biopipen 0.34.4__tar.gz → 0.34.6__tar.gz

{biopipen-0.34.4 → biopipen-0.34.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: biopipen
-Version: 0.34.4
+Version: 0.34.6
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

biopipen-0.34.6/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.34.6"

{biopipen-0.34.4 → biopipen-0.34.6}/biopipen/ns/tcr.py

@@ -1682,6 +1682,10 @@ class ScRepLoading(Proc):
         type (choice): The type of the data to load.
             - TCR: T cell receptor data
             - BCR: B cell receptor data
+            - auto: Automatically detect the type from the metadata.
+                If `auto` is selected, the type will be determined by the presence of
+                `TCRData` or `BCRData` columns in the metadata. If both columns are
+                present, `TCR` will be selected by default.
         combineTCR (type=json): The extra arguments for `scRepertoire::combineTCR`
             function.
             See also <https://www.borch.dev/uploads/screpertoire/reference/combinetcr>
@@ -1721,13 +1725,12 @@ class ScRepLoading(Proc):
     output = "outfile:file:{{in.metafile | stem}}.scRep.qs"
     lang = config.lang.rscript
     envs = {
-        "type": "TCR",  # or BCR
+        "type": "auto",  # or TCR/BCR
         "combineTCR": {"samples": True},
         "combineBCR": {"samples": True},
         "exclude": ["BCRData", "TCRData", "RNAData"],
         "format": None,
         "tmpdir": config.path.tmpdir,
-
     }
     script = "file://../scripts/tcr/ScRepLoading.R"
 
@@ -1750,7 +1753,7 @@ class ScRepCombiningExpression(Proc):
     Output:
         outfile: The `Seurat` object with the TCR/BCR data combined
             In addition to the meta columns added by
-            `scRepertoire::combineExpression()`, a new column `TCR_Presence` will be
+            `scRepertoire::combineExpression()`, a new column `VDJ_Presence` will be
             added to the metadata. It indicates whether the cell has a TCR/BCR
             sequence or not. The value is `TRUE` if the cell has a TCR/BCR sequence,
             and `FALSE` otherwise.

{biopipen-0.34.4 → biopipen-0.34.6}/biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R

@@ -111,7 +111,7 @@ if (file.exists(celltypist_outfile) &&
         command <- paste(command, "-v")
     }
     log$info("Running celltypist:")
-    log$debug("- {command}")
+    print("- {command}")
     rc <- system(command)
     if (rc != 0) {
         stop("Failed to run celltypist. Check the job.stderr file to see the error message.")

{biopipen-0.34.4 → biopipen-0.34.6}/biopipen/scripts/scrna/SeuratClusterStats-features.R

@@ -148,7 +148,7 @@ do_one_features <- function(name) {
     if (!is.null(case$comparisons)) {
         default_descr <- paste0(
             default_descr,
-            "Statistical comparisons were performed between groups using '{case$pairwise_method %||% 'wilcox.test'}' method."
+            glue("Statistical comparisons were performed between groups using \"{case$pairwise_method %||% 'wilcox.test'}\" method.")
         )
     }
     reporter$add2(

{biopipen-0.34.4 → biopipen-0.34.6}/biopipen/scripts/scrna/SeuratClusterStats-stats.R

@@ -47,7 +47,7 @@ do_one_stats <- function(name) {
     if (!is.null(case$comparisons)) {
         default_descr <- paste0(
             default_descr,
-            "Statistical comparisons were performed between groups using '{case$pairwise_method %||% 'wilcox.test'}' method."
+            glue("Statistical comparisons were performed between groups using \"{case$pairwise_method %||% 'wilcox.test'}\" method.")
         )
     }
     if (save_data) {

{biopipen-0.34.4 → biopipen-0.34.6}/biopipen/scripts/tcr/ScRepCombiningExpression.R

@@ -34,7 +34,7 @@ obj <- combineExpression(
     cloneSize = unlist(cloneSize),
     addLabel = addLabel
 )
-obj$TCR_Presence <- !is.na(obj$CTaa)
+obj$VDJ_Presence <- !is.na(obj$CTaa)
 
 log$info("Saving combined object ...")
 save_obj(obj, outfile)

{biopipen-0.34.4 → biopipen-0.34.6}/biopipen/scripts/tcr/ScRepLoading.R

@@ -21,6 +21,18 @@ log <- get_logger()
 
 log$info("Loading metadata ...")
 metadata <- read.table(metafile, header = TRUE, sep = "\t", row.names = NULL, check.names = FALSE)
+if (type == "AUTO") {
+    if ("TCRData" %in% colnames(metadata) && "BCRData" %in% colnames(metadata)) {
+        log$warn("Both TCRData and BCRData columns found in metadata. Defaulting to TCR.")
+        type <- "TCR"
+    } else if ("TCRData" %in% colnames(metadata)) {
+        type <- "TCR"
+    } else if ("BCRData" %in% colnames(metadata)) {
+        type <- "BCR"
+    } else {
+        stop("Error: Neither TCRData nor BCRData column found in metadata.")
+    }
+}
 
 data_column <- ifelse(type == "TCR", "TCRData", "BCRData")
 combine_fn <- ifelse(type == "TCR", combineTCR, combineBCR)

{biopipen-0.34.4 → biopipen-0.34.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.34.4"
+version = "0.34.6"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"

{biopipen-0.34.4 → biopipen-0.34.6}/setup.py

@@ -86,7 +86,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.34.4',
+    'version': '0.34.6',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.34.4/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.34.4"