[Bioc-sig-seq] readAligned and BAM format

[Sean Davis]

On Tue, Dec 8, 2009 at 6:06 PM, Pratap, Abhishek
<APratap at som.umaryland.edu> wrote:
> Sorry I could not find the way to install BioC dev version. I was looking here : http://www.bioconductor.org/docs/install/

Hi, Abhi.

Simply install the development version of R (available from the CRAN
website) and then use biocLite() as usual.  You will get the devel
versions of bioconductor packages.

Sean

> -----Original Message-----
> From: Sean Davis [mailto:seandavi at gmail.com]
> Sent: Tuesday, December 08, 2009 5:30 PM
> To: Pratap, Abhishek
> Cc: bioc-sig-sequencing at r-project.org
> Subject: Re: [Bioc-sig-seq] readAligned and BAM format
>
> On Tue, Dec 8, 2009 at 5:26 PM, Pratap, Abhishek
> <APratap at som.umaryland.edu> wrote:
>> If following a hint that I should move to R-devel for testing RSamtools.
>
> Yes.  You'll need to be using R-devel and the devel branch of bioconductor.
>
>> This is while trying to install RSAMTools
>>
>> Warning in .completeClassSlots(ClassDef, where) :
>>  undefined slot classes in definition of "Alignments0":
>> gapped_ranges(class "GappedRanges")
>> Error in setValidity2("Alignments0", .valid.Alignments0, where =
>> asNamespace("Rsamtools")) :
>>  unused argument(s) (where = asNamespace("Rsamtools"))
>> Error : unable to load R code in package 'Rsamtools'
>> ERROR: lazy loading failed for package 'Rsamtools'
>> * removing
>> '/local/projects/grc/devel/apratap/softwares/R-2.10.0/lib64/R/library/Rs
>> amtools
>>
>>
>> -Abhi
>>
>> -----Original Message-----
>> From: bioc-sig-sequencing-bounces at r-project.org
>> [mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf Of Pratap,
>> Abhishek
>> Sent: Tuesday, December 08, 2009 5:20 PM
>> To: Martin Morgan
>> Cc: bioc-sig-sequencing at r-project.org
>> Subject: Re: [Bioc-sig-seq] readAligned and BAM format
>>
>> Thanks Martin. Clearly shows I am just getting started :).
>>
>> -Abhi
>>
>> -----Original Message-----
>> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
>> Sent: Tuesday, December 08, 2009 5:17 PM
>> To: Pratap, Abhishek
>> Cc: Wu Wei; bioc-sig-sequencing at r-project.org
>> Subject: Re: [Bioc-sig-seq] readAligned and BAM format
>>
>> Pratap, Abhishek wrote:
>>> Hi Martin
>>>
>>> Just wondering if people outside the firewall/network without passw
>>> could download this package ?
>>
>> Hi Abhi -- there are short instructions on use of svn, including
>> password, at
>>
>>  http://wiki.fhcrc.org/bioc/SvnHowTo
>>
>> Important to note that this package is very much under active
>> development, so subject to frequent and unpredictable change.
>>
>> Martin
>>
>>>
>>>
>>> Thanks,
>>> -Abhi
>>>
>>> -----Original Message-----
>>> From: bioc-sig-sequencing-bounces at r-project.org
>>> [mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf Of Martin
>>> Morgan
>>> Sent: Monday, November 02, 2009 8:58 AM
>>> To: Wu Wei
>>> Cc: bioc-sig-sequencing at r-project.org
>>> Subject: Re: [Bioc-sig-seq] readAligned and BAM format
>>>
>>> Hi Wave --
>>>
>>> svn co
>>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools
>>>
>>> R CMD INSTALL --clean Rsamtools
>>>
>>> see the script in Rsamtools/inst/script/readAligned_prototype.R
>>>
>>> e.g.,
>>>
>>>   source(system.file("script", "readAligned_prototype.R",
>>>                      package="Rsamtools"))
>>>   .readAligned_bam(<...>) # args like the other readAligned
>>>
>>> see ?scanBam for additional ideas.
>>>
>>> Martin
>>>
>>> Wu Wei wrote:
>>>> Hi Martin,
>>>>
>>>> I am also looking for that. Would you please also forward that
>>>> additional info to me.
>>>>
>>>> Thanks,
>>>> Wave
>>>>
>>>> On 2 Nov 2009, at 14:34, Martin Morgan wrote:
>>>>
>>>>> Joern Toedling wrote:
>>>>>> Hi everyone,
>>>>>>
>>>>>> has anybody by chance already written a parser for importing
>>>>>> alignments in
>>>>>> BAM/SAM format into objects of class AlignedRead? This format seems
>>>>>> to be
>>>>>> gaining more and more support, yet it is still absent from the
>>>>>> options in
>>>>>> function readAligned. If one of you already has written such a
>>> parsing
>>>>>> function and would not mind sharing it, please let me know.
>>>>> Hi Joern -- there is a package in the Bioc svn repository that does
>>>>> this; it is not yet in the devel branch, there are some limitations
>>> in
>>>>> terms of AlignedRead (e.g., AlignedRead currently supports only
>>> ungapped
>>>>> alignments, whereas BAM allows gapped). I'll forward additional info
>>>>> off-list.
>>>>>
>>>>> Martin
>>>>>> Best regards,
>>>>>> Joern
>>>>>>
>>>>>> ---
>>>>>> Joern Toedling
>>>>>> Institut Curie -- U900
>>>>>> 26 rue d'Ulm, 75005 Paris, FRANCE
>>>>>> Tel. +33 (0)156246926
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-sig-sequencing mailing list
>>>>>> Bioc-sig-sequencing at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>>>
>>>>> --
>>>>> Martin Morgan
>>>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>>>> 1100 Fairview Ave. N.
>>>>> PO Box 19024 Seattle, WA 98109
>>>>>
>>>>> Location: Arnold Building M1 B861
>>>>> Phone: (206) 667-2793
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-sig-sequencing mailing list
>>>>> Bioc-sig-sequencing at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>>
>>>>
>>>> Wu Wei
>>>> Postdoctoral Fellow
>>>> Steinmetz Group, EMBL Heidelberg
>>>> Tex: +49 6221 387-8310 (8114)
>>>> Fax: +49 6221 387-8518
>>>> Email: wuwei at embl.de
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>> --
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>> _______________________________________________
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>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
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