From 9e0a6fbc3676af01f8a240d780aee23b0b70b12b Mon Sep 17 00:00:00 2001
From: Simeon <51403284+simeross@users.noreply.github.com>
Date: Fri, 27 Oct 2023 21:26:36 +0200
Subject: [PATCH] ORFik addition

---
 DESCRIPTION          | 1 +
 NAMESPACE            | 1 +
 R/find_longest_orf.R | 3 ++-
 3 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d286e2b..37f6494 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -32,6 +32,7 @@ Imports:
     ggplot2,
     ggtree,
     magrittr,
+    ORFik,
     phangorn,
     purrr,
     readr,
diff --git a/NAMESPACE b/NAMESPACE
index 484c11a..cbd2680 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -64,6 +64,7 @@ importFrom(DECIPHER,AlignSeqs)
 importFrom(DECIPHER,DistanceMatrix)
 importFrom(GenomicRanges,GRanges)
 importFrom(IRanges,ranges)
+importFrom(ORFik,findORFs)
 importFrom(ape,as.DNAbin)
 importFrom(cowplot,draw_label)
 importFrom(cowplot,get_legend)
diff --git a/R/find_longest_orf.R b/R/find_longest_orf.R
index 07b7eac..8f959d3 100644
--- a/R/find_longest_orf.R
+++ b/R/find_longest_orf.R
@@ -9,6 +9,7 @@
 #' @importFrom Biostrings DNAStringSet
 #' @importFrom GenomicRanges GRanges
 #' @importFrom IRanges ranges
+#' @importFrom ORFik findORFs
 #' @import dplyr tibble tidyr
 #'
 #' @examples
@@ -18,7 +19,7 @@
 #' @export
 find_longest_orf <- function(seqs = DNAStringSet) {
   # Find ORFs in the sequences, return longest ORF, and convert to a vector
-  orfs <- findORFs(seqs, longestORF = TRUE, startCodon = startDefinition(6)) %>%
+  orfs <- ORFik::findORFs(seqs, longestORF = TRUE, startCodon = startDefinition(6)) %>%
     unlist(use.names = TRUE)
   # Convert the ORFs to a GRanges object
   orfs <- GRanges(seqnames = names(seqs)[as.integer(names(orfs))],
-- 
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