[Bioc-devel] scanTabix coercion to data.frame
Hahne, Florian
florian.hahne at novartis.com
Wed Apr 18 08:42:20 CEST 2012
Ah, I see. I wasn't aware that we are supposed to develop on R-2.15,
although that makes perfect sense. How simple were the old days, when
biocDevel meant Rdevel. Sigh...
Florian Hahne
Novartis Institute For Biomedical Research
Translational Sciences / Preclinical Safety / PCS Informatics
Expert Data Integration and Modeling Bioinformatics
CHBS, WKL-135.2.26
Novartis Institute For Biomedical Research, Werk Klybeck
Klybeckstrasse 141
CH-4057 Basel
Switzerland
Phone: +41 61 6967127
Email : florian.hahne at novartis.com
On 4/16/12 10:17 PM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:
>On 04/16/2012 12:31 AM, Hahne, Florian wrote:
>> My bad, I updated all packages before trying this and never checked what
>> actually happened.
>> The odd thing is that I am running R-devel, I have the latest
>> BiocInstaller 1.5.6 installed but I still only get the bioc release
>> packages.:
>> > sessionInfo()
>> R Under development (unstable) (2012-04-16 r59045)
>> Platform: x86_64-unknown-linux-gnu/x86_64 (64-bit)
>
>R switched to an annual release cycle, whereas Bioc kept it's
>semi-annual release. Bioc during April - October uses 'release' R for
>both release and devel Bioc. So BiocInstaller was expecting you to have
>R-2-15 regardless of whether you were 'release' or 'devel' bioc.
>
>You can manage the two versions either with duplicate copies of R-2-15
>installed in different locations, or using the R_LIBS_USER (for example)
>environment variable to point to a user library that is different for
>Bioc release and for Bioc devel.
>
>Martin
>
>
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=C LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] rtracklayer_1.16.1 GenomicRanges_1.8.3 IRanges_1.14.2
>> [4] BiocGenerics_0.2.0 BiocInstaller_1.5.6
>>
>> loaded via a namespace (and not attached):
>> [1] Biostrings_2.24.1 bitops_1.0-4.1 BSgenome_1.24.0 RCurl_1.91-1
>> [5] Rsamtools_1.9.2 stats4_2.16.0 tools_2.16.0 XML_3.9-4
>> [9] zlibbioc_1.2.0
>>
>> I think I followed Dan's instructions carefully, any idea why this is
>> not working for me?
>>
>> The little bit of debugging I tried revealed that biocInstallRepos does
>> not give me the right repository path:
>> > biocinstallRepos()
>> BioCsoft
>> "http://www.bioconductor.org/packages/2.10/bioc"
>> CRAN
>> "http://cran.fhcrc.org"
>> BioCann
>> "http://www.bioconductor.org/packages/2.10/data/annotation"
>> BioCexp
>> "http://www.bioconductor.org/packages/2.10/data/experiment"
>> BioCextra
>> "http://www.bioconductor.org/packages/2.10/extra"
>>
>> Now in there I find:
>> > BiocInstaller:::biocinstallRepos
>> function (siteRepos = character())
>> {
>> .biocinstallRepos(siteRepos = siteRepos, devel = .isDevel())
>> }
>> <environment: namespace:BiocInstaller>
>>
>> And .isDevel is defined as
>>
>> > BiocInstaller:::.isDevel
>> function ()
>> {
>> isOdd <- (packageVersion("BiocInstaller")$minor%%2L) == 1L
>> isOdd && (R.version$status == "" || R.version$status == "Patched")
>> }
>> <environment: namespace:BiocInstaller>
>>
>> I may be wrong here, but how can I ever get TRUE unless I am running R
>> Patched or whatever R.version$status=="" refers to? Since I am running R
>> devel built from svn I have
>> > R.version$status
>> [1] "Under development (unstable)"
>>
>> So I will always and for all eternity get .isDevel()==FALSEŠ
>>
>> Florian
>>
>> Florian Hahne
>> Novartis Institute For Biomedical Research
>> Translational Sciences / Preclinical Safety / PCS Informatics
>> Expert Data Integration and Modeling Bioinformatics
>> CHBS, WKL-135.2.26
>> Novartis Institute For Biomedical Research, Werk Klybeck
>> Klybeckstrasse 141
>> CH-4057 Basel
>> Switzerland
>> Phone: +41 61 6967127
>> Email : florian.hahne at novartis.com <mailto:florian.hahne at novartis.com>
>>
>>
>> From: Michael Lawrence <lawrence.michael at gene.com
>> <mailto:lawrence.michael at gene.com>>
>> Date: Fri, 13 Apr 2012 09:19:20 -0700
>> To: NIBR <florian.hahne at novartis.com
>><mailto:florian.hahne at novartis.com>>
>> Cc: Michael Lawrence <lawrence.michael at gene.com
>> <mailto:lawrence.michael at gene.com>>, Sean Davis <sdavis2 at mail.nih.gov
>> <mailto:sdavis2 at mail.nih.gov>>, Martin Morgan <mtmorgan at fhcrc.org
>> <mailto:mtmorgan at fhcrc.org>>, "bioc-devel at r-project.org
>> <mailto:bioc-devel at r-project.org>" <bioc-devel at r-project.org
>> <mailto:bioc-devel at r-project.org>>
>> Subject: Re: [Bioc-devel] scanTabix coercion to data.frame
>>
>>
>>
>> On Fri, Apr 13, 2012 at 8:15 AM, Hahne, Florian
>> <florian.hahne at novartis.com <mailto:florian.hahne at novartis.com>> wrote:
>>
>> Yes, I tried this:
>> ff <-
>>
>>TabixFile("/CHBS/apps/itox/data/project_data_repository/1/1/project.tbx")
>> foo <- import(ff)
>> Error: evaluation nested too deeply: infinite recursion /
>> options(expressions=)?
>>
>> And this:
>>
>>
>> foo <- import(ff, which=GRanges(seqnames="chrX",
>>ranges=IRanges(start=1,
>> end=1e8)))
>> Error: evaluation nested too deeply: infinite recursion /
>> options(expressions=)?
>>
>> And then I gave up :-)
>>
>>
>>
>> Ok, well I said the devel version, i.e., 1.17.1, not 1.16.1.
>>
>> > sessionInfo()
>> R Under development (unstable) (2012-04-03 r58904)
>> Platform: x86_64-unknown-linux-gnu/x86_64 (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=C LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] rtracklayer_1.16.1 Rsamtools_1.9.2 Biostrings_2.24.1
>> [4] GenomicRanges_1.8.3 IRanges_1.14.2 BiocGenerics_0.2.0
>> [7] BiocInstaller_1.4.3
>>
>> loaded via a namespace (and not attached):
>> [1] bitops_1.0-4.1 BSgenome_1.24.0 RCurl_1.91-1 stats4_2.16.0
>> [5] tools_2.16.0 XML_3.9-4 zlibbioc_1.2.0
>>
>>
>>
>>
>>
>>
>>
>> Florian Hahne
>> Novartis Institute For Biomedical Research
>> Translational Sciences / Preclinical Safety / PCS Informatics
>> Expert Data Integration and Modeling Bioinformatics
>> CHBS, WKL-135.2.26
>> Novartis Institute For Biomedical Research, Werk Klybeck
>> Klybeckstrasse 141
>> CH-4057 Basel
>> Switzerland
>> Phone: +41 61 6967127 <tel:%2B41%2061%206967127>
>> Email : florian.hahne at novartis.com
>><mailto:florian.hahne at novartis.com>
>>
>>
>>
>>
>>
>>
>>
>> From: Michael Lawrence <lawrence.michael at gene.com
>> <mailto:lawrence.michael at gene.com>>
>> Date: Thu, 12 Apr 2012 10:07:31 -0700
>> To: NIBR <florian.hahne at novartis.com
>> <mailto:florian.hahne at novartis.com>>
>> Cc: Michael Lawrence <lawrence.michael at gene.com
>> <mailto:lawrence.michael at gene.com>>, Sean Davis
>> <sdavis2 at mail.nih.gov <mailto:sdavis2 at mail.nih.gov>>, Martin Morgan
>> <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>,
>> "bioc-devel at r-project.org <mailto:bioc-devel at r-project.org>"
>> <bioc-devel at r-project.org <mailto:bioc-devel at r-project.org>>
>> Subject: Re: [Bioc-devel] scanTabix coercion to data.frame
>>
>>
>> Did you try the latest devel version?
>>
>> On Thu, Apr 12, 2012 at 9:29 AM, Hahne, Florian
>> <florian.hahne at novartis.com <mailto:florian.hahne at novartis.com>>
>>wrote:
>>
>> Thanks, I gave it a shot and got this:
>> Error: evaluation nested too deeply: infinite recursion /
>> options(expressions=)?
>>
>>
>> Guess I'll stick with scanTabix for now :-)
>> Florian
>> Florian Hahne
>> Novartis Institute For Biomedical Research
>> Translational Sciences / Preclinical Safety / PCS Informatics
>> Expert Data Integration and Modeling Bioinformatics
>> CHBS, WKL-135.2.26
>> Novartis Institute For Biomedical Research, Werk Klybeck
>> Klybeckstrasse 141
>> CH-4057 Basel
>> Switzerland
>> Phone: +41 61 6967127 <tel:%2B41%2061%206967127>
>> <tel:%2B41%2061%206967127>
>> Email : florian.hahne at novartis.com
>><mailto:florian.hahne at novartis.com>
>>
>>
>>
>>
>>
>>
>>
>>
>> From: Michael Lawrence <lawrence.michael at gene.com
>> <mailto:lawrence.michael at gene.com>>
>> Date: Thu, 12 Apr 2012 06:54:19 -0700
>> To: NIBR <florian.hahne at novartis.com
>> <mailto:florian.hahne at novartis.com>>
>> Cc: Sean Davis <sdavis2 at mail.nih.gov <mailto:sdavis2 at mail.nih.gov>>,
>> Martin Morgan <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>,
>> "bioc-devel at r-project.org <mailto:bioc-devel at r-project.org>"
>> <bioc-devel at r-project.org <mailto:bioc-devel at r-project.org>>
>> Subject: Re: [Bioc-devel] scanTabix coercion to data.frame
>>
>>
>> You can use rtracklayer to import tabix files directly. If it's GFF
>>or
>> BED, you can just use import(). For arbitrary tabular files, first
>>cast
>> the path to a TabixFile, then pass it to import(). That last one is
>>not
>> well tested. It uses the header information
>> to know the starts, ends, etc.
>>
>> Michael
>>
>> On Thu, Apr 12, 2012 at 6:10 AM, Hahne, Florian
>> <florian.hahne at novartis.com <mailto:florian.hahne at novartis.com>>
>>wrote:
>>
>> Sean, Martin, thanks for the suggestions. I guess a combination of
>> the two
>> would work well for me. I create my own tabix files and could
>>certainly
>> stick the type information in the header. And I wasn't aware of
>> textConnection(), which seems to be performant enough to do what I
>>want.
>> At least it is much better than my manual parsing...
>> One problem remains, though: the tabix files are being created from
>> within
>> R, and I don't think there is any support to add arbitrary header
>>lines
>> available yet. Or is there?
>>
>> Florian
>>
>>
>> Florian Hahne
>> Novartis Institute For Biomedical Research
>> Translational Sciences / Preclinical Safety / PCS Informatics
>> Expert Data Integration and Modeling Bioinformatics
>> CHBS, WKL-135.2.26
>> Novartis Institute For Biomedical Research, Werk Klybeck
>> Klybeckstrasse 141
>> CH-4057 Basel
>> Switzerland
>> Phone: +41 61 6967127 <tel:%2B41%2061%206967127>
>> <tel:%2B41%2061%206967127>
>> Email : florian.hahne at novartis.com
>><mailto:florian.hahne at novartis.com>
>>
>>
>>
>>
>>
>>
>>
>>
>> On 4/12/12 2:08 PM, "Sean Davis" <sdavis2 at mail.nih.gov
>> <mailto:sdavis2 at mail.nih.gov>> wrote:
>>
>> >On Thu, Apr 12, 2012 at 7:57 AM, Martin Morgan <mtmorgan at fhcrc.org
>> <mailto:mtmorgan at fhcrc.org>> wrote:
>> > > On 04/12/2012 01:19 AM, Hahne, Florian wrote:
>> > >>
>> > >> Hi all,
>> > >> I frequently get into the situation that I import data from a
>>Tabix
>> > >>file
>> > >> using scanTabix and get a list of character vectors which I
>> first need
>> > >>to
>> > >> split back into columns using strsplit, followed by some type
>> coercion
>> > >>and
>> > >> lapply/sapply to actually get a list of data.frames which is
>> what I'd
>> > >> really want out in the first place. I may be missing something
>>here,
>> > >>but
>> > >> wouldn't it be possible to ask scanTabix for a list of
>>data.frames
>> > >> directly, and maybe even providing a vector of data types to
>>coerce
>> > >>into,
>> > >> a la 'colClasses' in read.table? It just seems to me that these
>> > >>operations
>> > >> could be done much more efficiently on the C level.
>> > >
>> > >
>> > > It's definitely poorly developed but one doesn't really want to
>> > >re-invent
>> > > too much of the parsing wheel. Does
>> > >
>> > > res <- scanTabix("/foo.tbx")
>> > > read.table(textConnection(res), header=TRUE, sep="\t")
>> > >
>> > > do the trick in a reasonably performant way? Obviously less than
>> ideal,
>> > >with
>> > > the data represented as character vectors and then as
>>data.frame. A
>> > >better
>> > > solution (colClasses ==> data.frame) wouldn't be impossible, but
>> > >guessing
>> > > column types would be a lot of redundant work.
>> >
>> >Since tabix allows arbitrary header lines, one could store
>>metadata in
>> >the first few lines and use that to store column info and classes.
>> >One can get at the header using Rsamtools
>> >headerTabix(TabixFile('foo.tbx')). This is getting more toward
>> >developer-land than end-user, though, since the tabix file would
>>need
>> >to be created with these uses in mind.
>> >
>> >Sean
>> >
>> >
>> > >> Thanks,
>> > >> Florian
>> > >>
>> > >>
>> > >> Florian Hahne
>> > >> Novartis Institute For Biomedical Research
>> > >> Translational Sciences / Preclinical Safety / PCS Informatics
>> > >> Expert Data Integration and Modeling Bioinformatics
>> > >> CHBS, WKL-135.2.26
>> > >> Novartis Institute For Biomedical Research, Werk Klybeck
>> > >> Klybeckstrasse 141
>> > >> CH-4057 Basel
>> > >> Switzerland
>> > >> Phone: +41 61 6967127 <tel:%2B41%2061%206967127>
>> <tel:%2B41%2061%206967127>
>> > >> Email : florian.hahne at novartis.com
>> <mailto:florian.hahne at novartis.com>
>> > >>
>> > >> _______________________________________________
>> > >> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>> mailing list
>> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >
>> > >
>> > >
>> > > --
>> > > Computational Biology
>> > > Fred Hutchinson Cancer Research Center
>> > > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>> > >
>> > > Location: M1-B861
>> > > Telephone: 206 667-2793 <tel:206%20667-2793>
>><tel:206%20667-2793>
>> > >
>> > >
>> > > _______________________________________________
>> > > Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>> mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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>
>
>--
>Computational Biology
>Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
>Location: M1-B861
>Telephone: 206 667-2793
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