[Bioperl-l] project ideas

[Jason Stajich]

exactly yes.  is there not an alignment component too?

Would be good to try and support more of jim's output formats too:
            psl -  Tab separated format without actual sequence
            pslx - Tab separated format with sequence
            axt -  blastz-associated axt format
            maf -  multiz-associated maf format

-j

On Tue, 21 Jan 2003, Aaron J Mackey wrote:

>
> On Tue, 21 Jan 2003, Jason Stajich wrote:
>
> > * Writing a SearchIO plugin for blastz parsing
>
> Do you mean a more generic LAJ parser?  Or something specific to blastz?
>
> I have some code that Webb Miller sent me that processes LAJ blastz output
> into lines that look like:
>
> Contig1010:329-1092: 3-766 of >316732 9421 bp 3 contigs (reverse complement) (764/9421 bp) 100%
> Contig1015:1-1033: 2593-3625 of >316222 3653 bp 2 contigs (reverse complement) (1033/3653 bp) 100%
> Contig1058:1-459: 790-1248 of >315908 1250 bp 1 contigs (reverse complement) (459/1250 bp) 100%
>
> Is that what you meant?  Regardless, the LAJ parsing code could be reused,
> if someone were interested.
>
> -Aaron
>
>

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