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Biostrings::pairwiseAlignment >>> pwalign::pairwiseAlignment #54

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Biostrings::pairwiseAlignment >>> pwalign::pairwiseAlignment #54

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Update DESCRIPTION
kullrich Feb 13, 2026
7da067a
Update pairwise_aln.R
kullrich Feb 13, 2026
3a70010
Update DESCRIPTION
kullrich Feb 13, 2026
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1 change: 1 addition & 0 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ Imports:
foreach,
Rcpp (>= 0.11.3),
Biostrings (>= 2.52.0),
pwalign (>= 1.6.0),
RSQLite (>= 0.11.4),
stringr (>= 0.6.2),
IRanges,
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18 changes: 9 additions & 9 deletions R/pairwise_aln.R
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Expand Up @@ -15,8 +15,8 @@
#' @author Sarah Scharfenberg and Hajk-Georg Drost
#' @details This function provides an interface between R and common pairwise alignment computation methods.
#'
#' The current version of this function computes pairwise alignments based on the \code{\link[Biostrings]{pairwiseAlignment}}
#' function implemented in the \pkg{Biostrings} package.
#' The current version of this function computes pairwise alignments based on the \code{\link[pwalign]{pairwiseAlignment}}
#' function implemented in the \pkg{pwalign} package.
#'
#' The default pairwise alignment method is based on the \emph{Needleman-Wunsch Algorithm}.
#'
Expand Down Expand Up @@ -85,7 +85,7 @@ pairwise_aln <- function(file,
)
}

# Needleman-Wunsch using Biostrings::pairwiseAlignment( type=global)
# Needleman-Wunsch using pwalign::pairwiseAlignment( type=global)
if (tool == "NW") {
#read file
if (is.element(seq_type, c("dna", "cds"))) {
Expand Down Expand Up @@ -122,25 +122,25 @@ pairwise_aln <- function(file,

# align
aln <-
Biostrings::pairwiseAlignment(pattern = seqs[[1]],
subject = seqs[[2]],
type = "global")
pwalign::pairwiseAlignment(pattern = seqs[[1]],
subject = seqs[[2]],
type = "global")

#write file -> comment Hajk: what does pattern() and subject() do in pattern(aln), subject(aln) ?
# pattern(aln) == get aligned sequence that was set as pattern input
# subject(aln) == get aligned sequence that was set as subject input
seqinr::write.fasta(
sequences = list(Biostrings::pattern(aln), IRanges::subject(aln)),
sequences = list(pwalign::pattern(aln), pwalign::subject(aln)),
names = names,
file.out = file.out
)

if (store_locally) {
local_store_path <- file.path("orthologr_alignment_files", "_pairwise_alignment_with_score")
Biostrings::writePairwiseAlignments(aln, file.path(local_store_path, paste0(pairwise_aln_name, "_", tool, "_", seqtype, ".aln")))
pwalign::writePairwiseAlignments(aln, file.path(local_store_path, paste0(pairwise_aln_name, "_", tool, "_", seqtype, ".aln")))
} else {
local_store_path <- file.path(tempdir(), "_pairwise_alignment_with_score")
Biostrings::writePairwiseAlignments(aln, file.path(local_store_path, paste0(pairwise_aln_name, "_", tool, "_", seqtype, ".aln")))
pwalign::writePairwiseAlignments(aln, file.path(local_store_path, paste0(pairwise_aln_name, "_", tool, "_", seqtype, ".aln")))
}

if (!quiet) {
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