I'm in favor of this display. The seqinfo output at the bottom has always been annoying (over-emphasized).
On Mon, Sep 8, 2014 at 10:08 PM, Vincent Carey <st...@channing.harvard.edu> wrote: > > > On Tue, Sep 9, 2014 at 12:30 AM, Hervé Pagès <hpa...@fhcrc.org> wrote: > >> On 09/08/2014 06:42 PM, Michael Lawrence wrote: >> >>> Instead of printing out multiple lines of a table that is rarely of >>> interest, could we develop Peter's idea toward something like: >>> >>> hg19:chr1 hg19:chr2 ... >>> [lengths ...] >>> >>> Not sure what condensed notation would be useful for circularity. >>> >> >> I don't know either. I'm worried that this would make the seqinfo >> stuff look like a named vector and that the user would expect >> hg19:chr1, hg19:chr2, etc... to be valid names. >> >> With the table-like layout, some screen real estate can always be >> saved by printing less lines: >> >> > What I had in mind was > > >> > gr >> GRanges with 3 ranges and 0 metadata columns: >> > genome: hg19 > >> seqnames ranges strand >> <Rle> <IRanges> <Rle> >> [1] chr14 [19069583, 19069654] + >> [2] chr14 [19363738, 19363809] + >> [3] chr14 [19363755, 19363826] - >> [4] chr14 [19369799, 19369870] + >> > > > you could then probably dispense with the seqlengths. i have > never found them too useful except as a key to the genome. > > if there are multiple genomes, we have something like > > genomes: hg19, mm9 > > the point is to make it prominent, particularly at a time of transition. > > > >> --- seqinfo: 60 seqlevels (2 circulars) on 2 genomes (hg19, mm10) --- >> seqlevels seqlengths isCircular genome >> chr1 249250621 <NA> hg19 >> chr10 135534747 <NA> hg19 >> ... ... ... ... >> chrX 155270560 <NA> hg19 >> chrY 59373566 <NA> hg19 >> >> I agree that the exact content of the seqinfo table itself is rarely >> of interest so printing only 3 or 4 lines is OK. IMO it's important >> to make the user aware of the existence of this hidden table and to >> display it like what it really is (i.e. a table). Also displaying the >> column names is a well established tradition and serves the purpose >> of providing a quick summary of the accessors that are available to >> access those fields. >> >> H. >> >> >>> >>> On Mon, Sep 8, 2014 at 5:21 PM, Peter Hickey <hic...@wehi.edu.au >>> <mailto:hic...@wehi.edu.au>> wrote: >>> >>> Perhaps it might be useful to have some way of highlighting if any >>> of the chromosomes are circular or highlighting if there are >>> multiple genomes present? Otherwise this information might be hidden >>> in the "…" >>> >>> Cheers, >>> Pete >>> >>> >>> On 09/09/2014, at 9:44 AM, Hervé Pagès <hpa...@fhcrc.org >>> <mailto:hpa...@fhcrc.org>> wrote: >>> >>> > On 09/08/2014 02:28 PM, Peter Hickey wrote: >>> >> Just a vote for still allowing for multiple genomes in a Seqinfo >>> object (in a GRanges object). My use case is in bisulfite-sequencing >>> experiments where there is often a spike-in of a lambda phage genome >>> along with the genome of interest (human or mouse). It's often >>> useful to keep all data from a single library together in the same >>> objet but process according to genome(x) for each seqlevel. >>> > >>> > Note taken. Thanks Pete! It's always great to know about concrete >>> use >>> > cases. >>> > >>> >> >>> >> FWIW, I like Vincent's proposal of selectSome(unique(genome(x))) >>> in the show method. >>> > >>> > Or what about displaying the genome next to the seqlevel it's >>> > associated with? Like e.g.: >>> > >>> > > gr >>> > GRanges with 3 ranges and 0 metadata columns: >>> > seqnames ranges strand >>> > <Rle> <IRanges> <Rle> >>> > [1] chr14 [19069583, 19069654] + >>> > [2] chr14 [19363738, 19363809] + >>> > [3] chr14 [19363755, 19363826] - >>> > [4] chr14 [19369799, 19369870] + >>> > --- >>> > seqinfo: >>> > seqlevels seqlengths isCircular genome >>> > chr1 249250621 <NA> hg19 >>> > chr10 135534747 <NA> hg19 >>> > chr11 135006516 <NA> hg19 >>> > ... ... ... ... >>> > chrUn_gl000249 38502 <NA> hg19 >>> > chrX 155270560 <NA> hg19 >>> > chrY 59373566 <NA> hg19 >>> > >>> > That way, we also raise awareness about the isCircular field. >>> > The current choice to only display the seqlengths pre-dates the >>> > existence of the seqinfo slot but might be a little bit misleading >>> > those days since it only exposes some arbitrary seqinfo fields. >>> > >>> > H. >>> > >>> >> >>> >> Cheers, >>> >> Pete >>> >> >>> >> >>> >>> I might have requested the genome annotation, but I'm pretty >>> sure it wasn't >>> >>> me who decide on tracking it on a per-sequence basis. I could >>> imagine use >>> >>> cases for that though, e.g., when diagnosing sequencing >>> contamination (like >>> >>> human vs. mouse). But most other tools and file formats expect >>> a single >>> >>> genome per "track", so, for example, rtracklayer has an >>> internal function >>> >>> singleGenome() to take care of this. >>> >>> >>> >>> On Mon, Sep 8, 2014 at 10:50 AM, Herv? Pag?s <hpa...@fhcrc.org >>> <mailto:hpa...@fhcrc.org>> wrote: >>> >>> >>> >>>> Hi Vince, >>> >>>> >>> >>>> Yes it would make sense to have the "show" method report the >>> genome >>> >>>> when genome(x) contains a unique non-NA value. I think the main >>> >>>> use case for having the genome defined at the sequence level >>> instead >>> >>>> of the whole object level is metagenomics. Maybe Michael has >>> some other >>> >>>> good use cases to share since IIRC he requested the addition >>> of the >>> >>>> genome field a couple of years ago and made the case for >>> having it >>> >>>> defined at the sequence level. >>> >>>> >>> >>>> Cheers, >>> >>>> H. >>> >>>> >>> >>>> >>> >>>> On 09/08/2014 07:21 AM, Vincent Carey wrote: >>> >>>> >>> >>>>> For GRanges x, my naive expectation is that genome(x) returns >>> a length- >>> >>>>> >>> >>>>> one tag identifying the genome to which chromosomal >>> coordinates >>> >>>>> >>> >>>>> correspond. The genome() method seems to have >>> sequence-specific >>> >>>>> >>> >>>>> semantics, which makes sense, but when we identify sequence >>> >>>>> >>> >>>>> with chromosome, it seems too complicated. Is there a use >>> case for >>> >>>>> >>> >>>>> a GRanges with sequences from several different genomes? >>> >>>>> >>> >>>>> >>> >>>>> One reason I am inquiring is that I feel it would be nice to >>> have the >>> >>>>> GRanges show() method report, prominently, the genome in use >>> (or NA >>> >>>>> >>> >>>>> if unspecified). This could be accomplished by reporting >>> >>>>> unique(genome(x)), and perhaps that would be satisfactory. >>> >>>>> >>> >>>>> after example(genome) : >>> >>>>> >>> >>>>> seqinfo(txdb) >>> >>>>>> >>> >>>>> >>> >>>>> Seqinfo of length 15 >>> >>>>> >>> >>>>> seqnames seqlengths isCircular genome >>> >>>>> >>> >>>>> CH2L 23011544 FALSE dm3 >>> >>>>> >>> >>>>> CH2R 21146708 FALSE dm3 >>> >>>>> >>> >>>>> CH3L 24543557 FALSE dm3 >>> >>>>> >>> >>>>> CH3R 27905053 FALSE dm3 >>> >>>>> >>> >>>>> CH4 1351857 FALSE dm3 >>> >>>>> >>> >>>>> ... ... ... ... >>> >>>>> >>> >>>>> CH3LHet 2555491 FALSE dm3 >>> >>>>> >>> >>>>> CH3RHet 2517507 FALSE dm3 >>> >>>>> >>> >>>>> CHXHet 204112 FALSE dm3 >>> >>>>> >>> >>>>> CHYHet 347038 FALSE dm3 >>> >>>>> >>> >>>>> CHUextra 29004656 FALSE dm3 >>> >>>>> >>> >>>>> genome(seqinfo(txdb)) >>> >>>>>> >>> >>>>> >>> >>>>> CH2L CH2R CH3L CH3R CH4 CHX >>> CHU M >>> >>>>> >>> >>>>> "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" >>> "dm3" "dm3" >>> >>>>> >>> >>>>> CH2LHet CH2RHet CH3LHet CH3RHet CHXHet CHYHet CHUextra >>> >>>>> >>> >>>>> "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" >>> >>>>> >>> >>>>> [[alternative HTML version deleted]] >>> >>>>> >>> >>>>> _______________________________________________ >>> >>>>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >>> mailing list >>> >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>>>> >>> >>>>> >>> >>>> -- >>> >>>> Herv? Pag?s >>> >>>> >>> >>>> 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: hpa...@fhcrc.org <mailto:hpa...@fhcrc.org> >>> >>>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> >>> >>>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> >>> >>>> >>> >>>> >>> >>>> _______________________________________________ >>> >>>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >>> mailing list >>> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>>> >>> >> >>> >> -------------------------------- >>> >> Peter Hickey, >>> >> PhD Student/Research Assistant, >>> >> Bioinformatics Division, >>> >> Walter and Eliza Hall Institute of Medical Research, >>> >> 1G Royal Parade, Parkville, Vic 3052, Australia. >>> >> Ph: +613 9345 2324 <tel:%2B613%209345%202324> >>> >> >>> >> hic...@wehi.edu.au <mailto:hic...@wehi.edu.au> >>> >> http://www.wehi.edu.au >>> >> >>> >> >>> ____________________________________________________________ >>> __________ >>> >> The information in this email is confidential and >>> intend...{{dropped:6}} >>> >> >>> >> _______________________________________________ >>> >>Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >>> mailing list >>> >>https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >>> > >>> > -- >>> > 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:hpa...@fhcrc.org <mailto:hpa...@fhcrc.org> >>> > Phone:(206) 667-5791 <tel:%28206%29%20667-5791> >>> > Fax:(206) 667-1319 <tel:%28206%29%20667-1319> >>> >>> -------------------------------- >>> Peter Hickey, >>> PhD Student/Research Assistant, >>> Bioinformatics Division, >>> Walter and Eliza Hall Institute of Medical Research, >>> 1G Royal Parade, Parkville, Vic 3052, Australia. >>> Ph: +613 9345 2324 <tel:%2B613%209345%202324> >>> >>> hic...@wehi.edu.au <mailto:hic...@wehi.edu.au> >>> http://www.wehi.edu.au >>> >>> >>> ____________________________________________________________ >>> __________ >>> The information in this email is confidential and >>> intend...{{dropped:8}} >>> >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing >>> list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> >>> >> -- >> 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: hpa...@fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel