biopipen 0.31.0__py3-none-any.whl → 0.31.1__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.31.0"
+__version__ = "0.31.1"

biopipen/scripts/scrna/SeuratMap2Ref.R

@@ -45,6 +45,10 @@ if (is.null(split_by)) {
     future::plan(strategy = "multicore", workers = ncores)
 }
 
+.is_sct <- function(x) {
+    return(Seurat:::IsSCT(assay = x@assays[[DefaultAssay(x)]]))
+}
+
 .expand_dims = function(args, name = "dims") {
     # Expand dims from 30 to 1:30
     if (is.numeric(args[[name]]) && length(args[[name]] == 1)) {
@@ -63,6 +67,8 @@ if (endsWith(ref, ".rds") || endsWith(ref, ".RDS")) {
 } else {
     reference = LoadH5Seurat(ref)
 }
+reference = UpdateSeuratObject(reference)
+reference = UpdateSCTAssays(reference)
 
 # check if refdata exists in the reference
 for (rname in names(mapquery_args$refdata)) {
@@ -84,9 +90,20 @@ for (rname in names(mapquery_args$refdata)) {
     }
 }
 
-if (refnorm == "auto" && DefaultAssay(reference) == "SCT") {
+if (refnorm == "auto" && .is_sct(reference)) {
     refnorm = "SCTransform"
 }
+if (refnorm == "SCTransform") {
+    # Check if the reference is SCTransform'ed
+    if (!.is_sct(reference)) {
+        stop("Reference is not SCTransform'ed")
+    }
+    n_models = length(x = slot(object = reference[[DefaultAssay(reference)]], name = "SCTModel.list"))
+    if (n_models == 0) {
+        stop("Reference doesn't contain SCTModel.")
+    }
+}
+
 log_info("  Normalization method used: {refnorm}")
 if (refnorm == "SCTransform") {
     findtransferanchors_args$normalization.method = "SCT"
@@ -307,14 +324,14 @@ sobj@meta.data = sobj@meta.data %>% mutate(
 Idents(sobj) = ident
 
 # Check if PrepSCTFindMarkers is done
-if (DefaultAssay(sobj) == "SCT") {
+if (.is_sct(sobj) && is.null(sobj@commands$PrepSCTFindMarkers)) {
     log_info("- Running PrepSCTFindMarkers ...")
     sobj <- PrepSCTFindMarkers(sobj)
     # compose a new SeuratCommand to record it to sobj@commands
     commands <- names(pbmc_small@commands)
     scommand <- pbmc_small@commands[[commands[length(commands)]]]
     scommand@time.stamp <- Sys.time()
-    scommand@assay.used <- "SCT"
+    scommand@assay.used <- DefaultAssay(sobj)
     scommand@call.string <- "PrepSCTFindMarkers(object = sobj)"
     scommand@params <- list()
     sobj@commands$PrepSCTFindMarkers <- scommand

{biopipen-0.31.0.dist-info → biopipen-0.31.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.31.0
+Version: 0.31.1
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.31.0.dist-info → biopipen-0.31.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=TJt1pYzTJuPE6GzDP1gxaeeVQlzcoUyEmSVSUPgYnIA,23
+biopipen/__init__.py,sha256=PB3hjnlSwoWLBLl2ge7lsrSRubKXRdIanr_Hg2t3ViA,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=7IXvviRicZ2D1h6x3BVgbLJ96nsh-ikvZ0sVlQepqFE,1944
@@ -164,7 +164,7 @@ biopipen/scripts/scrna/SeuratClustering-common.R,sha256=JX4Cn2FC6GOcBqaVyGDD3MM5
 biopipen/scripts/scrna/SeuratClustering.R,sha256=0OKRBQ5rFuupK7c03_sSt2HMwMdMnCYFqTvkRXFKchs,1706
 biopipen/scripts/scrna/SeuratFilter.R,sha256=BrYK0MLdaTtQvInMaQsmOt7oH_hlks0M1zykkJtg2lM,509
 biopipen/scripts/scrna/SeuratLoading.R,sha256=ekWKnHIqtQb3kHVQiVymAHXXqiUxs6KKefjZKjaykmk,900
-biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=-Jyd9O4IkVxZJRlskuaP_tOrI7Q1wwkot-YdmzRbLws,11452
+biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=KARt5IVBDYpNhLZ7_j0FEi1u5S8PxU_mB4THH26s7AM,12008
 biopipen/scripts/scrna/SeuratMetadataMutater.R,sha256=PMwG0Xvl_EEVKkicfrIi4arEqpY948PkYLkb59kTAXI,1135
 biopipen/scripts/scrna/SeuratPreparing-common.R,sha256=WuD7lGS17eAUQWSiIdAoV0EIeqS3Tnkkx-7PbP6Q3tc,16279
 biopipen/scripts/scrna/SeuratPreparing-doublet_detection.R,sha256=TNN2lfFjpnnO0rguMsG38JYCP1nFUhcPLJ1LqGj-Sc8,6674
@@ -279,7 +279,7 @@ biopipen/utils/reference.py,sha256=oi5evicLwHxF0KAIPNZohBeHJLJQNWFJH0cr2y5pgcg,5
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/single_cell.R,sha256=pJjYP8bIZpNAtTQ32rOXhZxaM1Y-6D-xUcK3pql9tbk,4316
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.31.0.dist-info/METADATA,sha256=OtaZr2FTKCeaK9H-yBmssBT6848_F1j1wa2e8D3wraE,882
-biopipen-0.31.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-biopipen-0.31.0.dist-info/entry_points.txt,sha256=69SbeMaF47Z2DS40yo-qDyoBKmMmumrNnsjEZMOioCE,625
-biopipen-0.31.0.dist-info/RECORD,,
+biopipen-0.31.1.dist-info/METADATA,sha256=uPOVUaGxNgT5ZJwJWBDXqmnxaBUxaMvyErjqFCRsV60,882
+biopipen-0.31.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+biopipen-0.31.1.dist-info/entry_points.txt,sha256=69SbeMaF47Z2DS40yo-qDyoBKmMmumrNnsjEZMOioCE,625
+biopipen-0.31.1.dist-info/RECORD,,