Hi, On 09/30/2013 04:53 AM, Julian Gehring wrote: > Hi Valerie and Herve, > > Your latest changes improve the speed of this greatly, thanks for your > work! > > Thinking more generally, do you think it would be worth generalizing the > readVcf in the way you described? I'm not just thinking about speed > here, but also about a more flexible way of interacting with the > functions (given that the user has to specify the genome name anyway). Yes. I'll aim to implement this before the next release. Valerie > > Best wishes > Julian > > > On 09/28/2013 12:57 AM, Hervé Pagès wrote: >> Hi Julian, >> >> With the latest devel version of GenomicRanges (1.13.48, should become >> available via biocLite() in the next 24 hours or so), setting the >> seqinfo of a big VCF object should be much faster but your mileage >> may vary. Let us know if you still find it slow enough to justify a >> mechanism for letting the user specify the seqinfo upfront when using >> readVcf() (e.g. the 'genome' arg could be renamed 'seqinfo' and accept >> everything it supports now plus a Seqinfo object). >> >> Cheers, >> H. >> >> On 09/24/2013 10:00 AM, Julian Gehring wrote: >>> Hi Valerie, >>> >>>> Thanks for clarifying. No, there is not currently a way to do this. >>>> >>>> The 'seqinfo' on the rowData(vcf) should not be difficult to change. >>>> Can >>>> you provide more detail as to (1) why you are changing it (did >>>> readVcf() >>>> import something incorrectly or ?) and (2) what operations on the >>>> 'seqinfo' are taking a long time. >>> >>> 'readVcf' did everything in a correct way. I needed to add the >>> information about the genome, circularity, and seqlengths based on >>> external annotitation, since it is not part of the VCF file. >>> >>> I can't tell you at the moment where 'seqinfo <-' spends most of its >>> time. I'll profile it and get back to you. >>> >>> Thank your for your quick answer and your help! >>> >>> Best wishes >>> Julian >>> >>> >>>> Thanks. >>>> Valerie >>>> >>>>> >>>>> Best wishes >>>>> Julian >>>>> >>>>> >>>>> On 09/24/2013 06:31 PM, Valerie Obenchain wrote: >>>>>> Hi Julian, >>>>>> >>>>>> On 09/24/2013 02:29 AM, Julian Gehring wrote: >>>>>>> Hi, >>>>>>> >>>>>>> Is there a direct way to specifiy the 'seqinfo' of a genome for the >>>>>>> import of a VCF file using 'readVcf'? >>>>>> >>>>>> I think the question is how to read in a subset of >>>>>> chromosomes/positions >>>>>> from a vcf file without an accompanying tabix index. You can't. >>>>>> readVcf() requires an index when subsets are defined by >>>>>> chromosome/position. However you can read in subsets defined by INFO >>>>>> and/or GENO fields without an index. >>>>>> >>>>>> Approaches: >>>>>> (1) create index with ?indexTabix and specify 'which' in ScanVcfParam >>>>>> (2) use ?filterVcf to write out a new file of records of interest >>>>>> >>>>>>> I'm aware that one can change it >>>>>>> with the 'seqinfo' method afterwards, but for large VCF files this >>>>>>> can >>>>>>> take a significant amount of time. >>>>>> >>>>>> What operation is taking along time? Subsetting the VCF object by >>>>>> chromosome? >>>>>> >>>>>> Valerie >>>>>> >>>>>>> >>>>>>> An alternative would be to sneak it in by the 'which' arguments, >>>>>>> such >>>>>>> as: >>>>>>> >>>>>>> readVcf(file, genome, ScanVcfParam(which = as(seq_info, "GRanges"))) >>>>>>> >>>>>>> but this requires the file to be indexed beforehand. >>>>>>> >>>>>>> Best wishes >>>>>>> Julian >>>>>>> >>>>>> >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>