merge

Merge branch 'main' of https://github.com/jakubkala/kmerFilters # Conflicts: # R/motifs.R
BioGenies · Aug 19, 2024 · 0571b1e · 0571b1e
2 parents f7450ad + 4d3e3ed
commit 0571b1e
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Showing 2 changed files with 13 additions and 1 deletion.
diff --git a/R/motifs.R b/R/motifs.R
@@ -79,10 +79,21 @@ add_motifs <- function(motifs, sequence, max_attempts = 20) {
     maximum_motifs_positions <- lapply(motifs, function(x)
         seq(sequence_len - length(x) + 1))
 
+<<<<<<< HEAD
     positions_to_sample <- maximum_motifs_positions
     motifs_positions <- numeric(length(motifs))
     attempt <- 1
     ith_motif <- 1
+=======
+    if(any(motifs_grid < 1)) {
+        stop("Some of positions are invalid!")
+    }
+
+    for (i in 1:nrow(motifs_grid)) {
+        list_of_masks <- list()
+        injected_sequence <- sequence
+        injected_positions <- logical(length(sequence))
+>>>>>>> 4d3e3ed55070425b5635338c4a6b18bc4f41fb1e
 
     while(attempt <= max_attempts & ith_motif <= length(motifs)) {
         dummy_ok <- TRUE

diff --git a/R/sequences.R b/R/sequences.R
@@ -76,6 +76,7 @@ generate_sequence_data <- function(n_seq,
     attr(sequences, "motifs_map") <- motifs_map
     attr(sequences, "masks") <- list_of_masks
     attr(sequences, "target") <- target
+    attr(sequences, "motifs_set") <- motifs
     sequences
 }
 
@@ -182,7 +183,7 @@ generate_kmer_data <- function(n_seq,
                                           nrow = nrow(test_dat),
                                           ncol = ncol(test_dat))
     attr(test_res, "max_injection") <- attr(test_dat, "max_injection")
-    attr(test_res, "motifs_set") <- motifs
+    attr(test_res, "motifs_set") <- attr(test_dat, "motifs_set")
     attr(test_res, "motifs_map") <- attr(test_dat, "motifs_map")
     attr(test_res, "masks") <- attr(test_dat, "masks")
     attr(test_res, "target") <- attr(test_dat, "target")