improved cli testing

scripts/clean_test.sh

@@ -4,12 +4,12 @@ source ~/miniconda3/etc/profile.d/conda.sh
 
 TEST_ENV_NAME="R-Test"
 
-mamba create --yes --name ${TEST_ENV_NAME} --channel bioconda \
-		r-essentials r-devtools bioconductor-biocinstaller bioconductor-genomicranges \
-		r-nloptr
+mamba create --yes --name ${TEST_ENV_NAME} --channel bioconda --channel conda-forge \
+		r-essentials r-devtools cooler r-nloptr
 conda activate ${TEST_ENV_NAME}
 
 R -e "devtools::install('.', dependencies=TRUE)"
+R -e "devtools::test()"
 
 conda deactivate 
 mamba env remove --yes --name ${TEST_ENV_NAME}

tests/testthat/test-main.R

@@ -1,67 +1,14 @@
-# Testing using Calder with a .cool file as input
-sanitize_chroms <- function(chroms){
-    res <- lapply(chroms, function(x){
-        if(startsWith(x, "chr")){
-            return(substring(x, 4))
-        } else{
-            return(x)
-        }
-    })
-    return(res)
-}
 
+CALDER_CLI=file.path(system.file("scripts", package="CALDER"), "calder")
 
-handle_input_cool <- function(input, 
-                              outpath, 
-                              bin_size=50000, 
-                              genome="hg38",  
-                              nproc=10,
-                              chroms_to_remove = c("MT", "M", 'chrMT', 'chrM', 'Y', 'chrY')){
-
-    intermediate_data_dir = file.path(outpath, "intermediate_data")
-    dir.create(intermediate_data_dir, recursive=TRUE, showWarnings=FALSE)
-
-    system(paste0("cooler dump --table chroms --out ", 
-                  file.path(intermediate_data_dir, "chroms.txt"), 
-                  " --header ", 
-                  input))
-    chroms <- read.table(file.path(intermediate_data_dir, "chroms.txt"), sep="\t", header=TRUE)
-    chroms <- chroms[!(chroms$name %in% chroms_to_remove), "name"]
-
-    dump_paths <- list()
-    for(chrom in chroms){
-        cat(paste0("[Pre-processing] Dumping ", chrom, "\n"))
-        chrom_dump_path <- file.path(intermediate_data_dir, paste0(chrom, "_dump.txt"))
-        dump_paths <- c(dump_paths, chrom_dump_path)
-        if(! file.exists(chrom_dump_path)){
-            system(paste0("cooler dump --table pixels --range ", 
-                          chrom, 
-                          " --join --balanced ",
-                          input,
-                          " | cut -f2,5,8 | awk '{if ($3) print;}' > ",
-                          chrom_dump_path))
-        }
-    }
-
-    chroms <- sanitize_chroms(chroms)
-    names(dump_paths) <- chroms
-
-    CALDER(contact_file_dump=dump_paths, 
-           chrs=chroms, 
-           bin_size=bin_size,
-           genome=genome,
-           save_dir=outpath,,
-           single_binsize_only=TRUE,
-           save_intermediate_data=TRUE,
-           n_cores=nproc,
-           sub_domains=TRUE)
-    file.remove(file.path(testthat::test_path(), "total_execution.time"))
-}
 
 test_that("CALDER works with cool files", {
     input_cool_path <- file.path(testthat::test_path("data"), "test.cool")
     output_path <- testthat::test_path("test-main-cool-out")
-    handle_input_cool(input_cool_path, output_path)
+
+    CMD = paste0(CALDER_CLI, " -i ", input_cool_path, " -t cool -g hg38 -o ", output_path)
+    system(CMD)
+
     expect_snapshot_file(file.path(output_path, "sub_compartments", "all_sub_compartments.bed"), name = "TestCool_all_sub_compartments.bed")
     expect_snapshot_file(file.path(output_path, "sub_compartments", "all_sub_compartments.tsv"), name = "TestCool_all_sub_compartments.tsv")
     expect_snapshot_file(file.path(output_path, "sub_domains", "all_nested_boundaries.bed"), name = "TestCool_all_nested_boundaries.bed")