replace callBasilisk with basilisk::basiliskRun

mritchielab · Oct 4, 2023 · fc64827 · fc64827
1 parent dfa2ba7
commit fc64827
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Showing 12 changed files with 40 additions and 65 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -90,8 +90,6 @@ importFrom(bambu,prepareAnnotations)
 importFrom(bambu,writeToGTF)
 importFrom(basilisk,BasiliskEnvironment)
 importFrom(basilisk,basiliskRun)
-importFrom(basilisk,basiliskStart)
-importFrom(basilisk,basiliskStop)
 importFrom(circlize,colorRamp2)
 importFrom(cowplot,get_legend)
 importFrom(cowplot,plot_grid)

diff --git a/R/BLAZE_demultiplexing.R b/R/BLAZE_demultiplexing.R
@@ -24,6 +24,7 @@
 #' blaze(expect_cells=10, fastq1, overwrite=TRUE)
 #' 
 #' @importFrom reticulate import_from_path dict
+#' @importFrom basilisk basiliskRun
 #' @export
 blaze <- function(expect_cells, fq_in, ...) {
         # prepare command-line-style arguments for blaze        
@@ -57,7 +58,7 @@ blaze <- function(expect_cells, fq_in, ...) {
 
         # run blaze
         ret <-
-            callBasilisk(flames_env, function(blaze_argv) {
+            basiliskRun(env = flames_env, fun = function(blaze_argv) {
                 # blaze_path <- system.file("blaze", package = "FLAMES")
                 cat("Running BLAZE...\n")
                 cat("Argument: ", blaze_argv, "\n")

diff --git a/R/call_basilisk.R b/R/call_basilisk.R
diff --git a/R/cutadapt.R b/R/cutadapt.R
@@ -7,12 +7,11 @@
 #' \dontrun{
 #'  cutadapt("-h")
 #' }
+#' @importFrom reticulate import_from_path
+#' @importFrom basilisk basiliskRun
 #' @export
 cutadapt <- function(args) {
-  callBasilisk(flames_env, function(x) {
-    # python_path <- system.file("python", package = "FLAMES")
-    # mod <- reticulate::import_from_path("cutadapt_wrapper", python_path)
-    # return(mod$wrapper(as.list(x)))
+  basiliskRun(env = flames_env, fun = function(x) {
     subprocess <- reticulate::import("subprocess")
     builtin <- reticulate::import_builtins()
     output <- subprocess$check_output(paste("cutadapt", as.list(x), sep=" "), shell=TRUE)
@@ -22,4 +21,4 @@ cutadapt <- function(args) {
   }, x = args)
 }
 
-#cutadapt -a 'CCCATGTACTCTGCGTTGATACCACTGCTT' -o cutadapt.fq  --untrimmed-output untrimmed.fq ../main/1k.out.fq
+# cutadapt usage: cutadapt -a 'CCCATGTACTCTGCGTTGATACCACTGCTT' -o cutadapt.fq  --untrimmed-output untrimmed.fq ../main/1k.out.fq
diff --git a/R/demultiplex_sockey.R b/R/demultiplex_sockey.R
@@ -6,8 +6,9 @@
 #' @return returns NULL
 #' @export
 #' @importFrom reticulate import_from_path
+#' @importFrom basilisk basiliskRun
 demultiplex_sockeye <- function(fastq_dir, sockeye_tsv, out_fq) {
-    callBasilisk(flames_env, function(fastq_dir_, sockeye_tsv_, out_fq_) {
+    basiliskRun(env = flames_env, fun = function(fastq_dir_, sockeye_tsv_, out_fq_) {
         python_path <- system.file("python", package = "FLAMES")
         demult <- reticulate::import_from_path("demultiplex_sockeye", python_path)
         ret <- demult$demultiplex_sockeye(fastq_dir_, sockeye_tsv_, out_fq_)

diff --git a/R/filter_gff.R b/R/filter_gff.R
@@ -1,12 +1,13 @@
 #' @importFrom reticulate import_from_path
+#' @importFrom basilisk basiliskRun
 annotate_filter_gff <-
     function(isoform_gff,
              ref_gff,
              isoform_out,
              anno_out,
              tr_cnt,
              min_sup_reads) {
-        callBasilisk(flames_env, function(isoform_gff,
+        basiliskRun(env = flames_env, fun = function(isoform_gff,
                                           ref_gff,
                                           isoform_out,
                                           anno_out,
@@ -34,10 +35,11 @@ annotate_filter_gff <-
     }
 
 
-
+#' @importFrom reticulate import_from_path
+#' @importFrom basilisk basiliskRun
 annotate_full_splice_match_all_sample <-
     function(anno_out, isoform_gff, ref_gff) {
-        callBasilisk(flames_env, function(anno_out, isoform_gff, ref_gff) {
+        basiliskRun(env = flames_env, fun = function(anno_out, isoform_gff, ref_gff) {
             python_path <- system.file("python", package = "FLAMES")
 
             filter <-
@@ -49,4 +51,4 @@ annotate_full_splice_match_all_sample <-
         )
 
         invisible()
-    }
+    }
diff --git a/R/find_isoform.R b/R/find_isoform.R
@@ -84,9 +84,10 @@ find_isoform_bambu <- function(annotation, genome_fa, genome_bam, outdir, config
 
 #' @importFrom reticulate import_from_path
 #' @importFrom Rsamtools indexFa
+#' @importFrom basilisk basiliskRun
 find_isoform_flames <- function(annotation, genome_fa, genome_bam, outdir, config) {
     if (length(genome_bam) == 1) {
-        ret <- callBasilisk(flames_env, function(gff3, genome, iso, tss, fa, tran, ds, conf, raw) {
+        ret <- basiliskRun(env = flames_env, fun = function(gff3, genome, iso, tss, fa, tran, ds, conf, raw) {
             python_path <- system.file("python", package = "FLAMES")
             find <- reticulate::import_from_path("find_isoform", python_path)
             ret <- find$find_isoform(gff3, genome, iso, tss, fa, tran, ds, conf, raw)
@@ -95,7 +96,7 @@ find_isoform_flames <- function(annotation, genome_fa, genome_bam, outdir, confi
         gff3 = annotation, genome = genome_bam, iso = file.path(outdir, "isoform_annotated.gff3"), tss = file.path(outdir, "tss_tes.bedgraph"), fa = genome_fa, tran = file.path(outdir, "transcript_assembly.fa"), ds = config$isoform_parameters$downsample_ratio, conf = config, raw = ifelse(config$isoform_parameters$generate_raw_isoform, file.path(outdir, "splice_raw.gff3"), FALSE)
         )
     } else {
-        ret <- callBasilisk(flames_env, function(gff3, genome, iso, tss, fa, tran, ds, conf, raw) {
+        ret <- basiliskRun(env = flames_env, fun = function(gff3, genome, iso, tss, fa, tran, ds, conf, raw) {
             python_path <- system.file("python", package = "FLAMES")
             find <- reticulate::import_from_path("find_isoform", python_path)
             ret <- find$find_isoform_multisample(gff3, genome, iso, tss, fa, tran, ds, conf, raw)

diff --git a/R/parse_gene_anno.R b/R/parse_gene_anno.R
@@ -10,6 +10,7 @@
 #' "chr_to_gene", "transcript_dict", "gene_to_transcript", "transcript_to_exon", containing
 #' the data parsed from the gff3 file.
 #' @importFrom reticulate import_from_path
+#' @importFrom basilisk basiliskRun
 #'
 #' @examples
 #' temp_path <- tempfile()
@@ -20,7 +21,7 @@
 #' \dontrun{parsed_gff <- parse_gff_tree(gff)}
 #' @export
 parse_gff_tree <- function(gff_file) {
-    ret <- callBasilisk(flames_env, function(args) {
+    ret <- basiliskRun(env = flames_env, fun = function(args) {
         python_path <- system.file("python", package = "FLAMES")
         parse <-
             reticulate::import_from_path("parse_gene_anno", python_path)

diff --git a/R/quantification.R b/R/quantification.R
@@ -1,4 +1,5 @@
 #' @importFrom reticulate import_from_path dict
+#' @importFrom basilisk basiliskRun
 parse_realigned_bam <-
     function(bam_in,
              fa_idx_f,
@@ -7,7 +8,7 @@ parse_realigned_bam <-
              min_read_coverage,
              bc_file) {
         ret <-
-            callBasilisk(flames_env, function(bam_in,
+            basiliskRun(env = flames_env, fun = function(bam_in,
                                               fa_idx_f,
                                               min_sup_reads,
                                               min_tr_coverage,
@@ -43,6 +44,7 @@ parse_realigned_bam <-
     }
 
 #' @importFrom reticulate import_from_path
+#' @importFrom basilisk basiliskRun
 #' @importFrom future plan
 wrt_tr_to_csv <-
     function(bc_tr_count_dict,
@@ -51,7 +53,7 @@ wrt_tr_to_csv <-
              transcript_dict_ref = NULL,
              has_UMI = TRUE) {
         future::plan(future::multisession)
-        callBasilisk(flames_env, function(bc_tr_count_dict,
+        basiliskRun(env = flames_env, fun = function(bc_tr_count_dict,
                                           transcript_dict,
                                           csv_f,
                                           transcript_dict_ref,
@@ -101,6 +103,7 @@ wrt_tr_to_csv <-
 #' \code{bulk} (bulk, single or multi-sample), or \code{sc_multi_sample} (single-cell, multiple samples)
 #' @return The count matrix will be saved in the output folder as \code{transcript_count.csv.gz}.
 #' @importFrom reticulate import_from_path dict
+#' @importFrom basilisk basiliskRun
 quantify_gene <- function(annotation, outdir, n_process, pipeline = "sc_single_sample") {
     cat(format(Sys.time(), "%X %a %b %d %Y"), "quantify genes \n")
 
@@ -116,7 +119,7 @@ quantify_gene <- function(annotation, outdir, n_process, pipeline = "sc_single_s
         stop("Incorrect number of genome alignment files found.\n")
     }
 
-    callBasilisk(flames_env, function(annotation, outdir,pipeline) {
+    basiliskRun(env = flames_env, fun = function(annotation, outdir,pipeline) {
         python_path <- system.file("python", package = "FLAMES")
         count <- reticulate::import_from_path("count_gene", python_path)
         count$quantification(annotation, outdir, pipeline, n_process)
@@ -135,6 +138,7 @@ quantify_gene <- function(annotation, outdir, n_process, pipeline = "sc_single_s
 #' @param pipeline The pipeline type as a character string, either \code{sc_single_sample} (single-cell, single-sample),
 #' \code{bulk} (bulk, single or multi-sample), or \code{sc_multi_sample} (single-cell, multiple samples)
 #' @return The count matrix will be saved in the output folder as \code{transcript_count.csv.gz}.
+#' @importFrom basilisk basiliskRun
 #' @importFrom reticulate import_from_path dict
 #' @examples
 #' temp_path <- tempfile()
@@ -173,7 +177,7 @@ quantify_transcript <- function(annotation, outdir, config, pipeline = "sc_singl
         stop("Incorrect number of realignment files found.\n")
     }
 
-    callBasilisk(flames_env, function(config_dict, annotation, outdir, pipeline) {
+    basiliskRun(env = flames_env, fun = function(config_dict, annotation, outdir, pipeline) {
         python_path <- system.file("python", package = "FLAMES")
         count <- reticulate::import_from_path("count_tr", python_path)
         count$quantification(config_dict, annotation, outdir, pipeline)

diff --git a/R/sc_longread.R b/R/sc_longread.R
@@ -1,6 +1,7 @@
 #' @importFrom reticulate import_from_path
+#' @importFrom basilisk basiliskRun
 blocks_to_junctions <- function(block) {
-    junctions <- callBasilisk(flames_env, function(block) {
+    junctions <- basiliskRun(env = flames_env, fun = function(block) {
         python_path <- system.file("python", package = "FLAMES")
 
         sc <-
@@ -12,11 +13,12 @@ blocks_to_junctions <- function(block) {
 }
 
 #' @importFrom reticulate import_from_path
+#' @importFrom basilisk basiliskRun
 remove_similar_tr <-
     function(gene_to_transcript,
              transcript_to_exon,
              thr = 10) {
-        callBasilisk(flames_env, function(gene_tran, tr_exon, thr) {
+        basiliskRun(env = flames_env, fun = function(gene_tran, tr_exon, thr) {
             python_path <- system.file("python", package = "FLAMES")
 
             sc <-
@@ -31,9 +33,10 @@ remove_similar_tr <-
     }
 
 #' @importFrom reticulate import_from_path
+#' @importFrom basilisk basiliskRun
 get_gene_flat <- function(gene_to_transcript, transcript_to_exon) {
     gene_flat <-
-        callBasilisk(flames_env, function(gene_tran, tran_exon) {
+        basiliskRun(env = flames_env, fun = function(gene_tran, tran_exon) {
             python_path <- system.file("python", package = "FLAMES")
 
             sc <-
@@ -45,12 +48,13 @@ get_gene_flat <- function(gene_to_transcript, transcript_to_exon) {
 }
 
 #' @importFrom reticulate import_from_path
+#' @importFrom basilisk basiliskRun
 get_gene_blocks <-
     function(gene_dict,
              chr_to_gene,
              gene_to_transcript) {
         gene_blocks <-
-            callBasilisk(flames_env, function(g_dict, chr_gene, gene_tran) {
+            basiliskRun(env = flames_env, fun = function(g_dict, chr_gene, gene_tran) {
                 python_path <- system.file("python", package = "FLAMES")
 
                 sc <-
@@ -63,6 +67,7 @@ get_gene_blocks <-
     }
 
 #' @importFrom reticulate import_from_path
+#' @importFrom basilisk basiliskRun
 group_bam2isoform <-
     function(bam_in,
              out_gff3,
@@ -76,7 +81,7 @@ group_bam2isoform <-
              config,
              downsample_ratio,
              raw_gff3 = NULL) {
-        callBasilisk(flames_env, function(bin,
+        basiliskRun(env = flames_env, fun = function(bin,
                                           o_gff3,
                                           o_stat,
                                           summary,
@@ -114,4 +119,4 @@ group_bam2isoform <-
         )
 
         c(out_gff3, out_stat) # output files
-    }
+    }
diff --git a/R/sc_mutations.R b/R/sc_mutations.R
@@ -53,6 +53,7 @@
 #'
 #' @importFrom utils write.csv
 #' @importFrom S4Vectors head
+#' @importFrom basilisk basiliskRun
 #'
 #' @examples
 #' outdir <- tempfile()
@@ -90,7 +91,7 @@ sc_mutations <- function(sce, barcode_tsv, bam_short, out_dir, genome_fa, annot,
     }
 
     python_path <- system.file("python", package = "FLAMES")
-    callBasilisk(flames_env, function(fa, bam, dir, barcode, gff, positions, mincov, reportpct) {
+    basiliskRun(env = flames_env, fun = function(fa, bam, dir, barcode, gff, positions, mincov, reportpct) {
         convert <- reticulate::import_from_path("sc_mutations", python_path)
         convert$sc_mutations(fa, bam, dir, barcode, gff, positions, mincov, reportpct)
     }, fa = genome_fa, bam = ifelse(missing("bam_short"), FALSE, bam_short), dir = out_dir, barcode = barcode_tsv, gff = annot, positions = known_positions, mincov = min_cov, reportpct = report_pct)

diff --git a/man/callBasilisk.Rd b/man/callBasilisk.Rd