[Bioc-devel] Request for comment metagenomeFeatures package

[Vincent Carey]

On Tue, Aug 4, 2015 at 3:00 PM, Martin Morgan <mtmorgan at fredhutch.org>
wrote:

> On 08/04/2015 06:43 AM, Nathan Olson wrote:
>
>> We are starting to work on an infrastructure for annotation of 16S
>> metagenomic
>> sequencing datasets and would like your comments and/or contributions.
>> Below are
>> links to two github repositories: metagenomeFeatures and
>> greengenes13.5MgDb.
>> The metagenomeFeatures package contains two classes; mgDb, for 16S
>> sequence
>> databases, and metagenomeAnnotation, for annotating a sequence dataset
>> with
>> taxonomic information from a mgDb object.  The greengenes13.5MgDb
>> package, loads
>> a mgDb object with the greengenes 13.5 database.  greengenes 13.5 was
>> used as an
>>
>
> does it make sense to use AnnotationHub to manage these resources?


I would think so.  At this time, trying to install greengenes13.5MgDb
package, the process "testing whether the package
can be loaded" takes a very long time -- I suspect it is doing some silent
downloading.  IMHO such activities
should be explicitly undertaken by the user.


> Instead of downloading and managing the fasta and taxonomy files in
> .onLoad and getGreenGenes13.5Db, .onLoad would be
>
>   hub = AnnotationHub()
>   db_seq = hub[["AH12345"]]
>   db_taxa_file = hub[["AH12346"]]
>
>
With this setup the first installation of the package could involve a long
download, silent by default.  It's feasible but
quite unusual.


> with a 'recipe' describing how the corresponding annotation hub resources
> are to be created. This would move download and management to
> AnnotationHub, and potentially allow use of the annotation hub records by
> people with other interests. If that sounds interesting we can work up a
> pull request.
>
> Martin
>
> example database, we plan on adding additional packages for other commonly
>> used
>> databases, e.g RDP and Silva.
>>
>> The metagenomeFeatures includes two vignettes to demonstrating the mgDb
>> and
>> metagenomeAnnotation class methods using the greengenes13.5MgDb as an
>> example
>> database.
>>
>> We are planning on adding additional methods for the mgDb and
>> metagenomeAnnotation classes.  For the mgDb class, assigning query
>> sequences to
>> database sequences using rRDP classifier, and/or sequence alignment
>> methods that
>> are part of the Biostrings package.  For the metagenomeAnnotation class
>> we plan
>> to include the ability to create a phylogenetic tree from a
>> metagenomeAnnotation
>> object.
>> We would appreciate comments on the package and suggestions for
>> additional features.
>>
>> Links to package github repositories
>>
>> https://github.com/HCBravoLab/metagenomeFeatures
>>
>> https://github.com/HCBravoLab/greengenes13.5MgDb
>>
>> Thanks
>>
>> Nate Olson and Hector Corrada Bravo
>>
>
>
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>
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>
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