| Title: | NCBI BLAST web client |
|---|---|
| Description: | NCBI BLAST web client. |
| Authors: | Pieter Provoost [cre, aut] |
| Maintainer: | Pieter Provoost <[email protected]> |
| License: | `use_mit_license()` |
| Version: | 0.0.1 |
| Built: | 2024-11-22 03:05:29 UTC |
| Source: | https://github.com/pieterprovoost/ghettoblaster |
Run a BLAST search
blast(sequence, max_num_seq = 100, verbose = FALSE, add_worms = FALSE)blast(sequence, max_num_seq = 100, verbose = FALSE, add_worms = FALSE)
sequence |
A DNA sequence |
max_num_seq |
The maximum number of sequences to return |
verbose |
Whether to print status messages |
add_worms |
Whether to add WoRMS taxonomy information |
A data frame with the BLAST results
Get the results of a BLAST request
get_results(rid)get_results(rid)
rid |
A request ID |
A data frame with the results
Get WoRMS taxonomy for a list of species names
get_taxonomy(species_names)get_taxonomy(species_names)
species_names |
A character vector of species names |
A data frame with the taxonomy, input names in column input
This package provides a simple interface to the NCBI BLAST web service.
Submit a sequence to NCBI BLAST
submit_sequence(sequence, program = "blastn", max_num_seq = 100)submit_sequence(sequence, program = "blastn", max_num_seq = 100)
sequence |
A DNA sequence |
program |
The BLAST program to use |
max_num_seq |
The maximum number of sequences to return |
A request ID
Wait until a BLAST request is ready
wait_until_ready(rid, verbose = FALSE)wait_until_ready(rid, verbose = FALSE)
rid |
A request ID |
verbose |
Whether to print status messages |
TRUE if the request is ready, FALSE in case of an unexpected status
Get WoRMS taxonomy for a list of species names
worms_for_names(...)worms_for_names(...)
species_names |
A character vector of species names |
A data frame with the taxonomy, input names in column input