[Bioperl-l] Problem with parsing ENSEMBL genbank flat file with genbank2gff3. pls

[Ewan Birney]

On Tue, 18 Jan 2005, Chris Mungall wrote:

> 
> OK, so it looks like EnsMart may solve Vladimir's problem by bypassing the
> genbank-format files altogether
> 
> Ewan - it'd be nice to see the GFF/GTFs appear in the main ftp download
> area too at some point, as well as via dynamic EnsMart download. As far as
> tweaking the ensembl genbank output, I think the addition of a feature of
> type 'gene', with a single location covering the maximal extent of all
> mRNAs, as is fairly-standard with genbank-format files - that should do
> it.

We can't do putting the GTF file on the ftp site as matter of general
principal - too many people ask for "why can't you just put XXXX on the
ftp site"  - and then we will run out of disk space too fast. Mart is far
more scaleable solution. We can't just keep putting every possible format
combination on our ftp site - it wont scale. (admittedly GTF files wont 
dent our disk space much, but you get the idea). 

Mart should work well for people and we have command line tools to address 
mart as well as the web form. Vladimir - does this work for you?



I've cc'd in Arne (software lead) and Glenn (release coordinator for 
March) - guys - we need to add a "gene" line in our EMBL and GenBank 
dumper so it plays better with parsing scripts out there. Chris - just for 
the avoidance of us screwing up could you give a concrete example of the 
right sort of gene line?