EntrezDownload: Download Public Sequence Data
In djwcisel/toast: Transcriptome Ortholog Alignment Sequence Tools
Description
Usage
Arguments
Value
Author(s)
Examples
View source: R/EntrezDownload.R
Description
Utility for downloading sequence data from NCBI for a user specified group of organisms
Usage
1
EntrezDownload(txid, fasta_dir, minimumSeq = 350, maximumSeq = NULL)
Arguments
txid
NCBI taxon ID. See https://ncbi.nlm.nih.gov and manual
fasta_dir
Place to store fasta sequences. Must end with */fasta/
minimumSeq
Minimum number of sequences a species must have to bother downloading
defaults to 350
maximumSeq
Maximum number of sequences to download per species.
Useful for testing scripts and troubleshooting TOAST/BUSCO
Value
Returns graphic of missing data based on defined threshold
Author(s)
Dustin J Wcisel, djwcisel@ncsu.edu
James Thomas Howard, jthowar3@ncsu.edu
Jeffrey A Yoder, jayoder@ncsu.edu
Alex Dornburg, dornburgalex@gmail.com
Examples
1
SequenceDownload(txid = 9721, fasta_dir = "path/to/fasta/", minimumSeq = 350)
djwcisel/toast documentation built on Nov. 4, 2019, 10:55 a.m.
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Description Usage Arguments Value Author(s) Examples
View source: R/EntrezDownload.R
Description
Utility for downloading sequence data from NCBI for a user specified group of organisms
Usage
1 | EntrezDownload(txid, fasta_dir, minimumSeq = 350, maximumSeq = NULL)
|
Arguments
txid |
NCBI taxon ID. See https://ncbi.nlm.nih.gov and manual |
fasta_dir |
Place to store fasta sequences. Must end with */fasta/ |
minimumSeq |
Minimum number of sequences a species must have to bother downloading defaults to 350 |
maximumSeq |
Maximum number of sequences to download per species. Useful for testing scripts and troubleshooting TOAST/BUSCO |
Value
Returns graphic of missing data based on defined threshold
Author(s)
Dustin J Wcisel, djwcisel@ncsu.edu
James Thomas Howard, jthowar3@ncsu.edu
Jeffrey A Yoder, jayoder@ncsu.edu
Alex Dornburg, dornburgalex@gmail.com
Examples
1 | SequenceDownload(txid = 9721, fasta_dir = "path/to/fasta/", minimumSeq = 350)
|
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.
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