[Bioperl-l] Sim4 output parsing using Bioperl

[Jason Stajich]

On Tue, 1 Jul 2003, Arnaud Kerhornou wrote:

> Hi
>
> I'd like to use Bioperl to parse Sim4 output.
> I run sim4 using this command, "sim4 genomicDNA.fa cDNAs.fa P=1 A=4"
>
> I can't get the parsing going through the all sim4 output, it stops on
> this type of result:
>
> ------------------>
> seq1 = DICTY6P4_0001.gfseq.masked, 145194 bp
> seq2 = CONTIGS.fa (>AU275246), 258 bp
>
>  >DICTY6P4_0001
>  >AU275246  FC-IC Dictyostelium discoideum cDNA clone FC-IC1786, mRNA
> sequence

THERE SHOULD BE LOCATION INFORMATION HERE

Are you sure you you expect to see an alignment between these two
sequences.

>
> seq1 = DICTY6P4_0001.gfseq.masked, 145194 bp
> <------------------
>
> There is a "last" statement in the method "parse_next_alignment" in
> Bio::Tools::Sim4::Results.pm
>
>  /^seq1/ && do {
>        if($started) {
>            $self->_pushback($_);
>            last;
>        }
> ...
> }
>
> Why this last statement ?
>
Because we trying to detect the end of a report in case you've stored more
than one report in a single file.  The next time you see seq1 it means a
new report has started.

> Thanks
> Arnaud
>
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu