[Bioperl-l] NT_xxxxx contigs file info

[Jason Stajich]

On Wed, 24 Jul 2002, Damien Mattei wrote:

> thank you i ain't got any answer since your.
> Perheaps i could have find the answer in the doc but it's not really

I don't think this has been written up in the doc yet - waiting for
someone to get to it eventually

> easy to find what we want in it.I will try the NT_xxxxx contig later as
> i have enought to do already with standard genbank sequence.
> Sometimes i rewrite code that perheaps
> was already in bioperl,for example i spend a lot of time to write a
>    perl program using Tk to display BACs and contigs graphically before
> discovering bioperl-gui which althought isn't more supported , i just
> discover too gff in bioperl which could help me and i will be
Also see Bio::Graphics and the example script: scripts/render_sequence.pl

> interesting in examples programs if someone have. I also want to
> contribute in bioperl but i just discover perl programming few month ago
> and i know not about perl modules and lacks time to dig in a lot.

Keep working at it and feel free to post questions relating to perl
programming for biological problems here.

>
> Damien.
>
> Jason Stajich wrote:
>
>  > 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