Add findermethod parameter to get_orfs_dna and get_orfs_aa functions

camilogarciabotero · Mar 29, 2024 · 92b0e22 · 92b0e22
1 parent 80a8918
commit 92b0e22
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Showing 2 changed files with 165 additions and 149 deletions.
diff --git a/src/getorfs.jl b/src/getorfs.jl
@@ -19,10 +19,11 @@ This function takes a `NucleicSeqOrView{DNAAlphabet{N}}` sequence and identifies
 """
 function get_orfs_dna(
     sequence::NucleicSeqOrView{DNAAlphabet{N}};
+    findermethod::Function = naivefinder,
     alternative_start::Bool = false,
     min_len::Int64 = 6
 ) where {N}
-    orfs = findorfs(sequence; alternative_start, min_len)
+    orfs = findorfs(sequence; findermethod, alternative_start, min_len)
     seqs = Vector{LongSubSeq{DNAAlphabet{N}}}(undef, length(orfs)) #Vector{}(undef, length(orfs)) # todo correct the output type
     @inbounds for (i, orf) in enumerate(orfs)
         seqs[i] = sequence[orf]
@@ -47,11 +48,12 @@ This function takes a `NucleicSeqOrView{DNAAlphabet{N}}` sequence and identifies
 """
 function get_orfs_aa(
     sequence::NucleicSeqOrView{DNAAlphabet{N}};
+    findermethod::Function = naivefinder,
     alternative_start::Bool = false,
     code::GeneticCode = ncbi_trans_table[1],
     min_len::Int64 = 6
 ) where {N}
-    orfs = findorfs(sequence; alternative_start, min_len)
+    orfs = findorfs(sequence; findermethod, alternative_start, min_len)
     aas = Vector{LongSubSeq{AminoAcidAlphabet}}(undef, length(orfs))
     @inbounds for (i, orf) in enumerate(orfs)
         aas[i] = translate(sequence[orf]; code)