[Bioperl-l] Problem with StandAloneBlastPlus

[Mark A. Jensen]

This is a bug, and fairly deep. I have made 
https://github.com/bioperl/bioperl-run/issues/12.
(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
> [1]> wrote:
>
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>> 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
>> > http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>> >
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>
>
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