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<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>You’re right, it was the
comma. Sorry!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>De:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
bioperl-l-bounces+dcarball=tandar.cnea.gov.ar@mailman.open-bio.org
[mailto:bioperl-l-bounces+dcarball=tandar.cnea.gov.ar@mailman.open-bio.org] <b><span
style='font-weight:bold'>En nombre de </span></b>Mark A Jensen<br>
<b><span style='font-weight:bold'>Enviado el:</span></b> martes, 29 de julio de
2014 0:57<br>
<b><span style='font-weight:bold'>Para:</span></b> Darío Carballido<br>
<b><span style='font-weight:bold'>CC:</span></b> <st1:PersonName w:st="on">bioperl-l@mailman.open-bio.org</st1:PersonName><br>
<b><span style='font-weight:bold'>Asunto:</span></b> Re: [Bioperl-l] Problem
with StandAloneBlastPlus</span></font><o:p></o:p></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Dario,
looking just at the error message,I think you might be missing a comma in the
list of params before -outformat.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><font size=3 color="#787878" face="Times New Roman"><span
style='font-size:12.0pt;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:<o:p></o:p></span></font></p>
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12.0pt'><o:p> </o:p></span></font></p>
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id=oldcontent>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'>
<p style='background:white'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>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: <st1:PersonName w:st="on">bioperl-l@mailman.open-bio.org</st1:PersonName>
<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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http://mailman.open-bio.org/mailman/listinfo/bioperl-l <o:p></o:p></span></font></p>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'
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Versión: 2014.0.4716 / Base de datos de virus: 3986/7937 - Fecha de la versión:
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