[Bioperl-l] Parsing Blast output for nohit sequences

[Marc Logghe]

Hi,
I had the same problem a while ago, at least when using Bio::Tools::Blast.
You should try Bio::Tools::BPLite, this 'no hits' bug appears not to show up
there.
Hope this helps,
Marc

> -----Original Message-----
> From: Sammons, Scott [mailto:zno6@cdc.gov]
> Sent: Wednesday, October 31, 2001 6:04 PM
> To: 'bioperl-l@bioperl.org'
> Subject: [Bioperl-l] Parsing Blast output for nohit sequences
> 
> 
> Greetings:
> 
> I am a relatively new bioperler.  I am trying to parse a 
> large batch of
> blast
> searches and build a fasta file of the subjects that have no 
> hits.  The code
> 
> below works fine when I want to do something with the hits.  
> But by the time
> 
> process_blast gets to the data, the nohits are already parsed 
> out.  I can't 
> seem to get to the blast parse while the nohits are still 
> there. Any help
> would 
> be appreciated.
> 
> -Scott Sammons
> Centers for Disease Control and Prevention
> 1600 Clifton Rd, NE
> MS G36
> Atlanta, GA 30333
> 404-639-3560 (Voice)
> 404-639-1331 (FAX)
> ssammons@cdc.gov
> 
> ==============
> use Bio::Index::Fasta;
> use Bio::SeqIO;
> use Bio::Tools::Blast qw(:obj);
> 
> my ($inx, $seqobj, $outputfile, $blastobj, $params);
> 
> # parse blast output and create a fasta file from subject 
> sequences with
> nohits
> # First, we create a index from the fasta file that was used 
> to create the
> blast output
> # call this with  cat blastoutfile | nohit_blast2fasta.pl fastafile
> 
> sub process_blast {
>         my $hit;
>         my $blast_object = shift;
>         if ($blast_object->num_hits('total') == 0) {
>                 $seqobj = $inx->fetch($blast_object->name);
>                 printf ">%s %s\n",$seqobj->display_id,$seqobj->desc;
>                 printf "%s\n", $seqobj->seq;
>         }
>         $blast_object->destroy;
> }
> 
> $inx = Bio::Index::Fasta->new(
>         -filename => "/tmp/t$$.idx",
>         -write_flag => 1);
> $inx->make_index(@ARGV);
> 
> $Blast->parse(  -parse => 1,
>                 -exec_func => \&process_blast,
>                 );
>                 
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