[Bioperl-l] Problem with StandAloneBlastPlus

[Mark A. Jensen]

Ok Dario,
This should be fixed in the master branch -- you need the fixes in both 
bioperl-live and bioperl-run.

  -method_args => [ '-outfmt' => '"7 std qcovs"' ]

should work now, and also the standard factory argument:

  -outformat => '"7 std qcovs"'

(and, as it turns out

  -outformat => '7 std qcovs'

should work. That's a longer story.)

Pls try and let us know-

MAJ

On 2014-07-23 12:13, Fields, Christopher J wrote:
> 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 [9]>
> wrote:
>
>> This is a bug, and fairly deep. I have made
>> https://github.com/bioperl/bioperl-run/issues/12 [6].
>> (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 [4]
>>> [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 [1]
>>>> > http://mailman.open-bio.org/mailman/listinfo/bioperl-l [2]
>>>> >
>>>> -----BEGIN PGP SIGNATURE-----
>>>> Version: GnuPG v1
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>>>> iD8DBQFTzVHiF9UIceSIYeoRAmLRAJsFCbynO5sZ8FWb8zAOtSVHTMKTDgCfeG3c
>>>> 356E0nxLltTzB+msEwRJ5ZY=
>>>> =5Y5m
>>>> -----END PGP SIGNATURE-----
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>>>
>>> Links:
>>> ------
>>> [1] mailto:abelew at gmail.com [5]
>>
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>
>
>
> Links:
> ------
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> [5] mailto:abelew at gmail.com
> [6] https://github.com/bioperl/bioperl-run/issues/12
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