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<div>Yep, that’s where to send it. I’ll post an official (belated) announcement.</div>
<div><br>
</div>
<div>chris</div>
<br>
<div>
<div>On Jul 22, 2014, at 10:38 PM, Mark A. Jensen <<a href="mailto:maj@fortinbras.us">maj@fortinbras.us</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
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This is a bug, and fairly deep. I have made<span class="Apple-converted-space"> </span><a href="https://github.com/bioperl/bioperl-run/issues/12">https://github.com/bioperl/bioperl-run/issues/12</a>.<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>
<blockquote type="cite">Almost positive this will require a mod in SABP. I will try to have a<br>
look. MAJ<br>
<br>
On Mon, Jul 21, 2014 at 1:54 PM, Ashton Trey Belew <<a href="mailto:abelew@gmail.com">abelew@gmail.com</a><br>
[1]> wrote:<br>
<br>
<blockquote type="cite">-----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 your<br>
<br>
question, but I hope it will be similar enough to prove 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 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, 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 coverage<br>
<br>
> in the output (among other values). For that to work, the 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 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 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 work.<br>
<br>
><br>
><br>
><br>
> Any help?<br>
><br>
><br>
><br>
> Thanks,<br>
><br>
> Darío Carballido<br>
><br>
><br>
><br>
> _______________________________________________ Bioperl-l mailing<br>
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> list <a href="mailto:Bioperl-l@mailman.open-bio.org">Bioperl-l@mailman.open-bio.org</a><br>
> <a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-l">http://mailman.open-bio.org/mailman/listinfo/bioperl-l</a><br>
><br>
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</blockquote>
<br>
<br>
Links:<br>
------<br>
[1]<span class="Apple-converted-space"> </span><a href="mailto:abelew@gmail.com">mailto:abelew@gmail.com</a><br>
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