[Bioperl-l] RE:Segmentation fault

[Jason Stajich]

I really have no idea what you are doing....


If you want to initialize a SearchIO parser to read in HMMER output
results you do

my $in = Bio::SearchIO(-file => 'hmmerresultfile.out',
                       -format => 'hmmer');

# an loop through each result (a single result per query sequence)
while( my $result = $in->next_result ) {
  # print the query name
  # for hmmpfam this will be each sequence in the input set
  # for hmmsearch this will be the name of the HMM file you
  # used to search
  print $result->query_name, "\n";

  # now print all the hits (for HMMPFAM this will be the Pfam domains
  # for hmmsearch this will be the sequences in the db that had good
  # alignments
  while ( my $hit = $result->next_hit ) {
    # print the name, indented with a tab
    print "\t", $hit->name, "\n";
  }
}

This is all covered in the HOWTO.  Did you try the example code in there?

-jason
On Mon, 12 Apr 2004, stephan rosecker wrote:

>  > If $result->query_name() is indeed the right call to make in
>  > the inner loop (according to the Bio::SearchIO documentation,
>  > $result is an object with the Bio::Search::Hit::HitI interface,
>  > which from what I can see contains no query_name() method), then
>  > I would suggest that you try your program with a newer version
>  > of Perl.  I believe the latest version is 5.8.3.
>
> Hi,
> like i wrote a'm not a perl guru so please correct me.
> $result is a "pointer" to my current seq object.
> ($result = $in->next_result)
> $hit is a "pointer" to my current hit object.
> (my $hit = $result->next_hit)
> So "$result->query_name" has to be visible inside my while-loop.
> (I want only the seq object that contains hit's)
>
> old code:
> ----------------------------------------------
> while( my $result = $in->next_result )
>          {
>                  while( my $hit = $result->next_hit )
>                          {
>                          print $result->query_name."\n";
>                          wait;
>                          last;
>                          }
>          }
> ----------------------------------------------
>
> After i read your mail i rewrote the code and
> it shoud be more conform... but also sementation fault:-( .
>
> new code:
> ----------------------------------------------
>
> use Bio::Search::Result::HMMERResult;
>      my $result = new Bio::Search::Result::HMMERResult
>      ( -hmm_name => 'pfam',
>            -sequence_file => 'uniprot_sprot.dat',
>                  -hits => \@hits);
> # I'm not realy understand the args here -
> # pfam for hmmpfam ?
> # -sequence_file = source hmmpfam file ?
>
>      use Bio::SearchIO;
>          my $in = new Bio::SearchIO(-format => 'hmmer',
>                  -file   => 'uniprot_sprot_hmmer.out');
>       while( my $result = $in->next_result ) {
>            $result->num_hits(), " hits\n";
>                 if ($result->num_hits()>0)
>                       {print $result->query_name."\n";}
> }
>
> greets,
> stephan
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu