Bioperl: running local blasts
Joey Morris
rjmorris@unity.ncsu.edu
Thu, 22 Jun 2000 14:59:53 -0400
Well, see the thing is that I get this undefined subroutine error that
really shouldn't be affected by my implementations of the _validate_seqs or
_blast_files subroutines, should it? The call to _rearrange that is
generating the error occurs in the blast_local function in LocalBlast.pm,
code that I didn't touch.
Joey
Alan Williams wrote on Jun 22 at 09:29 am:
>
> Aside:
> Why does LocalBlast.pm throw an error in some situations and just
> print an error message in others in the _validate_seq method?
>
> Your _run_local looks fine.
>
> In LocalBlast.pm:
>
> * increased $maximumLength
> * changed _validate_options to only check for a known blast program
> (ie no checking for whether the database exists or not and no
> checking if the right program is used with the requested database)
> * Changed _validate_seq to NOT check for a correct sequence type and
> database program combination
> * I don't set the environmental variable stuff in the perl modules --
> we depend on the user having a proper environment to start with
> ( ie BLASTDB points to a dir with blast databases and the
> ~/.ncbirc file exists)
> * I implemented the blast_seq only (see below)
>
> Hope this helps.
>
> -Alan
>
>
> #---------------
> sub _blast_seqs {
> #---------------
>
> #% HACK!
>
> my $seq;
> my $tmp_seq_file;
> my $id;
> my $baseFileName;
> my $blast_cmd;
> my $sequence;
>
> $blast_cmd = "blastall ";
>
> # Linux Hack to check for more than one processor
> my @procs;
> if (-e "/proc/cpuinfo") { @procs=`grep processor /proc/cpuinfo` }
> $blast_cmd .= "-a " . @procs ." "; # For using both processors
>
> $blast_cmd .= "-p $program ";
> $blast_cmd .= "-d $database ";
> if($expect) {$blast_cmd .= "-e $expect ";}
> if($gappedAlignmentFlag) {$blast_cmd .= "-g $gappedAlignmentFlag ";}
> if($filter) {$blast_cmd .= "-F $filter ";}
> if($matrix) {$blast_cmd .= "-M $matrix ";}
> if($alignments) {$blast_cmd .= "-b $alignments ";}
> if($descriptions) {$blast_cmd .= "-v $descriptions ";}
>
> foreach $seq (@seq_queue) {
>
> next unless &_validate_seq($seq);
>
> $tmp_seq_file = POSIX::tmpnam();
> my $out = Bio::SeqIO->new(-file => ">$tmp_seq_file", -format=>
> 'Fasta');
> $out->write_seq($seq);
> $out->close();
>
> # get temp filename and final filename
> $id = $seq->id;
> $id =~ s/[|:\/\\<>]/_/g; # remove special chars that could confuse
> shell
> #$id =~ s/\.\w+?$//; # trim off the extension if id is a filename.
> $baseFileName = "$_out_dir$id.$database.$program";
>
>
> system("echo '$blast_cmd -i $tmp_seq_file > $baseFileName'
> >/tmp/bioperl_blast_cmd");
>
> system("$blast_cmd -i $tmp_seq_file > $baseFileName");
> unlink $tmp_seq_file;
>
> push @_outFiles, $baseFileName;
>
> }
> }
>
> ---------------------------------
> Alan Williams
> Neomorphic, Inc.
> Alan@Neomorphic.com
> 510-981-8513
> ---------------------------------
>
> On Wed, 21 Jun 2000, Joey Morris wrote:
>
> > Date: Wed, 21 Jun 2000 19:55:44 -0400
> > From: Joey Morris <rjmorris@unity.ncsu.edu>
> > To: Alan Williams <alan@neomorphic.com>
> > Cc: vsns-bcd-perl@lists.uni-bielefeld.de
> > Subject: Re: Bioperl: running local blasts
> >
> > Well, I did both of those things (I think). For (1), I set the arrays
> > Blast_dbp_local, Blast_dbn_local, and Blast_matrix_local, I set some of the
> > default values (program, database, etc), and I wrote the functions
> > _get_environment and _blast_files. I left the function _blast_seqs as is
> > because I knew we wouldn't be using it for now. The function definitions for
> > _get_environment and _blast_files were the same as the ones I used in 0.05.1
> > (which worked). For (2), I changed _run_local to be
> >
> > sub _run_local {
> > my ($self, %param) = @_;
> >
> > require Bio::Tools::Blast::Run::LocalBlast;
> > Bio::Tools::Blast::Run::LocalBlast->import(qw(&blast_local));
> >
> > &blast_local($self, %param);
> > }
> >
> > Let me know if I skipped something.
> >
> > Thanks,
> > Joey
> >
> >
> > Alan Williams wrote on Jun 21 at 02:46 pm:
> > >
> > > I am. However it required:
> > > 1) implementing the appropriate stub in the LocalBlast.pm module
> > > 2) fixing Blast.pm to call LocalBlast.pm
> > > This was with 0.5 and 0.6 (not sure about 0.6.1). You may also want to
> > > change the MIN/MAX sequence size constraints set in the LocalBlast.pm as
> > > well.
> > >
> > > If you need more detailed pointers let me know.
> > >
> > > -Alan
> > >
> > > ---------------------------------
> > > Alan Williams
> > > Neomorphic, Inc.
> > > Alan@Neomorphic.com
> > > 510-981-8513
> > > ---------------------------------
> > >
> > > On Wed, 21 Jun 2000, Joey Morris wrote:
> > >
> > > > Date: Wed, 21 Jun 2000 15:58:13 -0400
> > > > From: Joey Morris <rjmorris@unity.ncsu.edu>
> > > > To: vsns-bcd-perl@lists.uni-bielefeld.de
> > > > Subject: Bioperl: running local blasts
> > > >
> > > > Can anyone tell me if they are successfully running local blast searches
> > > > using the LocalBlast.pm module? I just downloaded 0.6.1 and I get this error
> > > > when running a local blast:
> > > >
> > > > *** 1 Blast reports produced fatal errors:
> > > > Undefined subroutine &Bio::Root::Object::_rearrange called at
> > > > /local/lib/perl/lib/Bio/Tools/Blast/Run/LocalBlast.pm line 309.
> > > >
> > > > I experienced the same issue with 0.6.0 but not with the 0.05.1 release.
> > > > I've reported it as a bug but there's been no progess on it apparently.
> > > >
> > > > Thanks,
> > > > Joey
> > > >
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> >
>
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