[Bioperl-l] process_sgd.PLS trouble

[Jason Stajich]

actually you can download SGD data as already formed GFF.
ftp://ftp.yeastgenome.org/pub/yeast/data_download/chromosomal_feature/s_cerevisiae.gff2

(and when the GFF3 parsers are ready)
ftp://ftp.yeastgenome.org/pub/yeast/data_download/chromosomal_feature/s_cerevisiae.gff3

So no need to do that step anymore, the tutorial will be updated in the
future.

On Tue, 29 Jul 2003, Venky Nandagopal wrote:

> Hi,
> I'm trying to set up a Bio::DB::GFF feature database for the SGD data.
> I downloaded the chromosomal_feature.tab file at ftp://genome-
> ftp.stanford.edu/pub/yeast/data_download/chromosomal_feature/chromosomal_feature.tab
>  and ran process_sgd.PLS as instructed --
>
> process_sgd.PLS chromosomal_feature.tab > yeast.gff.
>
> I got this error message:
> Strand logic is messed up at ./process_sgd.PLS line 69, <> line 6.
>
> I looked at the script and it screams and dies when $stop<$start at line
> 69.
>
> So I modified the script to save away $_, the line being processed and
> print it out before dying and here it is:
>
> ARS1001                        ARS     10      65      577
> S0028438               Autonomously Replicating Sequence        2002-12-16
>     2002-12-16
>
>
> I'm not really sure what I should do to fix this -- any suggestions?
>
> Venky
>
>
>

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