1. NanoMethViz
  2. R
  3. get_read_entropy.R
Browse code

Linting

shians authored on 29/02/2024 05:18:23
Showing 1 changed files
R/get_read_entropy.R
History View file @ 19dc3f0
... ... 
@@ -15,7 +15,7 @@ get_read_entropy <- function(bam_path, sample = fs::path_file(bam_path)) {
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             chr = factor(reads$rname),
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             pos = reads$pos,
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             width = Biostrings::width(reads$seq),
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-            center = as.integer(.data$pos + .data$width/2),
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+            center = as.integer(.data$pos + .data$width / 2),
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             cg_count = purrr::map_int(as.character(reads$seq), count_cg_cpp),
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             crossings = purrr::map_int(reads$tag$ML, count_crossings),
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             entropy = .data$crossings / .data$cg_count
Browse code

Updated tests

shians authored on 13/10/2023 00:31:06
Showing 1 changed files
R/get_read_entropy.R
History View file @ 308ad71
... ... 
@@ -1,4 +1,5 @@
1 1 
 #' @importFrom Biostrings width
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+# nocov start
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 get_read_entropy <- function(bam_path, sample = fs::path_file(bam_path)) {
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     # helper functions ----
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     count_crossings <- function(numbers) {
... ... 
@@ -48,3 +49,4 @@ get_read_entropy <- function(bam_path, sample = fs::path_file(bam_path)) {
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     bind_rows(df_list)
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 }
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+# nocov end
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Added dependencies

Shians authored on 27/06/2023 02:00:44
Showing 1 changed files
R/get_read_entropy.R
History View file @ 4d80667
... ... 
@@ -1,3 +1,4 @@
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+#' @importFrom Biostrings width
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 get_read_entropy <- function(bam_path, sample = fs::path_file(bam_path)) {
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     # helper functions ----
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     count_crossings <- function(numbers) {
... ... 
@@ -13,10 +14,10 @@ get_read_entropy <- function(bam_path, sample = fs::path_file(bam_path)) {
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             chr = factor(reads$rname),
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             pos = reads$pos,
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             width = Biostrings::width(reads$seq),
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-            center = as.integer(pos + width/2),
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+            center = as.integer(.data$pos + .data$width/2),
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             cg_count = purrr::map_int(as.character(reads$seq), count_cg_cpp),
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             crossings = purrr::map_int(reads$tag$ML, count_crossings),
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-            entropy = crossings / cg_count
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+            entropy = .data$crossings / .data$cg_count
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         )
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     }
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Refactored modbam reading

Shians authored on 22/06/2023 07:40:28
Showing 1 changed files
R/get_read_entropy.R
History View file @ ee042ba
... ... 
@@ -5,10 +5,6 @@ get_read_entropy <- function(bam_path, sample = fs::path_file(bam_path)) {
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         return(crossings)
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     }
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-    read_chunk <- function(bam_file) {
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-        Rsamtools::scanBam(bam_file, param = modbam_param())[[1]]
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-    }
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-
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     parse_chunk <- function(reads, sample) {
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         reads <- reads[!is.null(reads$seq)]
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         tibble::tibble(
... ... 
@@ -42,7 +38,7 @@ get_read_entropy <- function(bam_path, sample = fs::path_file(bam_path)) {
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     df_list <- list()
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     open(bam_file)
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     while (Rsamtools::isIncomplete(bam_file)) {
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-        reads <- read_chunk(bam_file)
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+        reads <- read_bam(bam_file)[[1]]
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         df_list[[i]] <- parse_chunk(reads, sample)
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         i <- i + 1
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         cli::cli_progress_update(length(reads[[1]]))
Browse code

Fixed stuck progress bar

Shians authored on 09/06/2023 06:53:24
Showing 1 changed files
R/get_read_entropy.R
History View file @ 57f4eaf
... ... 
@@ -45,7 +45,7 @@ get_read_entropy <- function(bam_path, sample = fs::path_file(bam_path)) {
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         reads <- read_chunk(bam_file)
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         df_list[[i]] <- parse_chunk(reads, sample)
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         i <- i + 1
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-        cli::cli_progress_update(length(reads[[1]][[1]]))
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+        cli::cli_progress_update(length(reads[[1]]))
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     }
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     close(bam_file)
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Browse code

Fixed incorrect function name

Shians authored on 09/06/2023 06:31:11
Showing 1 changed files
R/get_read_entropy.R
History View file @ 7f4623a
... ... 
@@ -18,7 +18,7 @@ get_read_entropy <- function(bam_path, sample = fs::path_file(bam_path)) {
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             pos = reads$pos,
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             width = Biostrings::width(reads$seq),
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             center = as.integer(pos + width/2),
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-            cg_count = purrr::map_int(as.character(reads$seq), count_cg),
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+            cg_count = purrr::map_int(as.character(reads$seq), count_cg_cpp),
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             crossings = purrr::map_int(reads$tag$ML, count_crossings),
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             entropy = crossings / cg_count
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         )
Browse code

Added missing namespace

Shians authored on 09/06/2023 06:25:46
Showing 1 changed files
R/get_read_entropy.R
History View file @ 0e19a6f
... ... 
@@ -18,7 +18,7 @@ get_read_entropy <- function(bam_path, sample = fs::path_file(bam_path)) {
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             pos = reads$pos,
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             width = Biostrings::width(reads$seq),
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             center = as.integer(pos + width/2),
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-            cg_count = map_int(as.character(reads$seq), count_cg),
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+            cg_count = purrr::map_int(as.character(reads$seq), count_cg),
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             crossings = purrr::map_int(reads$tag$ML, count_crossings),
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             entropy = crossings / cg_count
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         )
Browse code

Added get_read_entropy feature

Shians authored on 09/06/2023 03:02:40
Showing 1 changed files
R/get_read_entropy.R
History View file @ 1e9b7ab
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,53 @@
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+get_read_entropy <- function(bam_path, sample = fs::path_file(bam_path)) {
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+    # helper functions ----
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+    count_crossings <- function(numbers) {
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+        crossings <- sum(((numbers[-1] - 127.5) * (numbers[-length(numbers)] - 127.5)) < 0)
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+        return(crossings)
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+    }
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+
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+    read_chunk <- function(bam_file) {
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+        Rsamtools::scanBam(bam_file, param = modbam_param())[[1]]
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+    }
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+
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+    parse_chunk <- function(reads, sample) {
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+        reads <- reads[!is.null(reads$seq)]
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+        tibble::tibble(
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+            sample = factor(sample),
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+            read_name = reads$qname,
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+            chr = factor(reads$rname),
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+            pos = reads$pos,
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+            width = Biostrings::width(reads$seq),
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+            center = as.integer(pos + width/2),
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+            cg_count = map_int(as.character(reads$seq), count_cg),
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+            crossings = purrr::map_int(reads$tag$ML, count_crossings),
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+            entropy = crossings / cg_count
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+        )
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+    }
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+
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+    # function body ----
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+    fname <- fs::path_file(bam_path)
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+        cli::cli_progress_bar(
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+            glue::glue("Parsing file: {fname}"),
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+            total = get_bam_total_reads(bam_path),
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+            format_done = paste0(
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+                "{.alert-success Data parsed: ", fname, " {.timestamp {cli::pb_elapsed}}}"),
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+            format_failed = paste0(
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+                "{.alert-danger Data parsing failed: ", fname, " {.timestamp {cli::pb_elapsed}}}"),
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+            clear = FALSE
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+        )
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+
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+    bam_file <- Rsamtools::BamFile(bam_path, yieldSize = 15000)
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+
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+    i <- 1
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+    df_list <- list()
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+    open(bam_file)
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+    while (Rsamtools::isIncomplete(bam_file)) {
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+        reads <- read_chunk(bam_file)
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+        df_list[[i]] <- parse_chunk(reads, sample)
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+        i <- i + 1
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+        cli::cli_progress_update(length(reads[[1]][[1]]))
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+    }
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+    close(bam_file)
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+
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+    bind_rows(df_list)
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+}