[Bioperl-l] Problem with StandAloneBlastPlus

[Fields, Christopher J]

Yep, that’s where to send it.  I’ll post an official (belated) announcement.

chris

On Jul 22, 2014, at 10:38 PM, Mark A. Jensen <maj at fortinbras.us<mailto:maj at fortinbras.us>> wrote:

This is a bug, and fairly deep. I have made https://github.com/bioperl/bioperl-run/issues/12.
(I hope that's what we do around here now...)
cheers MAJ

On 2014-07-21 15:24, Mark A Jensen wrote:
Almost positive this will require a mod in SABP. I will try to have a
look. MAJ

On Mon, Jul 21, 2014 at 1:54 PM, Ashton Trey Belew <abelew at gmail.com<mailto:abelew at gmail.com>
[1]> wrote:

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello Dario,
Below is a portion of a little script which I use for
StandAloneBlast and which uses -m 7. It doesn't exactly answer your

question, but I hope it will be similar enough to prove helpful.
My ignorant thought is that you can modify my use of -m to suit
your
purpose; but after rereading your message I am guessing you already

tried something similar.
-Trey

my @params = (-program => 'blastn', -b => $max_hits,
-I => 't', -a => $processors,
-database => $library_db, -m => 7,);

my $query_count = 0;
while (my $query_seq = $query_library->next_seq()) {
$query_count++;
my $search = new Bio::Tools::Run::StandAloneBlast(
-_READMETHOD => 'blastxml', @params);
$search->m(7);
my $blast_output = new Bio::SearchIO(
-format => 'blastxml', -verbose => 1,);
$blast_output = $search->blastall($query_seq,
-format=>'blastxml', -verbose => 1,);
my $result_count = 0;
while (my $result = $blast_output->next_result()) {
## Collect alignments
} ## End of results by query
} ## End of queries

On 07/21/2014 11:57 AM, Darío Carballido wrote:
> Hello,
>
>
>
> I’m working with this script that uses StandAloneBlastPlus, and
I
> would like to take advantage of a new feature in the latest
> releases of blast+, which allows me to present the query coverage

> in the output (among other values). For that to work, the value
of
> –outfmt needs to be quoted (for example, -outfmt “7 std
qcovs”), so
> I’m passing the outfmt parameter via
>
>
>
> -method_args => [ '-outfmt' => '"7 std qcovs"' ]
>
>
>
> (I’m using single quotes with doubles inside, so that the
double
> quotes are passed literally).
>
>
>
> But when I run it, the quotes seem to get lost and I end up with
> the error I get when I pass that value without the quotes:
>
>
>
> Error: Too many positional arguments (1), the offending value:
std
>
>
>
>
> I have tried lots of combinations with single, double quotes,
> character escaping and I couldn’t find the way to make it work.

>
>
>
> Any help?
>
>
>
> Thanks,
>
> Darío Carballido
>
>
>
> _______________________________________________ Bioperl-l mailing

> list Bioperl-l at mailman.open-bio.org<mailto:Bioperl-l at mailman.open-bio.org>
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1

iD8DBQFTzVHiF9UIceSIYeoRAmLRAJsFCbynO5sZ8FWb8zAOtSVHTMKTDgCfeG3c
356E0nxLltTzB+msEwRJ5ZY=
=5Y5m
-----END PGP SIGNATURE-----
_______________________________________________
Bioperl-l mailing list
Bioperl-l at mailman.open-bio.org<mailto:Bioperl-l at mailman.open-bio.org>
http://mailman.open-bio.org/mailman/listinfo/bioperl-l


Links:
------
[1] mailto:abelew at gmail.com

_______________________________________________
Bioperl-l mailing list
Bioperl-l at mailman.open-bio.org<mailto:Bioperl-l at mailman.open-bio.org>
http://mailman.open-bio.org/mailman/listinfo/bioperl-l

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/bioperl-l/attachments/20140723/ac35e964/attachment.html>