[BioC] I need help making a dcf seed file to encapsulate a genome assembly im using.

ashteyma at andrew.cmu.edu ashteyma at andrew.cmu.edu
Tue Jan 14 22:43:05 CET 2014

To Herve,
   Thank you, that helped. I tried searching in window explorer for a dcf
file, but couldnt find anything i looked for the folder you mentioned
and found it and i see an example now. It should be easy to modify it.
thank you for the help.
> Hi Alan,
> [I'm cc'ing the list so others can benefit from this.]
> On 01/14/2014 08:13 AM, ashteyma at andrew.cmu.edu wrote:
>> Hello,
>>      I am working on a research project and I need to use a particular
>> assembly of the yeast genome. I tried figuring out how to make a DCF
>> file, But i was confused. I looked in the documentation but I'm
>> confused about the correct way to make a dcf file from a text file.
> You don't need to make a DCF file from a text file. A DCF file *is* a
> text file. More precisely a DCF file is just a text file where the
> content is organized as a collection of key/value pairs.
>> If
>> you have an example DCF file I could look at,
> The BSgenomeForge vignette contains the full seed file that was used to
> forge the BSgenome.Rnorvegicus.UCSC.rn4 package.
> If you need more examples of seed files, the vignette also gives you a
> list of more than 30 seed files that you can look at. All these seed
> files are text files in the DCF format, that is, the information in
> them is organized using the DCF syntax.
>> some guaranteed method
>> of making a seed file correctly, a video tutorial or anything that
>> would help, can you please send it in response. Thank you.
> No video tutorial sorry! The best way to make your own seed file is to
> pick-up one of the seed files provided in the BSgenome package itself
> (located in the extdata/GentlemanLab/ folder) and to modify it for your
> own needs. In your case, the seed file for sacCer1, sacCer2, or sacCer3
> should be close enough to what you need.
> Finally note that the BSgenomeForge vignette in the devel version
> of the BSgenome package has been reorganized to reflect the fact that,
> starting with BioC 2.14, the BSgenome data packages don't contain
> masks anymore (by default). As a consequence, the vignette is simpler
> and probably a little bit easier to follow.
> Hope this helps,
> H.
>> Sincerely,
>> Alan Shteyman
>> Carnegie Mellon University
> --
> Hervé Pagès
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319

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