[Bioperl-l] Problem with StandAloneBlastPlus

Tue Jul 29 16:16:53 UTC 2014

You’re right, it was the comma. Sorry!

  _____  

De: bioperl-l-bounces+dcarball=tandar.cnea.gov.ar at mailman.open-bio.org
[mailto:bioperl-l-bounces+dcarball=tandar.cnea.gov.ar at mailman.open-bio.org]
En nombre de Mark A Jensen
Enviado el: martes, 29 de julio de 2014 0:57
Para: Darío Carballido
CC: bioperl-l at mailman.open-bio.org
Asunto: Re: [Bioperl-l] Problem with StandAloneBlastPlus

Dario, looking just at the error message,I think you might be missing a
comma in the list of params before -outformat.

On Mon, Jul 28, 2014 at 1:15 PM, Darío Carballido
<dcarball at tandar.cnea.gov.ar> wrote:

Hello Mark, 

When using 

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

It worked perfectly. When using 

-outformat => '"7 std qcovs"' (or '7 std qcovs') 

I got this: 

Argument "outformat" isn't numeric in subtraction (-) at 
./new_orthoparahomlist.pl line 180. 
Can't use string ("46534816") as an ARRAY ref while "strict refs" in use at 
/usr/local/share/perl/5.14.2/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.

pm line 236. 

BlastMethods.pm has been updated properly (I checked before writing). 

Thanks for your help, 

Darío Carballido 

-----Mensaje original----- 
De: bioperl-l-bounces+dcarball=tandar.cnea.gov.ar at mailman.open-bio.org 
[mailto:bioperl-l-bounces+dcarball=tandar.cnea.gov.ar at mailman.open-bio.org] 
En nombre de Mark A. Jensen 
Enviado el: sábado, 26 de julio de 2014 0:06 
Para: bioperl-l at mailman.open-bio.org 
Asunto: Re: [Bioperl-l] Problem with StandAloneBlastPlus 

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 
>>>> 
>>>> iD8DBQFTzVHiF9UIceSIYeoRAmLRAJsFCbynO5sZ8FWb8zAOtSVHTMKTDgCfeG3c 
>>>> 356E0nxLltTzB+msEwRJ5ZY= 
>>>> =5Y5m 
>>>> -----END PGP SIGNATURE----- 
>>>> _______________________________________________ 
>>>> Bioperl-l mailing list 
>>>> Bioperl-l at mailman.open-bio.org [3] 
>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l 
>>> 
>>> Links: 
>>> ------ 
>>> [1] mailto:abelew at gmail.com [5] 
>> 
>> _______________________________________________ 
>> Bioperl-l mailing list 
>> Bioperl-l at mailman.open-bio.org [7] 
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l [8] 
> 
> 
> 
> Links: 
> ------ 
> [1] mailto:Bioperl-l at mailman.open-bio.org 
> [2] http://mailman.open-bio.org/mailman/listinfo/bioperl-l 
> [3] mailto:Bioperl-l at mailman.open-bio.org 
> [4] mailto:abelew at gmail.com 
> [5] mailto:abelew at gmail.com 
> [6] https://github.com/bioperl/bioperl-run/issues/12 
> [7] mailto:Bioperl-l at mailman.open-bio.org 
> [8] http://mailman.open-bio.org/mailman/listinfo/bioperl-l 
> [9] mailto:maj at fortinbras.us 

_______________________________________________ 
Bioperl-l mailing list 
Bioperl-l at mailman.open-bio.org 
http://mailman.open-bio.org/mailman/listinfo/bioperl-l 
----- 
Se certificó que el correo no contiene virus. 
Comprobada por AVG - www.avg.es 
Versión: 2014.0.4716 / Base de datos de virus: 3986/7918 - Fecha de la 
versión: 07/25/2014 

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

  _____  

Se certificó que el correo no contiene virus.
Comprobada por AVG - www.avg.es
Versión: 2014.0.4716 / Base de datos de virus: 3986/7937 - Fecha de la
versión: 07/28/2014

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/bioperl-l/attachments/20140729/c84a6bd8/attachment.html>