Hi Michael,
This is now supported in Biostrings 2.31.17.
Cheers,
H.
On 03/18/2014 11:42 AM, Hervé Pagès wrote:
Hi,
On 03/18/2014 10:04 AM, Michael Lawrence wrote:
On Tue, Mar 18, 2014 at 7:54 AM, Gabriel Becker mailto:gmbec...@ucdavis.edu>> wrote:
Or going the positive declarative r
Hi,
On 03/18/2014 10:04 AM, Michael Lawrence wrote:
On Tue, Mar 18, 2014 at 7:54 AM, Gabriel Becker mailto:gmbec...@ucdavis.edu>> wrote:
Or going the positive declarative route but arguably more
informative: skip.to.fasta or fasta.only
skip.to.fasta might work. A different algorith
On Tue, Mar 18, 2014 at 7:54 AM, Gabriel Becker wrote:
> Or going the positive declarative route but arguably more informative:
> skip.to.fasta or fasta.only
>
>
skip.to.fasta might work. A different algorithm that would work for GFF3
would be skip.to.pragma="##FASTA", which would skip until it hi
Or going the positive declarative route but arguably more informative:
skip.to.fasta or fasta.only
I don't know the GFF format spec, are we guaranteed that there will be only
one embedded fasta file and that it will be contiguous within the file? If
not the skip.to._ terminology would not technica
For direct reading of the sequence, the skip.non.fasta idea sounds good. An
alternative for the name would be "skip.to.first.record". Up to you.
Michael
On Mon, Mar 17, 2014 at 5:33 PM, Hervé Pagès wrote:
> Hi Michael,
>
>
> On 03/17/2014 04:15 PM, Michael Lawrence wrote:
>
>> Hi Herve,
>>
>>
Hi Michael,
On 03/17/2014 04:15 PM, Michael Lawrence wrote:
Hi Herve,
What would be a clean way for rtracklayer to extract the (optional) FASTA
data embedded in a GFF3 file and parse it as an XStringSet? Is there a
low-level way to pass in-memory data to the parser in Biostrings?
Not that it
Hi Herve,
What would be a clean way for rtracklayer to extract the (optional) FASTA
data embedded in a GFF3 file and parse it as an XStringSet? Is there a
low-level way to pass in-memory data to the parser in Biostrings?
In terms of the API, import,GFFFile could return a GRanges with the
DNAStrin
