[Bioperl-l] How to get Remote BLAST results in a single out
José Luis Lavín
jluis.lavin at unavarra.es
Mon Nov 14 16:23:31 EST 2011
Thank you very much for your answers, but due to them, I'm afraid I didn't
explained myself good enough.
I'm not looking for another tool to perform a BLAST task. I was just
wondering if there was a way to simply change the way the module writes the
outputs, so that I can get multiple searches in a single report file
instead of having a report for each BLAST search.
Maybe there's some issue I ignore, that makes you recommend the use of
other tools instead of the Bioperl Remote BLAST module...it would be
appreciated if you let me know about that (NCBI server problems with
web-services or so)...
Thank you for your answers anyway
Best wishes
2011/11/14 Fields, Christopher J <cjfields at illinois.edu>
> Re: a BLAST+ equivalent for blastcl3, I believe there is an option for the
> various 'blast*' indicating the search is to use a remote database. I
> haven't used it, though...
>
> chris
>
> On Nov 14, 2011, at 8:07 AM, Jason Stajich wrote:
>
> > Please keep this on list discussions
> >
> > Sent from my iPhone-please excuse typos
> >
> > --
> > Jason Stajich
> >
> > Begin forwarded message:
> >
> >> From: José Luis Lavín <jluis.lavin at unavarra.es>
> >> Date: November 14, 2011 8:04:25 AM EST
> >> To: Jason Stajich <jason.stajich at gmail.com>
> >> Subject: Re: [Bioperl-l] Fwd: How to get Remote BLAST results in a
> single out
> >>
> >> Hello Jason,
> >>
> >> As answering your question:
> >>
> >> " If you want to do this within this code I guess the question is what
> format you want the data in - a BLAST report or something more like a
> table?"
> >>
> >> A concatenation of BLAST (default format) reports should be OK, since I
> have a script to parse that kind of results. Anyway formats 1 or 2 will
> also do the trick.
> >> I'll be happy to get assistance on how to change the OUTFILE from "a
> query a report" to "all queries in the same report", because I don't seem
> to be able to do it myself after reading the module documentation.
> >>
> >> Thanks in advance
> >>
> >> El 14 de noviembre de 2011 12:59, Jason Stajich <
> jason.stajich at gmail.com> escribió:
> >> if you want to do a bunch of BLASTs remotely on the cmdline you should
> also just use the NCBI's blastcl3 tool (not sure if there is a BLAST+
> equivalent). This might be faster to do and easier since you need to learn
> the programming part too.
> >>
> >> If you want to do this within this code I guess the question is what
> format you want the data in - a BLAST report or something more like a table?
> >>
> >> On Nov 14, 2011, at 6:14 AM, José Luis Lavín wrote:
> >>
> >>> Hello everybody,
> >>>
> >>> I've been using "Bio::Tools::Run::RemoteBlast" for a time and it has
> >>> worked fine for me. Now I need to perform a multiple BLAST search, but
> this
> >>> time I'd just like to get all the BLAST results in a single out file
> >>> instead of having each sequence's report written individually. I've
> read
> >>> the documentation of the module, but due to my short
> >>> experience/understanding on complex modules as this one seems to be I
> can't
> >>> figure out where to change the script to achieve my previously
> mentioned
> >>> aim.
> >>> Here I post the script I've been using (it's basically the one posted
> on
> >>> the module cookbook).
> >>>
> >>> #!/c:/Perl -w
> >>> use Bio::Tools::Run::RemoteBlast;
> >>> use Bio::SearchIO;
> >>> use Data::Dumper;
> >>>
> >>> #Here i set the parameters for blast
> >>> print "Enter your BLAST choice (blastn, blastp, blastx, tblastn,
> >>> tblastx):\n";
> >>> my $blst = <STDIN>;
> >>> my $prog = "$blst";
> >>> print "Enter a database to search (nr, refseq_protein, swissprot, pat,
> pdb,
> >>> env_nr):\n";
> >>> my $dtb = <STDIN>;
> >>> $db = "$dtb";
> >>> print "Enter your cutt off score (1e-n):\n";
> >>> my $cut = <STDIN>;
> >>> my $e_val = "$cut";
> >>>
> >>> my @params = ( '-prog' => $prog,
> >>> '-data' => $db,
> >>> '-expect' => $e_val,
> >>> '-readmethod' => 'SearchIO' );
> >>>
> >>> my $remoteBlast = Bio::Tools::Run::RemoteBlast->new(@params);
> >>>
> >>>
> >>> #Select the file and make the blast.
> >>> print "Enter your FASTA file:\n";
> >>> chomp(my $infile = <STDIN>);
> >>> my $r = $remoteBlast->submit_blast($infile);
> >>> my $v = 1;
> >>>
> >>> print STDERR "waiting..." if( $v > 0 ); ######## WAIT FOR THE
> RESULTS
> >>> TO RETURN!!!!!
> >>> while ( my @rids = $remoteBlast->each_rid ) {
> >>> foreach my $rid ( @rids ) {
> >>> my $rc = $remoteBlast->retrieve_blast($rid);
> >>> if( !ref($rc) ) {
> >>> if( $rc < 0 ) {
> >>> $remoteBlast->remove_rid($rid);
> >>> }
> >>> print STDERR "." if ( $v > 0 );
> >>> sleep 5;
> >>> } else {
> >>> my $result = $rc->next_result();
> >>> #save the output
> >>> my $filename =
> >>> $result->query_name()."\.out";##################open SALIDA,
> >>> '>>'."$^T"."Report"."\.out";
> >>> $remoteBlast->save_output($filename);#############
> >>> $remoteBlast->remove_rid($rid);
> >>> print "\nQuery Name: ", $result->query_name(), "\n";
> >>> while ( my $hit = $result->next_hit ) {
> >>> next unless ( $v > 0);
> >>> print "\thit name is ", $hit->name, "\n";
> >>> while( my $hsp = $hit->next_hsp ) {
> >>> print "\t\tscore is ", $hsp->score, "\n";
> >>> }
> >>> }
> >>> }
> >>> }
> >>> }
> >>>
> >>>
> >>> May any of you please explain me how to solve my question?
> >>>
> >>> Thanks in advence
> >>>
> >>> With best wishes
> >>>
> >>> --
> >>> --
> >>> Dr. José Luis Lavín Trueba
> >>>
> >>> Dpto. de Producción Agraria
> >>> Grupo de Genética y Microbiología
> >>> Universidad Pública de Navarra
> >>> 31006 Pamplona
> >>> Navarra
> >>> SPAIN
> >>>
> >>>
> >>>
> >>> --
> >>> --
> >>> Dr. José Luis Lavín Trueba
> >>>
> >>> Dpto. de Producción Agraria
> >>> Grupo de Genética y Microbiología
> >>> Universidad Pública de Navarra
> >>> 31006 Pamplona
> >>> Navarra
> >>> SPAIN
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
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> >>
> >>
> >>
> >> --
> >> --
> >> Dr. José Luis Lavín Trueba
> >>
> >> Dpto. de Producción Agraria
> >> Grupo de Genética y Microbiología
> >> Universidad Pública de Navarra
> >> 31006 Pamplona
> >> Navarra
> >> SPAIN
> >
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--
--
Dr. José Luis Lavín Trueba
Dpto. de Producción Agraria
Grupo de Genética y Microbiología
Universidad Pública de Navarra
31006 Pamplona
Navarra
SPAIN
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