<p dir="ltr">Almost positive this will require a mod in SABP. I will try to have a look. MAJ</p>
<br/><div class="cm_quote" style=" color: #787878">On Mon, Jul 21, 2014 at 1:54 PM, Ashton Trey Belew <<a href="mailto:abelew@gmail.com">abelew@gmail.com</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">-----BEGIN PGP SIGNED MESSAGE-----
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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>
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 your
<br>
purpose; but after rereading your message I am guessing you already
<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;
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while (my $query_seq = $query_library->next_seq()) {
<br>
$query_count++;
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my $search = new Bio::Tools::Run::StandAloneBlast(
<br>
-_READMETHOD => 'blastxml', @params);
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$search->m(7);
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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
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} ## End of results by query
<br>
} ## End of queries
<br>
<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 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>
> in the output (among other values). For that to work, the value of
<br>
> –outfmt needs to be quoted (for example, -outfmt “7 std 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 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: 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>
> Any help?
<br>
>
<br>
>
<br>
>
<br>
> Thanks,
<br>
>
<br>
> Darío Carballido
<br>
>
<br>
>
<br>
>
<br>
> _______________________________________________ Bioperl-l mailing
<br>
> list Bioperl-l@mailman.open-bio.org
<br>
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
<br>
>
<br>
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