downloadPubmlst_seq: Download Genes for a Given MLST Scheme
In iferres/quickMLST: Quick Multi Locus Sequence Typing Analisys
Description
Usage
Arguments
Value
Author(s)
References
View source: R/pubmlstInterface.R
Description
This function takes a genus, as returned by listPubmlst_orgs,
and a mlst scheme as either an integer or as a vector of locus names
as returned by listPubmlst_schemes, and downloads the fasta files for
the given genus and mlst scheme.
Usage
1
downloadPubmlst_seq(org = "leptospira", scheme = "", dir = ".", n_threads = 1L)
Arguments
org
character. A genus (lowercase).
scheme
Either an integer specifiying the scheme number to
download, or a vector of the locus names of that organism.
dir
Where to put the fasta files.
n_threads
integer. The number of cores to use.
Value
A vector of paths to the downloaded fasta files.
Author(s)
Ignacio Ferres
References
Jolley KA, Bray JE, Maiden MCJ. A RESTful application programming
interface for the PubMLST molecular typing and genome databases. Database:
The Journal of Biological Databases and Curation. 2017;2017:bax060.
doi:10.1093/database/bax060.
iferres/quickMLST documentation built on Dec. 22, 2020, 5:10 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Author(s) References
View source: R/pubmlstInterface.R
Description
This function takes a genus, as returned by listPubmlst_orgs,
and a mlst scheme as either an integer or as a vector of locus names
as returned by listPubmlst_schemes, and downloads the fasta files for
the given genus and mlst scheme.
Usage
1 | downloadPubmlst_seq(org = "leptospira", scheme = "", dir = ".", n_threads = 1L)
|
Arguments
org |
|
scheme |
Either an |
dir |
Where to put the fasta files. |
n_threads |
|
Value
A vector of paths to the downloaded fasta files.
Author(s)
Ignacio Ferres
References
Jolley KA, Bray JE, Maiden MCJ. A RESTful application programming interface for the PubMLST molecular typing and genome databases. Database: The Journal of Biological Databases and Curation. 2017;2017:bax060. doi:10.1093/database/bax060.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.