BioPerl

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 ... [More] 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 < at >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', < at >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()) { ## C [Less]

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 ... [More] 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: [Less]

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Would this do the same thing? $rc = $hsp->hit->revcom->seq ie. I think the hit() method returns a Seq object, so no need to convert between strings? --Torsten Seemann --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash ... [More] University, AUSTRALIA _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]

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It almost works, Just a little correction if this can help someone else: $rc = Bio::Seq->new( -seq => $hsp->hit_string )->revcom->seq; Thanks! -- View this message in context: http://bioperl.996286.n3.nabble.com/Problem-with-revcom-tp17581p17583.html Sent from the Bioperl-L mailing list archive at Nabble.com.

Antony, hit_string() returns a string, not a sequence obj. Something like $rc = Bio::Seq->new( -seq => $hsp->hit_string )->revcom; should work. MAJ On 2014-07-17 20:14, Antony03 wrote:

Hello, I try to reverse complement a sequence found with fasta36: if ( $hsp->strand('query') == -1 ) { my $rev_output=$hsp->hit_string->revcom(); print "$rev_output"; } And I get an error like: Can't locate object method ... [More] "revcom" via package Can someone know what is wrong with my code? Thanks, Antony -- View this message in context: http://bioperl.996286.n3.nabble.com/Problem-with-revcom-tp17581.html Sent from the Bioperl-L mailing list archive at Nabble.com. [Less]

It’s been moved to a separate github distribution, namely Bio-FeatureIO, but it was also being largely rewritten as the original implementation was never completed. We can probably set up a branch with the relevant version of the code that should ... [More] work with the script. Scott, is this the recommended way of loading Chado data in still? Do we need a working version of Bio::FeatureIO on CPAN so it’s available? For some reason I thought users started going with Bio::Chado::Schema... chris On Jul 17, 2014, at 12:23 PM, George Hartzell <hartzell< at >alerce.com> wrote: [Less]

I'm following instructions on the GMOD site to install the Chado schema and related tools. I used cpanm to install BioPerl, which gives me the current version. Various Chado-related tools, e.g. load/bin/gmod_bulk_load_gff3, require Bio::FeatureIO ... [More] , which is no longer in the BioPerl distribution. I've found a GitHub repo for it, but I can't find any sign of it on CPAN. Has it ever been released? Thanks. g. Sent from a device that makes me type with two fingers. [Less]