On Tue, Aug 4, 2015 at 3:00 PM, Martin Morgan <mtmor...@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 >> > > > -- > 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-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
