blastp: Blast query sequences against reference sequences

Description Usage Arguments

View source: R/blast.R

Description

requires makeblastdb and blastp from blast+ to be on the path

Usage

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blastp(ref, query, run_id, cmd_makeblastdb = "makeblastdb",
  cmd_blastp = "blastp", blastp_num_threads = "16", verbose = F)

Arguments

ref

list of vector of chars where each element is a sequence object of class SeqFastadna or SeqFastaAA, e.g. what is returned by seqinr::read.fasta

query

list of vector of chars where each element is a sequence object of class SeqFastadna or SeqFastaAA, e.g. what is returned by seqinr::read.fasta

run_id

character string used to name temporary files etc.

cmd_makeblastdb

the command used to make the reference database e.g. makeblastdb from the blast+ package

cmd_blastp

the command used to blast the queries against the reference sequences e.g. blastp blastp_num_threads the number of threads to use while running blast

verbose

write out additional information while executing.


momeara/Bethany documentation built on Aug. 6, 2019, 9:26 a.m.