biopipen 0.33.0__tar.gz → 0.33.1__tar.gz

{biopipen-0.33.0 → biopipen-0.33.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: biopipen
-Version: 0.33.0
+Version: 0.33.1
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

biopipen-0.33.1/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.33.1"

{biopipen-0.33.0 → biopipen-0.33.1}/biopipen/ns/scrna.py

@@ -2628,3 +2628,20 @@ class SlingShot(Proc):
         "seed": 8525,
     }
     script = "file://../scripts/scrna/SlingShot.R"
+
+
+class LoomTo10X(Proc):
+    """Convert Loom file to 10X format
+
+    Input:
+        loomfile: The Loom file
+
+    Output:
+        outdir: The output directory for the 10X format files,
+            including the `matrix.mtx.gz`, `barcodes.tsv.gz` and `features.tsv.gz`
+            files.
+    """
+    input = "loomfile:file"
+    output = "outdir:dir:{{in.loomfile | stem}}.10X"
+    lang = config.lang.rscript
+    script = "file://../scripts/scrna/LoomTo10X.R"

{biopipen-0.33.0 → biopipen-0.33.1}/biopipen/scripts/delim/SampleInfo.R

@@ -54,7 +54,16 @@ get_plotthis_fn <- function(plot_type, gglogger_register = TRUE, return_name = F
         pie = "PieChart",
         wordcloud = "WordCloudPlot",
         venn = "VennDiagram",
-        paste0(tools::toTitleCase(plot_type), "Plot")
+        {
+            title_case_plot_type <- tools::toTitleCase(plot_type)
+            if (endsWith(title_case_plot_type, "Plot")) {
+                title_case_plot_type
+            } else if (endsWith(title_case_plot_type, "plot")) {
+                paste0(substr(title_case_plot_type, 1, nchar(title_case_plot_type) - 4), "Plot")
+            } else {
+                paste0(title_case_plot_type, "Plot")
+            }
+        }
     )
     if (return_name) {
         return(fn_name)

biopipen-0.33.1/biopipen/scripts/scrna/LoomTo10X.R

@@ -0,0 +1,51 @@
+library(loomR)
+library(DropletUtils)
+library(Matrix)
+
+loomfile <- {{in.loomfile | r}}
+outdir <- {{out.outdir | r}}
+
+lfile <- connect(filename = loomfile, mode = "r")
+
+# Extract the expression matrix (genes x cells)
+expr_matrix <- t(lfile[["matrix"]][, ])
+if (!inherits(expr_matrix, "dgCMatrix")) {
+    expr_matrix <- Matrix::Matrix(expr_matrix, sparse = TRUE)
+}
+
+# Extract gene names and IDs
+gene_names <- lfile[["row_attrs/Gene"]][]
+
+gene_ids <- tryCatch({
+   lfile[["row_attrs/GeneID"]][]
+}, error = function(e) {
+   NULL
+})
+
+if (is.null(gene_ids)) {
+  gene_ids <- gene_names
+}
+
+# Extract cell barcodes
+cell_barcodes <- lfile[["col_attrs/CellID"]][]
+
+# Close the LOOM file connection
+lfile$close_all()
+
+# Create a data frame for gene information
+gene_info <- data.frame(
+    gene_id = gene_ids,
+    gene_name = gene_names
+)
+
+# Write the data to 10X format
+
+write10xCounts(
+    path = outdir,
+    x = expr_matrix,
+    gene.id = gene_info$gene_id,
+    gene.symbol = gene_info$gene_name,
+    barcodes = cell_barcodes,
+    version = "3",
+    overwrite = TRUE
+)

{biopipen-0.33.0 → biopipen-0.33.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.33.0"
+version = "0.33.1"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"

{biopipen-0.33.0 → biopipen-0.33.1}/setup.py

@@ -85,7 +85,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.33.0',
+    'version': '0.33.1',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.33.0/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.33.0"