R: Extracts seed amplicon sequence from blast databases using...

run_blastdbcmd {rCRUX}

R Documentation

Extracts seed amplicon sequence from blast databases using blastdbcmd and primer start and end coordinates stored in the seeds table

Given a row from a blast_seed formatted data.frame, extracts arguments for blastdbcmd, then returns the output of the blastdbcmd call.

run_blastdbcmd(query_row, db, ncbi_bin = NULL)

`query_row`	a row from get_seeds_local or get_seeds_remote
`db`	a directory with a blast-formatted database
`ncbi_bin`	is the path to blast+ tools if not in the user's path. Specify only if blastn and blastdbcmd are not in your path. The default is ncbi_bin = NULL - if not specified in path do the following: ncbi_bin = "/my/local/ncbi-blast-2.10.1+/bin/".

a fasta-formatted character vector

[Package rCRUX version 0.0.1.000 ]