[Bioperl-l] Is there a parser for "seq_contig.md"?

[Ewan Birney]

On Thu, 6 Mar 2003, Hilmar Lapp wrote:

> I'm afraid no, but maybe the file's format matches a standard one
> supported by bioperl. Have you checked what the precise format is?

It is not - it is a pretty simple file to understand, but the data
consequence of it is quite extreme (ie, assembled chromosomes). Parsing
this into an object which does something more than just give back out the
lines in the .md file would be fine.


Sang - have you checked out the Ensembl system, either EnsMART
(www.ensembl.org/EnsMART) which is a powerful, flexible, web accessible
data mining system and/or the Ensembl Perl API, which is a Bioperl
compliant Perl API to genome sequence (go to www.ensembl.org, click on
documentation, and there is an up to date tutorial there)




>
> 	-hilmar
>
> On Thursday, March 6, 2003, at 04:04  PM, Sang Chul Choi wrote:
>
> > Hi!
> >
> > The contig layout file, 'seq_contig.md' from NCBI ftp server is said
> > to provide information on the order and orientation of the contigs
> > along the chromosome.
> >
> > Is there any parser for the file in bioperl?
> >
> > Sincerely yours,
> >
> > Sang Chul Choi
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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