[Bioc-sig-seq] readAligned and BAM format

Pratap, Abhishek APratap at som.umaryland.edu
Wed Dec 9 00:06:06 CET 2009


Sorry I could not find the way to install BioC dev version. I was looking here : http://www.bioconductor.org/docs/install/


-Abhi

-----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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