Merge branch 'release/v0.0.5'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MonocleScripts
 Title: Command line scripts for Monocle3
-Version: 0.0.4
+Version: 0.0.5
 Authors@R: c(
     person('Ni', 'Huang', email='[email protected]', role=c('aut', 'cre')),
     person('Krzysztof', 'Polanski', email='[email protected]', role='aut'))

R/cmd_methods.R

@@ -127,9 +127,9 @@ monocle_create <- function(
             else if (toupper(substr(file, nchar(file)-2, nchar(file))) == 'MTX')
                 assign(var, Matrix::readMM(file))
             else if (toupper(substr(file, nchar(file)-2, nchar(file))) == 'TSV')
-                assign(var, read.delim(file, row.names = 1, stringsAsFactors = FALSE))
+                assign(var, as.matrix(read.delim(file, row.names = 1, stringsAsFactors = FALSE)))
             else
-                assign(var, read.csv(file, row.names = 1, stringsAsFactors = FALSE))
+                assign(var, as.matrix(read.csv(file, row.names = 1, stringsAsFactors = FALSE)))
         }
     }
 

monocle-scripts-post-install-tests.bats

@@ -14,6 +14,12 @@ setup() {
     var_rds="${data_dir}/var.rds"
     create_opt="--expression-matrix $exprs_mtx --cell-metadata $obs_rds --gene-annotation $var_rds"
     create_rds="${output_dir}/create.rds"
+    tsv_file="${test_dir}/matrix.tsv"
+    tsv_opt="--expression-matrix $tsv_file"
+    tsv_rds="${output_dir}/tsv.rds"
+    csv_file="${test_dir}/matrix.csv"
+    csv_opt="--expression-matrix $csv_file"
+    csv_rds="${output_dir}/csv.rds"
     preprocess_opt="-f cds3 --method PCA --num-dim 50 --norm-method log --pseudo-count 1"
     preprocess_rds="${output_dir}/preprocess.rds"
     reduceDim_opt="--max-components 2 --reduction-method UMAP --preprocess-method PCA"
@@ -72,6 +78,30 @@ setup() {
     [ -f "$create_rds" ]
 }
 
+@test "Create from .csv" {
+    if [ "$resume" = 'true' ] && [ -f "$csv_rds" ]; then
+        skip "$csv_rds exists and resume is set to 'true'"
+    fi
+
+    echo "$monocle create $csv_rds $csv_opt"
+    run eval "printf 'genes,MGH100-P5-A01,MGH100-P5-A03\nA1BG,4.13,2.17\nA1BG-AS1,0,5.57\n' > $csv_file" && $monocle create $csv_rds $csv_opt
+
+    [ "$status" -eq 0 ]
+    [ -f "$csv_rds" ]
+}
+
+@test "Create from .tsv" {
+    if [ "$resume" = 'true' ] && [ -f "$tsv_rds" ]; then
+        skip "$tsv_rds exists and resume is set to 'true'"
+    fi
+
+    echo "$monocle create $tsv_rds $tsv_opt"
+    run eval "printf 'genes\tMGH100-P5-A01\tMGH100-P5-A03\nA1BG\t4.13\t2.17\nA1BG-AS1\t0\t5.57\n' > $tsv_file" && $monocle create $tsv_rds $tsv_opt
+
+    [ "$status" -eq 0 ]
+    [ -f "$tsv_rds" ]
+}
+
 # Preprocess data
 
 @test "Preprocess" {