biopipen 0.34.15__tar.gz → 0.34.16__tar.gz

{biopipen-0.34.15 → biopipen-0.34.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biopipen
-Version: 0.34.15
+Version: 0.34.16
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

biopipen-0.34.16/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.34.16"

{biopipen-0.34.15 → biopipen-0.34.16}/biopipen/ns/scrna.py

@@ -96,6 +96,8 @@ class SeuratPreparing(Proc):
             `RNAData` to assign the path of the data to the samples
             The path will be read by `Read10X()` from `Seurat`, or the path
             to the h5 file that can be read by `Read10X_h5()` from `Seurat`.
+            It can also be an RDS or qs2 file containing a `Seurat` object.
+            Note that it must has a column named `Sample` in the meta.data to specify the sample names.
 
     Output:
         outfile: The qs2 file with the Seurat object with all samples integrated.
@@ -111,11 +113,11 @@ class SeuratPreparing(Proc):
         min_cells (type=int): The minimum number of cells that a gene must be
             expressed in to be kept. This is used in `Seurat::CreateSeuratObject()`.
             Futher QC (`envs.cell_qc`, `envs.gene_qc`) will be performed after this.
-            It doesn't work when data is loaded from loom files.
+            It doesn't work when data is loaded from loom files or RDS/qs2 files.
         min_features (type=int): The minimum number of features that a cell must
             express to be kept. This is used in `Seurat::CreateSeuratObject()`.
             Futher QC (`envs.cell_qc`, `envs.gene_qc`) will be performed after this.
-            It doesn't work when data is loaded from loom files.
+            It doesn't work when data is loaded from loom files or RDS/qs2 files.
         cell_qc: Filter expression to filter cells, using
             `tidyrseurat::filter()`.
             It can also be a dictionary of expressions, where the names of the list are
@@ -607,7 +609,7 @@ class SeuratClusterStats(Proc):
                 `ActivationScore` in the metadata.
                 You may also specify the literal order of the clusters by a list of strings (at least two).
             - subset: An expression to subset the cells, will be passed to `tidyrseurat::filter()`.
-            - devpars (ns): The device parameters for the plots. Does not work for `table`.
+            - devpars (ns): The device parameters for the plots.
                 - res (type=int): The resolution of the plots.
                 - height (type=int): The height of the plots.
                 - width (type=int): The width of the plots.

{biopipen-0.34.15 → biopipen-0.34.16}/biopipen/scripts/scrna/SeuratPreparing.R

@@ -38,19 +38,27 @@ reporter$add(
     h1 = "Filters and QC"
 )
 
-metadata <- read.table(
-    metafile,
-    header = TRUE,
-    row.names = NULL,
-    sep = "\t",
-    check.names = FALSE
-)
+metadata <- tryCatch({
+    log$debug("Trying to read Seurat object from metafile ...")
+    read_obj(metafile)
+}, error = function(e) {
+    log$debug("Failed to read Seurat object from metafile: {e$message}")
+    log$debug("Reading metafile as a table (sample info) ...")
+    read.table(
+        metafile,
+        header = TRUE,
+        row.names = NULL,
+        sep = "\t",
+        check.names = FALSE
+    )
+})
+is_seurat <- inherits(metadata, "Seurat")
 
-meta_cols = colnames(metadata)
+meta_cols <- if (is_seurat) colnames(metadata@meta.data) else colnames(metadata)
 if (!"Sample" %in% meta_cols) {
-    stop("Error: Column `Sample` is not found in metafile.")
+    stop("Error: Column `Sample` is not found in ", ifelse(is_seurat, "Seurat object's meta.data.", "metafile."))
 }
-if (!"RNAData" %in% meta_cols) {
+if (!"RNAData" %in% meta_cols && !is_seurat) {
     stop("Error: Column `RNAData` is not found in metafile.")
 }
 

{biopipen-0.34.15 → biopipen-0.34.16}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.34.15"
+version = "0.34.16"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"

{biopipen-0.34.15 → biopipen-0.34.16}/setup.py

@@ -86,7 +86,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.34.15',
+    'version': '0.34.16',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.34.15/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.34.15"