[Bioperl-l] blastxml format

Massimo Ubaldi massimo.ubaldi at gmail.com
Wed Oct 25 11:20:49 EDT 2006


Thanks for the reply. I've already tried this but I got exactly the same
results as before.
What other can I try?
Massimo

On 10/25/06, Chris Fields <cjfields at uiuc.edu> wrote:
>
> Iterations (which are related to PSIBLAST) aren't currently handled in
> blastxml, which is why the tag isn't being parsed.  I'll give it a look
> but
> I don't think it will be properly fixed anytime soon, since we're gearing
> up
> for a developer release and are sorting out various bugs in relation to
> that.
>
> In the meantime, you could always try changing the relevant tag in the
> %MAPPING hash in your local copy of Bio::SearchIO::blastxml from
> 'BlastOutput_query-def' to 'Iteration_query-def', which may do the trick
> for
> you.  I'm a bit reluctant to change this in CVS as it would be better to
> add
> this in when iterations are handled properly by blastxml, and I'm not sure
> all BLAST XML varieties have the <Iteration_query-def> tag.
>
> If you want you can add this to the bioperl bugzilla as an enhancement
> request to remind us:
>
> http://bugzilla.open-bio.org/
>
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
>
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Massimo Ubaldi
> > Sent: Wednesday, October 25, 2006 9:29 AM
> > To: bioperl-l List
> > Subject: [Bioperl-l] blastxml format
> >
> > Hi
> > I'm using the script below to parse a blastn output to multiple
> sequences
> > I got the output from the blast web interface asking for xml formatted
> > output.
> > Everything work fine except that I cannot print the name of each input
> > sequence (see below).
> > That is, using the line (see below) $result->query_description I got
> just
> > the name of the first sequence. Infact this is defined by the
> > <BlastOutput_query-def> tag.
> > What I really want is to extract the name that is defined by the
> > <Iteration_query-def> tag.
> > Now I digged out the bioperl mailing list and other sources but I did
> not
> > find anything to solve this.
> > Can somebody help me?
> > Thanks alot
> > Massimo
> >
> >
> >  This is an example of ouput I got
> >
> > MRDNA_probe
> > 46.1    PREDICTED: Danio rerio similar to mineralocorticoid receptor
> form
> > B
> > (LOC562171), mRNA    68354945    XM_685568
> > 81.8    Danio rerio VDR-B mRNA, partial cds    68132043    DQ017633
> > PREDICTED: Danio rerio similar to Rarab protein (LOC560679), mRNA
> > 68420187    XM_684078
> >
> > This what I'd like to get
> > MRDNA_probe
> > 46.1    PREDICTED: Danio rerio similar to mineralocorticoid receptor
> form
> > B
> > (LOC562171), mRNA    68354945    XM_685568
> > VDRacterm_probe
> > 81.8    Danio rerio VDR-B mRNA, partial cds    68132043    DQ017633
> > ARalpcterm_probe
> > PREDICTED: Danio rerio similar to Rarab protein (LOC560679), mRNA
> > 68420187    XM_684078
> >
> > This is the script
> > #!/usr/bin/perl
> > use strict;
> > use Bio::SearchIO;
> > my $in = new Bio::SearchIO(-format => 'blast',
> >                             -file   => 'Blastn_danio.bls');
> > open OUTFILE, ">parsed_blastn_danio.txt" or die "Could not open file,
> > stopped";
> > my $result = $in->next_result;
> > print OUTFILE $result->algorithm, "\n";
> > print OUTFILE $result->database_name, "\n";
> >
> > print OUTFILE "Score", "\t", "Description", "\t", "NCBI gi identifiers",
> > "\t", "GenBank Accession", "\n";
> >
> > while($result = $in->next_result ) {
> >     print OUTFILE $result->query_description, "\n";
> >       while( my $hit = $result->next_hit ) {
> >            while( my $hsp = $hit->next_hsp ) {
> >
> >                 my $acc=$hit->name;
> >                 my $description= $hit->description;
> >
> >                 $acc =~ /gi\|(\d+)\|\w+\|(\w+)\.\d/;
> >
> >                 print OUTFILE
> >
> >                   $hit->raw_score, "\t", # Score
> >                   $hit->description, "\t", # Description
> >
> >                 $1, "\t", $2, "\n";
> >          }
> >       }
> > }
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


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