putto at gmail.com> wrote:
> > yes replacing '-' by 'stdin' works :)
> >
> > seq_record = SeqIO.read(open("alpha.fasta"), "fasta")  #or a sequence
> object
> > water_cline = WaterCommandline(asequence="stdin", bsequence="beta.fasta",
> > gapopen=10, gapextend=0.5, outfile="water.txt")
> > stdout, stderr =water_cline(stdin=seq_record.format("fasta"))
>
> Good - thanks for letting us know.
>
> I can probably make the tutorial text a little clearer here.
>
>
> > but I tried to replace bsequence also by 'stdin' and it shows error
> >
> #----------------------------------------------------------------------------------------------------------------------
> > seq_record = SeqIO.read(open("alpha.fasta"), "fasta")  #or a sequence
> object
> > seq_record2 = SeqIO.read(open("beta.fasta"), "fasta")
> > water_cline = WaterCommandline(asequence="stdin", bsequence="stdin",
> > gapopen=10, gapextend=0.5, outfile="water.txt", auto=True)
>
> That won't work - there is only one stdin pipe in a Unix style command
> line environment.
> You have to use either two input files, or stdin and one file, (or one
> file and stdin).
>
> > stdout, stderr =water_cline(stdin=seq_record.format("fasta"),
> > stdin=seq_record2.format("fasta"))
> > #  File "<stdin>", line 1 # <the error msg.
> > #SyntaxError: keyword argument repeated
>
> That is a python syntax error message because you tried to use the stdin
> argument twice. Named Python function arguments can only be used once.
>
> I hope that makes sense.
>
> Peter
>