Hi all,
I just realized that serialized PairwiseAlignmentsSingleSubject objects
grow ridiculously large:
x <- "xxxabcdefghijklmnopqyyy"
y <- "abcdhijklmnpqr"
pa <- pairwiseAlignment(x,y)
save(pa, file="~/tmp/pa.rda")
file.info("~/tmp/pa.rda")
size isdir mode mtim
it)
>>>
>>> locale:
>>> [1] C
>>>
>>> attached base packages:
>>> [1] parallel stats graphics grDevices utils datasets methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] Biostrings_2.
"subject" "type" "score"
>"gapOpening"
> [6] "gapExtension"
> > validObject(pa)
> [1] TRUE
> > object.size(pa)
> 35528 bytes
>
>... instead of 35308996 bytes! 3 orders of magnitude smaller :-)
Hi Herve,
a while ago I was asking about the possibility to store the reverse
mapping in the resulting GRanges object after a reduce operation, and as
far as I remember you agreed to put this on the to-do list for 2.11. I
can't find any documentation about it in the man pages, and the code of
the G
I've hacked up some code that uses BatchJobs but makes it look like a
normal parLapply operation. Currently the main R process is checking the
state of the queue in regular intervals and fetches results once a job has
finished. Seems to work quite nicely, although there certainly are more
elaborate
I am interested in all three, and for many of our large genomics
experiments 3) seems to become more and more important. All large
centralized clusters seem to rely on scheduling systems these days.
--
On 11/15/12 7:53 PM, "Henrik Bengtsson" wrote:
>Is there any write up/discussion/plans o
Hi Anita,
it seems that FilterRules is defined in the IRanges package. If you want
to use it you will have to explicitly import it. Can't quite see how this
is related to importing or not importing ShortRead. The only reason why
this works when you require ShortRead is because it depends on IRanges
Oh wait, correction. Not your fault. I thought you call FilterRules
directly. So ShortRead is using it internally in methods-SRFilter.R and
never imports it from IRanges. Looks like a simple fix in there.
Florian
--
On 11/16/12 12:40 PM, "Anita Lerch" wrote:
>Hi,
>
>I have two problems whe
evel] BiocParallel
This sounds very useful when mixing batch jobs with an interactive session. In
fact, it's something I was planning to do, since I noticed their execution
model is completely asynchronous. Is it actually a new cluster backend for the
parallel package?
Michael
O
a related note, it might be nice to add Bioconductor-compatible
>versions of foreach and the plyr functions to BiocParallel if they're
>not already compatible.
>
>On 11/16/2012 12:18 AM, Hahne, Florian wrote:
>> I've hacked up some code that uses BatchJobs but makes it look l
Hi Henrik,
I have now come up now with a relatively generic version of this
SGEcluster approach. It does indeed use BatchJobs under the hood and
should thus support all available cluster queues, assuming that the
necessary batchJobs routines are available. I could only test this on our
SGE cluster,
Hi Michael,
I realized that rtracklayer does not handle path expansion in file names
well:
export.2bit(seqs, con="~/test.2bit")
Error in .TwoBits_export(mapply(.DNAString_to_twoBit, object, seqnames),
:
UCSC library operation failed
In addition: Warning message:
In .TwoBits_export(mapply(.DNASt
Hi Dario,
the most efficient way to transform between list-like structures of
GRanges objects and single GRanges is to use the GRangesList class in the
first place. Not sure how you came up with your initial list, but assuming
that blockRanges is already a GRangesList object, unlist(blockRanges) wi
Hi all,
Novartis in Cambridge is hiring a data analyst to work on large scale
genomics data with a background in R/Bioconductor. Take a look if you are
interested:
https://sjobs.brassring.com/2057/ASP/TG/cim_jobdetail.asp?partnerid=13617&s
iteid=5260&jobid=1907772&codes=novcom
Florian
--
You've probably already spotted this, but GenomicRanges seems to be
broken, and because I just upgraded to the latest R I now can't build most
of the Bioconductor packages that depend on it.
> biocLite("GenomicRanges")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInsta
roject in
>>>> progress to address this.
>>>>
>>>> http://www.bioconductor.org/developers/gsoc2013/ (towards the bottom)
>>>>
>>>> Dan
>>>>
>>>>
>>>> > /Henrik
>>>> >
>>>> &
Thanks for the info, the package now installs. Looks pretty cool. Attached
is my first hack at this from a couple of months ago. In a way it is very
similar to what you guys are doing, only that It predates the times of a
formal registry for parallel backends. I just tried to make it look like a
cl
Hi List, Martin,
I just wanted to quickly ask about the status of the BiocParallel package and
the cluster support in particular. Is this project finished? And are there
plans to having BiocParallel as a proper package again, or will it remain a GIT
project?
Florian
[[alternative HTML v
Great, thanks for the feedback. I will give it a try asap.
Am Sep 3, 2013 um 15:03 schrieb "Martin Morgan" :
> On 09/03/2013 05:25 AM, Hahne, Florian wrote:
>> Hi List, Martin,
>> I just wanted to quickly ask about the status of the BiocParallel package and
>> th
Hi all,
I used to be able to do this:
as.data.frame(DataFrame(), stringsAsFactors=TRUE)
now I get a warning:
Warning in as.data.frame(DataFrame(), stringsAsFactors = TRUE) :
Arguments in '...' ignored
Do I have the guarantee nowadays that coercing a DataFrame to a data.frame does
not cast cha
Hi Marc,
I saw these warnings in Gviz, but they stem from GenomicFeatures
Warning messages:
1: 'isActiveSeq' is deprecated.
Use 'seqlevels' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
2: 'isActiveSeq' is deprecated.
Use 'seqlevels' instead.
See help("Deprecated") and he
lto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] coercing DataFrame to data.frame
On Fri, Sep 13, 2013 at 7:35 AM, Hahne, Florian
mailto:florian.ha...@novartis.com>> wrote:
Hi all,
I used to be able to do this:
as.data.frame(DataFrame(), stringsAsFactors=TRUE)
now I get a war
eSeq() just so that
users have less to learn about. The reason why isActiveSeq was different from
seqlevels was just because it was born for a TranscriptDb (which is based on an
annotation database) instead of being born on a GRanges object. So seqlevels
was the more general tool.
Marc
n for a TranscriptDb (which is based on an
annotation database) instead of being born on a GRanges object. So seqlevels
was the more general tool.
Marc
On 09/13/2013 07:24 AM, Hahne, Florian wrote:
Hi Marc,
I saw these warnings in Gviz, but they stem from GenomicFeatures
Warning mess
- a little bit more user-friendly on
>>> those objects.
>>>
>>> Thanks,
>>> H.
>>>
>>>
>>> On 09/13/2013 10:38 AM, Marc Carlson wrote:
>>>> Hi Florian,
>>>>
>>>> Yes we are trying to make things mo
Same view here,
with all the different data types that are around in the Bioconductor
world these days it seems to me that a consistent behaviour is preferable.
Florian
On 9/24/13 8:22 AM, "Hervé Pagès" wrote:
>Hi Florian, Marc,
>
>On 09/18/2013 11:55 PM, Hahne, Floria
Hi Herve,
is there really a hard requirement on the input files to forgeBSgenomeDataPkg
to be unzipped? Even though one would usually only build a particular BSGenome
package once, this seems to be such an arcane requirement nowadays with gzip
connections and the like.
Florian
[[altern
We discussed with Michael Lang at the Cambridge meeting and he agreed to
think about potential abstractions for nested parallelization requests in
BatchJobs. Not sure whether that ever took off. Ideally one would be able
to infer the number of requested nodes AND cpus directly from the
BiocParallel
Hi Sebastian,
Hm, this looks odd indeed. I am wondering whether this is some sort of
name space problem. Does the same happen when you create your ³A² dummy
class and the ³[³ method in a little dummy package with its own name
space? Something seems to be messing up the methods table when you define
Hi Sebastian,
This could be a rounding error. I will have to take a closer look at it
and will get back to you asap.
Thanks for reporting,
Florian
PS: Pviz looks nice. Already have a couple of use cases :-)
On 02/05/14 21:52, "Sebastian Gibb" wrote:
>sTrack <- SequenceTrack(Hsapiens)
>
__
Hi Lance,
Sorry for the late reply, I was out of office for the last two weeks. Looks
like you indeed discovered a bug which I may have introduced during the last
changes to the ylim code. Thanks for the report, and even more so for the
patch! I will make the necessary code changes in both the r
uot; (default). There are probably use
>case I have not thought about and I have not done extensive testing,
>maybe Florian can explain why the letters are set this way.
>
>Best.
>Renan
>
>
>From: Hahne, Florian [florian.ha...@novartis.com]
&
Thanks Martin,
Btw, is there some sort of disconnect on BioC Devel right now with regards
to the latest package versions? Since the release there are some rather
strict requirements in my DESCRIPTION file, but some of the packages
versions are not available from BiocLite:
[s_itoxadm@chbslx1501:~/R
Hi all,
I was wondering whether some of the rather arbitrary restrictions on input
files for the process of forging as new Bsgenome package could be liftet. In
particular:
Why do we need all chromosomes in individual files? Couldn�t the function be
smart enough to just extract the relevant bits
l now says:
>
> The sequence data must be in a single twoBit file (e.g. musFur1.2bit)
> or in a collection of FASTA files (possibly gzip-compressed).
>
>I guess I should also support a single FASTA file.
>
>H.
>
>On 09/29/2014 01:36 AM, Hahne, Florian wrote:
>>
Hi Tiphaine,
You can follow Vince¹s advice and transform all the data into proper ASCII
character. Or you can just get rid of the culprit (being the @biomart slot
of the object) before serialising. The easiest way to do that is:
foo@biomart <- NULL
The slot is only present to cache the BiomaRt conn
Hi Laurent,
I had a similar issue a couple of days ago, but the error would only show
up when building the vignette of a package, rather than during package
loading. I tried to dig around for a while but really could not find the
bottom of this. In the end I decided to update my R-devel version, an
I think there is indeed something more fundamentally broken here:
> R.version
_
platform x86_64-apple-darwin13.4.0
arch x86_64
os darwin13.4.0
system x86_64, darwin13.4.0
status Under development (unstable)
major 3
minor
That might well be. I can't recall doing anything special, but I'll try to
uninstall BiocInstaller the next time I run into a similar issue to test
this.
Florian
On 05/11/14 18:02, "Dan Tenenbaum" wrote:
>Taking a closer look at your email...
>
>> - Original Message -
>> > From: "Floria
Hi Michael,
I'll take a look. In order to improve my code: what exactly do you think
should be part of the initialiser, and what should be in the constructor?
There don't seem to bee any clear guidelines out there anywhere. And if
all logic goes in the constructor, how does one deal with more compl
gt;Hope that helps,
>Michael
>
>
>
>
>
>On Mon, Jan 26, 2015 at 12:38 AM, Hahne, Florian
> wrote:
>> Hi Michael,
>> I'll take a look. In order to improve my code: what exactly do you think
>> should be part of the initialiser, and what should be in
Hi Vince,
I haven't looked too much at the OrganismDb stuff yet. Just let me know
when you run into any major roadblocks for a Gviz patch. We could refactor
some things to make it work.
FLorian
On 13/02/15 19:01, "Vincent Carey" wrote:
>Gviz has a nice way of working with TxDb instances to deriv
Hi Johannes,
Great! This is really useful and something I wanted to do since a while.
I am doing all of my development on the svn repository. Not sure about the
githup clone.
If you want to you can just send the files you changes by mail and I will
take a look at the diff.
FLorian
On 04/11/15 15:
Wow, you are busy :-)
I will just wait until I receive all of you patches before adding them to
the official package release.
Florian
On 09/11/15 16:08, "Bioc-devel on behalf of Rainer Johannes"
wrote:
>Dear All, dear Florian,
>
>I¹m currently working on a Gviz-hack that would enable to use the
This is a problem with the biomaRt package and its connection to the Ensembl
archives, not Gviz. Here’s the call the fails:
listMarts(host="feb2012.archive.ensembl.org", path="/biomart/martservice")
It looks like Ensembl is no longer providing a download for the feb2012
archive. You could try th
though the assembly name could be parsed and
compared with the ENSEMBL genome version string.
Florian
we
On 26/07/16 21:27, "Obenchain, Valerie"
wrote:
>Hi Florian,
>
>On 07/21/2016 01:47 AM, Hahne, Florian wrote:
>> This is a problem with the biomaRt package and its
On 26/07/16 21:27, "Obenchain, Valerie"
wrote:
>Hi Florian,
>
>On 07/21/2016 01:47 AM, Hahne, Florian wrote:
>> This is a problem with the biomaRt package and its connection to the Ensembl
>> archives, not Gviz. Here’s the call the fails:
>> listMarts(hos
versions (Dasnov2.0 and
ARMA). A one to many mapping only makes sense for minor releases (e.g., human
or mouse). UCSC will always assign a new genome identifier to each major
release.
Florian
On 27/07/16 16:57, "Obenchain, Valerie"
wrote:
>Hi,
>
>On 07/27/2016 04:49 AM, H
I thought that this all originates in biovizBase? So there’s nothing to change
in Gviz unless I miss a crucial point here.
Florian
On 06.04.17, 19:10, "Bioc-devel on behalf of Stian Lågstad"
wrote:
How does the error deadline tomorrow (http://www.bioconductor.org/
developers/release-sc
Thanks, Rainer. Always happy if I don’t have to fix anything ☺
From: Rainer Johannes
Date: Thursday, 6 April 2017 at 22:07
To: "Obenchain, Valerie"
Cc: Stian Lågstad , Michael Lawrence
, "bioc-devel@r-project.org"
, Florian Hahne
Subject: Re: [Bioc-devel] Filter classes moved from ensembldb t
And by Rainer I mean Johannes. It is late…
From: Rainer Johannes
Date: Thursday, 6 April 2017 at 22:07
To: "Obenchain, Valerie"
Cc: Stian Lågstad , Michael Lawrence
, "bioc-devel@r-project.org"
, Florian Hahne
Subject: Re: [Bioc-devel] Filter classes moved from ensembldb to
AnnotationFilter
And why exactly is it becoming defunct? That is the first time I hear that it
will be. The warning message is:
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'GenomeAxisTrack,ANY,ANY,ANY'
All user-level objects in a package (including S
52 matches
Mail list logo
