requires makeblastdb and blastp from blast+ to be on the path
1 2 | blastp(ref, query, run_id, cmd_makeblastdb = "makeblastdb",
cmd_blastp = "blastp", blastp_num_threads = "16", verbose = F)
|
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. |
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