biopipen 0.31.0__py3-none-any.whl → 0.31.2__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.31.0"
+__version__ = "0.31.2"

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/scripts/tcr/CDR3AAPhyschem.R

@@ -170,6 +170,8 @@ immdata = readRDS(immdatafile)
 merge_data = function(sam) {
     # Merge the data for one sample from immdata and metadata
     out = immdata$data[[sam]] %>%
+        separate_rows(chain, CDR3.aa, V.name, J.name, sep = ";") %>%
+        filter(chain == "TRB") %>%
         mutate(
             Sample = sam,
             locus = "TCRB",

biopipen/scripts/tcr/TCRClustering.R

@@ -34,9 +34,17 @@ if (is.null(prefix)) { prefix = immdata$prefix }
 if (is.null(prefix)) { prefix = "" }
 
 get_cdr3aa_df = function() {
-    expand_immdata(immdata, cell_id = "Barcode") %>%
+    out = expand_immdata(immdata, cell_id = "Barcode") %>%
         mutate(Barcode = glue(paste0(prefix, "{Barcode}"))) %>%
-        select(Barcode, CDR3.aa)
+        select(Barcode, CDR3.aa, chain)
+
+    if (on_multi) {
+        out$CDR3.aa = sub(";", "", out$CDR3.aa)
+    } else {
+        out = out %>% separate_rows(chain, CDR3.aa, sep = ";") %>%
+            filter(chain == "TRB")
+    }
+    out %>% select(Barcode, CDR3.aa)
 }
 cdr3aa_df = get_cdr3aa_df()
 
@@ -159,12 +167,14 @@ prepare_input = function() {
     # cdr3col = if (!on_multi) "cdr3" else "CDR3.aa"
     cdr3col = "CDR3.aa"
     for (sample in names(seqdata)) {
-        # cdr3 = bind_rows(cdr3, seqdata[[sample]] %>%
-        #     transmute(aminoAcid=CDR3.aa, vMaxResolved=paste0(V.name, "*01"), Sample=sample))
-        cdr3 = union(
-            cdr3,
-            seqdata[[sample]] %>% pull(cdr3col) %>% unique()
-        )
+        sdata = seqdata[[sample]]
+        if (on_multi) {
+            sdata[[cdr3col]] = sub(";", "", sdata[[cdr3col]])
+        } else {
+            sdata = sdata %>% separate_rows(chain, cdr3col, sep = ";") %>%
+                filter(chain == "TRB")
+        }
+        cdr3 = union(cdr3, unique(sdata[[cdr3col]]))
     }
     cdr3 = unique(cdr3)
 

{biopipen-0.31.0.dist-info → biopipen-0.31.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.31.0
+Version: 0.31.2
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.31.0.dist-info → biopipen-0.31.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=TJt1pYzTJuPE6GzDP1gxaeeVQlzcoUyEmSVSUPgYnIA,23
+biopipen/__init__.py,sha256=Me03yXizCG2hXimVttvq6I-XoZSxSRE2J-NrK4My4cU,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
@@ -202,7 +202,7 @@ biopipen/scripts/tcgamaf/Maf2Vcf.py,sha256=Cxh7fiSNCxWDTfIJqZDOOnaSrw-85S_fH2U-P
 biopipen/scripts/tcgamaf/MafAddChr.py,sha256=V10HMisl12O3ZfXuRmFNdy5p-3mr43WCvy0GHxSpwfA,494
 biopipen/scripts/tcgamaf/maf2vcf.pl,sha256=hJKcH-NbgWK6fmK7f3qex7ozJJl-PqCNPXqpwfcHwJg,22707
 biopipen/scripts/tcr/Attach2Seurat.R,sha256=0KZaBkuPvqOBXq4ZG3pzIIua5HL-161K5dVXRoCysy4,1366
-biopipen/scripts/tcr/CDR3AAPhyschem.R,sha256=3fWmoTwxVHM3CNnwxdKxy6-7Jul1UltoN4ic39aGTH0,16649
+biopipen/scripts/tcr/CDR3AAPhyschem.R,sha256=_eg5Ep-Zt-J-VklYrklDPYAvZTBH_RIxbLTPJDqS4KE,16753
 biopipen/scripts/tcr/CloneResidency.R,sha256=KAcFB39vTYsk8IEj44s8oSFVhKjpAdJ8hkpKxtdWzRA,21540
 biopipen/scripts/tcr/CloneSizeQQPlot.R,sha256=hds1C80Q_W40Ikp-BrFfvh_aBf_V61lz-1YAvkDESyk,4569
 biopipen/scripts/tcr/GIANA/GIANA.py,sha256=0qLhgCWxT8K-4JvORA03CzBPTT5pd4Di5B_DgrHXbFA,47198
@@ -225,7 +225,7 @@ biopipen/scripts/tcr/ImmunarchLoading.R,sha256=Vw2oIza3mDJzg9kuo-w5jvwdivk4AtDA6
 biopipen/scripts/tcr/ImmunarchSplitIdents.R,sha256=FGCeGV0uSmFU91lKkldUAeV4A2m3hHw5X4GNi8ffGzI,1873
 biopipen/scripts/tcr/SampleDiversity.R,sha256=oipN4-2nQZe8bYjI0lZ0SvZ7T8GZ_FWkpkobi1cwmWE,2664
 biopipen/scripts/tcr/TCRClusterStats.R,sha256=QhXgfKSh27VHO901hDizyGYTXMYFJxW22StchQUq3uE,12906
-biopipen/scripts/tcr/TCRClustering.R,sha256=LOdq6NjKcRydGSSoYehILgH4vPCeHIbVpSEYev05578,9278
+biopipen/scripts/tcr/TCRClustering.R,sha256=J3cBAK3PRN54iQHMISVSbldhVDWPIWfeO8Vrjr9qwyE,9571
 biopipen/scripts/tcr/TCRDock.py,sha256=jjzxMWp-hs0LDtA1mVbiWDvUieSO7X-F9yeKGy1LSTM,3026
 biopipen/scripts/tcr/TESSA.R,sha256=XFC2P_e_Gm83jG5EjzVIW6KcyG5IieAaK7sXDA3_oZ0,6864
 biopipen/scripts/tcr/TESSA_source/Atchley_factors.csv,sha256=SumqDOqP67P54uM7Cuc5_O_rySTWcGo7eX3psMSPX9s,763
@@ -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-0.31.2.dist-info/METADATA,sha256=3C7vpZEWG0ySF1H298xWctBRl77fl7NZluVa7Q65jUc,882
+biopipen-0.31.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+biopipen-0.31.2.dist-info/entry_points.txt,sha256=69SbeMaF47Z2DS40yo-qDyoBKmMmumrNnsjEZMOioCE,625
+biopipen-0.31.2.dist-info/RECORD,,