Re: [Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

2016-01-19 Thread Rainer Johannes
Thanks Hervé! I’ll check it out but don’t expect any problems. cheers, jo > On 19 Jan 2016, at 22:31, Hervé Pagès wrote: > > Hi Jo, > > In GenomicFeatures 1.23.18 I've modified the default > "extractTranscriptSeqs" method so it can be called with additional > arguments when the 2nd argument i

Re: [Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

2016-01-19 Thread Hervé Pagès
Hi Jo, In GenomicFeatures 1.23.18 I've modified the default "extractTranscriptSeqs" method so it can be called with additional arguments when the 2nd argument in not a GRangesList object. These additional arguments then get passed to the internal call to exonsBy(). With this change, the user shou

[Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

2016-01-18 Thread Rainer Johannes
Dear all, I’m having hard times to extend the extractTranscriptSeqs method implemented in GenomicFeatures. Basically, I would like to implement a method for signature(x="ANY”, transcripts="EnsDb”), so that I can re-use the method from GenomicFeatures and add the optional parameter “filter” whic