[Bioperl-pipeline] Genewise matters(start,stop modification)

[Elia Stupka]

> the alternative is to get the db_file name from the analysis object,
> read the sequence directly from the flat file we blast against
> using Bio::DB::Fasta. but of course, using a db is preferred but since
> the flat file exist anyways.....

No, definitely not the case. Don't forget you could easily have an ensembl
database sittign somewhere that's got nothing to do with where your
analysis was run, e.g. shaggy, e.g. any mirror in the world.... therefore,
not nice assumption to make....

and also it does take much longer to scan a file even with
Bio-Lincoln-magic ;)

> I will got ahead and do it thru biosql, 

Yep :)

Elia

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