effector_annot.r 562 B
library(effectR)
# fasta_prot <- seqinr::read.fasta(commandArgs(trailingOnly = TRUE)[1])
test <- seqinr::read.fasta("/home/nibio/Documents/Git/DivGene-genome-annotation/Mid_test_data/test_prot.fa")
fasta_prot <- test
rxlr_cand <- regex.search(fasta_prot)
crn_cand <- regex.search(fasta_prot, motif = "CRN")
rxlrs <- hmm.search(original.seq = fasta_prot, regex.seq = rxlr_cand,
mafft.path = "/home/nibio/miniconda3/envs/funannotate/bin/mafft")
crns <- hmm.search(fasta_prot, rxlr_cand,
mafft.path = "/home/nibio/miniconda3/envs/funannotate/bin/mafft")