[Bioperl-l] NT_xxxxx contigs file info

[Jason Stajich]

Damien - not sure if you got a satifactory answer - we can parse these
files in Bioperl and there is code in Bio::DB::RefSeq I believe to
put them back together.  However it is still not a heavily tested system
and probably needs someone going through it in more detail.  Part of the
problem is the need to assume a real Genbank or EMBL database is available
to suck in the data.



On Tue, 16 Jul 2002, Damien Mattei wrote:

>
> is there a way in bioperl to retrieve and parse contigs
> such as NT_xxxxx ,for example:
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NT_033929.1
>   to get the info on BACs assembly :
> CONTIG   join(AP003965.2:1..121852,AP000439.5:51986..105963,
> AP001824.4:7542..124888,AP001888.4:3798..161505,
> AP000850.4:9247..48539,AP003555.2:16283..121600,
> AP000879.4:2012..169725,AP002336.3:1993..112484,
> AP000487.5:52296..177074,AP001271.4:23675..210402,
> AP000590.6:22311..114287,AP001648.4:25262..166013)
>
> does someone already write something doing that or should it be?
>
> Damien
>
> -----------------------------
> Damien Mattei
> C.N.R.S / U.N.S.A - UMR 6549
> mailto:mattei@unice.fr
> http://www-iag.unice.fr/
> -----------------------------
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu