[Bioperl-l] Bio::Tools:Sim4::Results

[Jason Stajich]

Did you try Bio::SearchIO::sim4?  More effort for proper sim4 parsing has
been paid there.

I don't know if it handles this situation - if it doesn't we'd need you
submit an example report file that isn't working to buzilla.

-jason
On Tue, 24 Aug 2004, Miroslava Cuperlovic-Culf wrote:

> Dear All,
> I am trying to parse output from sim4  to gff format using something like:
>     while(my $exonset = $sim4->next_exonset()) {
>
>        foreach my $exon ( $exonset->sub_SeqFeature() ) {
> .....
> }
> }
>
> This works fine if exon alignment is in the the first group of seq1/seq2  :
> seq1 = ..
> seq2 = ..
>
>  >fasta info
>  >fasta info
>
> 1-66  (31346313-31346378)   100% ->
> 67-222  (31372915-31373070)   100% ->
> 223-798  (31376360-31376935)   100%
>
> But  if the sim4 outputs shows alignment to multiple sections of the
> Chromosome input and if the exon info is not in the first group of data
> (seq1 \n seq2 ...) this loop doesn't find it. parse_next_alignment
> didn't seem to be able to solve this problem either.
> Is there any way to loop around all seq1/seq2 parts of the input from
> Bioperl or not to write the empty alignments from sim4?
> Sorry for this most likely trivial question!
> Thanks for the on-going help
> Mira
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu