<p dir="ltr">Dario, looking just at the error message,I think you might be missing a comma in the list of params before -outformat.</p>
<br/><div class="cm_quote" style=" color: #787878">On Mon, Jul 28, 2014 at 1:15 PM, Darío Carballido <<a href="mailto:dcarball@tandar.cnea.gov.ar">dcarball@tandar.cnea.gov.ar</a>> wrote:</div><br><div id="oldcontent" style="background-color: rgb(255, 255, 255); background-position: initial initial; background-repeat: initial initial;"><blockquote style=""><p dir="ltr">Hello Mark,
<br>
<br>
When using
<br>
<br>
-method_args => [ '-outfmt' => '"7 std qcovs"' ]
<br>
<br>
It worked perfectly. When using
<br>
<br>
-outformat => '"7 std qcovs"' (or '7 std qcovs')
<br>
<br>
I got this:
<br>
<br>
Argument "outformat" isn't numeric in subtraction (-) at
<br>
./new_orthoparahomlist.pl line 180.
<br>
Can't use string ("46534816") as an ARRAY ref while "strict refs" in use at
<br>
/usr/local/share/perl/5.14.2/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.
<br>
pm line 236.
<br>
<br>
BlastMethods.pm has been updated properly (I checked before writing).
<br>
<br>
Thanks for your help,
<br>
<br>
Darío Carballido
<br>
<br>
-----Mensaje original-----
<br>
De: bioperl-l-bounces+dcarball=tandar.cnea.gov.ar@mailman.open-bio.org
<br>
[mailto:bioperl-l-bounces+dcarball=tandar.cnea.gov.ar@mailman.open-bio.org]
<br>
En nombre de Mark A. Jensen
<br>
Enviado el: sábado, 26 de julio de 2014 0:06
<br>
Para: bioperl-l@mailman.open-bio.org
<br>
Asunto: Re: [Bioperl-l] Problem with StandAloneBlastPlus
<br>
<br>
Ok Dario,
<br>
This should be fixed in the master branch -- you need the fixes in both
<br>
bioperl-live and bioperl-run.
<br>
<br>
-method_args => [ '-outfmt' => '"7 std qcovs"' ]
<br>
<br>
should work now, and also the standard factory argument:
<br>
<br>
-outformat => '"7 std qcovs"'
<br>
<br>
(and, as it turns out
<br>
<br>
-outformat => '7 std qcovs'
<br>
<br>
should work. That's a longer story.)
<br>
<br>
Pls try and let us know-
<br>
<br>
MAJ
<br>
<br>
On 2014-07-23 12:13, Fields, Christopher J wrote:
<br>
> Yep, that’s where to send it. I’ll post an official (belated)
<br>
> announcement.
<br>
>
<br>
> chris
<br>
>
<br>
> On Jul 22, 2014, at 10:38 PM, Mark A. Jensen <maj@fortinbras.us [9]>
<br>
> wrote:
<br>
>
<br>
>> This is a bug, and fairly deep. I have made
<br>
>> https://github.com/bioperl/bioperl-run/issues/12 [6].
<br>
>> (I hope that's what we do around here now...)
<br>
>> cheers MAJ
<br>
>>
<br>
>> On 2014-07-21 15:24, Mark A Jensen wrote:
<br>
>>
<br>
>>> Almost positive this will require a mod in SABP. I will try to
<br>
>>> have a
<br>
>>> look. MAJ
<br>
>>>
<br>
>>> On Mon, Jul 21, 2014 at 1:54 PM, Ashton Trey Belew
<br>
>>> <abelew@gmail.com [4]
<br>
>>> [1]> wrote:
<br>
>>>
<br>
>>>> -----BEGIN PGP SIGNED MESSAGE-----
<br>
>>>> Hash: SHA1
<br>
>>>>
<br>
>>>> Hello Dario,
<br>
>>>> Below is a portion of a little script which I use for
<br>
>>>> StandAloneBlast and which uses -m 7. It doesn't exactly answer
<br>
>>>> your
<br>
>>>>
<br>
>>>> question, but I hope it will be similar enough to prove
<br>
>>>> helpful.
<br>
>>>> My ignorant thought is that you can modify my use of -m to suit
<br>
>>>> your
<br>
>>>> purpose; but after rereading your message I am guessing you
<br>
>>>> already
<br>
>>>>
<br>
>>>> tried something similar.
<br>
>>>> -Trey
<br>
>>>>
<br>
>>>> my @params = (-program => 'blastn', -b => $max_hits,
<br>
>>>> -I => 't', -a => $processors,
<br>
>>>> -database => $library_db, -m => 7,);
<br>
>>>>
<br>
>>>> my $query_count = 0;
<br>
>>>> while (my $query_seq = $query_library->next_seq()) {
<br>
>>>> $query_count++;
<br>
>>>> my $search = new Bio::Tools::Run::StandAloneBlast(
<br>
>>>> -_READMETHOD => 'blastxml', @params);
<br>
>>>> $search->m(7);
<br>
>>>> my $blast_output = new Bio::SearchIO(
<br>
>>>> -format => 'blastxml', -verbose => 1,);
<br>
>>>> $blast_output = $search->blastall($query_seq,
<br>
>>>> -format=>'blastxml', -verbose => 1,);
<br>
>>>> my $result_count = 0;
<br>
>>>> while (my $result = $blast_output->next_result()) {
<br>
>>>> ## Collect alignments
<br>
>>>> } ## End of results by query
<br>
>>>> } ## End of queries
<br>
>>>>
<br>
>>>> On 07/21/2014 11:57 AM, Darío Carballido wrote:
<br>
>>>> > Hello,
<br>
>>>> >
<br>
>>>> >
<br>
>>>> >
<br>
>>>> > I’m working with this script that uses StandAloneBlastPlus,
<br>
>>>> and
<br>
>>>> I
<br>
>>>> > would like to take advantage of a new feature in the latest
<br>
>>>> > releases of blast+, which allows me to present the query
<br>
>>>> coverage
<br>
>>>>
<br>
>>>> > in the output (among other values). For that to work, the
<br>
>>>> value
<br>
>>>> of
<br>
>>>> > –outfmt needs to be quoted (for example, -outfmt “7 std
<br>
>>>> qcovs”), so
<br>
>>>> > I’m passing the outfmt parameter via
<br>
>>>> >
<br>
>>>> >
<br>
>>>> >
<br>
>>>> > -method_args => [ '-outfmt' => '"7 std qcovs"' ]
<br>
>>>> >
<br>
>>>> >
<br>
>>>> >
<br>
>>>> > (I’m using single quotes with doubles inside, so that the
<br>
>>>> double
<br>
>>>> > quotes are passed literally).
<br>
>>>> >
<br>
>>>> >
<br>
>>>> >
<br>
>>>> > But when I run it, the quotes seem to get lost and I end up
<br>
>>>> with
<br>
>>>> > the error I get when I pass that value without the quotes:
<br>
>>>> >
<br>
>>>> >
<br>
>>>> >
<br>
>>>> > Error: Too many positional arguments (1), the offending
<br>
>>>> value:
<br>
>>>> std
<br>
>>>> >
<br>
>>>> >
<br>
>>>> >
<br>
>>>> >
<br>
>>>> > I have tried lots of combinations with single, double quotes,
<br>
>>>> > character escaping and I couldn’t find the way to make it
<br>
>>>> work.
<br>
>>>>
<br>
>>>> >
<br>
>>>> >
<br>
>>>> >
<br>
>>>> > Any help?
<br>
>>>> >
<br>
>>>> >
<br>
>>>> >
<br>
>>>> > Thanks,
<br>
>>>> >
<br>
>>>> > Darío Carballido
<br>
>>>> >
<br>
>>>> >
<br>
>>>> >
<br>
>>>> > _______________________________________________ Bioperl-l
<br>
>>>> mailing
<br>
>>>>
<br>
>>>> > list Bioperl-l@mailman.open-bio.org [1]
<br>
>>>> > http://mailman.open-bio.org/mailman/listinfo/bioperl-l [2]
<br>
>>>> >
<br>
>>>> -----BEGIN PGP SIGNATURE-----
<br>
>>>> Version: GnuPG v1
<br>
>>>>
<br>
>>>> iD8DBQFTzVHiF9UIceSIYeoRAmLRAJsFCbynO5sZ8FWb8zAOtSVHTMKTDgCfeG3c
<br>
>>>> 356E0nxLltTzB+msEwRJ5ZY=
<br>
>>>> =5Y5m
<br>
>>>> -----END PGP SIGNATURE-----
<br>
>>>> _______________________________________________
<br>
>>>> Bioperl-l mailing list
<br>
>>>> Bioperl-l@mailman.open-bio.org [3]
<br>
>>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
<br>
>>>
<br>
>>> Links:
<br>
>>> ------
<br>
>>> [1] mailto:abelew@gmail.com [5]
<br>
>>
<br>
>> _______________________________________________
<br>
>> Bioperl-l mailing list
<br>
>> Bioperl-l@mailman.open-bio.org [7]
<br>
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l [8]
<br>
>
<br>
>
<br>
>
<br>
> Links:
<br>
> ------
<br>
> [1] mailto:Bioperl-l@mailman.open-bio.org
<br>
> [2] http://mailman.open-bio.org/mailman/listinfo/bioperl-l
<br>
> [3] mailto:Bioperl-l@mailman.open-bio.org
<br>
> [4] mailto:abelew@gmail.com
<br>
> [5] mailto:abelew@gmail.com
<br>
> [6] https://github.com/bioperl/bioperl-run/issues/12
<br>
> [7] mailto:Bioperl-l@mailman.open-bio.org
<br>
> [8] http://mailman.open-bio.org/mailman/listinfo/bioperl-l
<br>
> [9] mailto:maj@fortinbras.us
<br>
<br>
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</p>
</blockquote></div>