biopipen 0.33.0__py3-none-any.whl → 0.33.1__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.33.0"
+__version__ = "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/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/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.dist-info → biopipen-0.33.1.dist-info}/METADATA

@@ -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-0.33.0.dist-info → biopipen-0.33.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=6K931DiWIOR94oP_7w9oZPyA0wEqkdgU1lkcLFyRTMU,23
+biopipen/__init__.py,sha256=NGQajgIUpsHZBmlrDBG3bxWb5zT8ur6HMm3aE6rnc7M,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=lZV_vbYWk6uqm19ZWJcsZCcSNqAdIfN2fOfamzxZpg4,2148
@@ -22,7 +22,7 @@ biopipen/ns/plot.py,sha256=XzLq0A8qCIQRbxhPEdWhEfbRZ8g3e4KriVz0RP8enNY,18078
 biopipen/ns/protein.py,sha256=YJtlKoHI2p5yHdxKeQnNtm5QrbxDGOq1UXOdt_7tlTs,6391
 biopipen/ns/regulatory.py,sha256=gJjGVpJrdv-rg2t5UjK4AGuvtLNymaNYNvoD8PhlbvE,15929
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
-biopipen/ns/scrna.py,sha256=bZjIppqwmFb7Sc3GLyed8jd0tsvybSBq80uanmzU9WE,127673
+biopipen/ns/scrna.py,sha256=rsbBD81wGHlrrOcmjyToYSbd8tM7-q7ugAO62Y1usx4,128130
 biopipen/ns/scrna_metabolic_landscape.py,sha256=6AhaynGG3lNRi96N2tReVT46BJMuEwooSSd2irBoN80,28347
 biopipen/ns/snp.py,sha256=iXWrw7Lmhf4_ct57HGT7JGTClCXUD4sZ2FzOgsC2pTg,28123
 biopipen/ns/stats.py,sha256=DlPyK5Vsg6ZEkV9SDS3aAw21eXzvOHgqeZDkXPhg7go,20509
@@ -113,7 +113,7 @@ biopipen/scripts/cnvkit/CNVkitScatter.py,sha256=jDbYlMMuedih8qhbC65cqrNsNflWXSnH
 biopipen/scripts/cnvkit/CNVkitSegment.py,sha256=YIgLo6ka8fBG1Ylb8pmbquwUl5B7SY42YlzZHgmp8y0,1656
 biopipen/scripts/cnvkit/guess_baits.py,sha256=mTy3AmyH5tkC_Mb_5IhQ_c0RssEGaCmoLPEVsW81yrY,10691
 biopipen/scripts/delim/RowsBinder.R,sha256=1QtRiPdUoxR8st1nxBMyVXgpcLfeF-iGsMYHz-66L2s,1465
-biopipen/scripts/delim/SampleInfo.R,sha256=EyvpLHCn2jpMKKw7MvMPZVSmkV7ZBp02q93ZQxg_RPU,4296
+biopipen/scripts/delim/SampleInfo.R,sha256=KCdjLQ744bfp3ho3ZPoyZxM5kLB6tqi76CHEKvfk6b0,4673
 biopipen/scripts/gene/GeneNameConversion.R,sha256=Jy2ykhCj9ClSdQUfdYavh2LaBm0nOIXY2kJKmpsqOlI,1818
 biopipen/scripts/gene/GenePromoters.R,sha256=0ukq3-wpN6uq_cyJlQvKDVvy0Dv8cI5Htd9t2xpkEyk,2021
 biopipen/scripts/gsea/Enrichr.R,sha256=gqN93oE3OeqW_TXZiE_gNH89_o_XFwnOWcHxhTUMvNs,724
@@ -161,6 +161,7 @@ biopipen/scripts/scrna/ExprImputation-alra.R,sha256=xNdQiXgY13-iF16o2KgCJWfPIy4P
 biopipen/scripts/scrna/ExprImputation-rmagic.R,sha256=jYIfqZpnvjKJkvItLnemPVtUApHBYQi1_L8rHVbEe1M,735
 biopipen/scripts/scrna/ExprImputation-scimpute.R,sha256=mg40qCUW7-nP5oHPvARq7dmtoahM0GRFWXQpum0BXVk,1082
 biopipen/scripts/scrna/ExprImputation.R,sha256=GcdZJpkDpq88hRQjtLZY5-byp8V43stEFm5T-pQbU6A,319
+biopipen/scripts/scrna/LoomTo10X.R,sha256=c6F0p1udsL5UOlb84-53K5BsjSDWkdFyYTt5NQmlIec,1059
 biopipen/scripts/scrna/MarkersFinder.R,sha256=D3vhxVYAc6kgPLjw05_D5yaXOaYKHoiZ-4OvQ7RdZ6s,13297
 biopipen/scripts/scrna/MetaMarkers.R,sha256=gJexrokGg0Q53N4Y4UA6707mn9Jxv-g_Qpp4Pi6xrs8,12438
 biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=QJ_E6qjRC8GazoopcxZfT5cKxlubf4dK-V7KLBB-yRE,4210
@@ -299,7 +300,7 @@ biopipen/utils/repr.R,sha256=GO5F5FFE4XjFXO5JODAJ7Nwvr00yiPMG34vIPMkKkrU,4016
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/single_cell.R,sha256=3jmTV9-kHTXyBA6GRlRf_Ig0jx_5jRr6E1THoa1869k,7564
 biopipen/utils/vcf.py,sha256=MmMbAtLUcKPp02jUdk9TzuET2gWSeoWn7xgoOXFysK0,9393
-biopipen-0.33.0.dist-info/METADATA,sha256=J_5O1LtSrQUaYsnmwkw8Hh9IjwULZZGlsmGfbWJU6lc,930
-biopipen-0.33.0.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-biopipen-0.33.0.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
-biopipen-0.33.0.dist-info/RECORD,,
+biopipen-0.33.1.dist-info/METADATA,sha256=6HmgRewJOLTI8m8x9R6rLCfOOhHNsyLLepXq-DyKrX0,930
+biopipen-0.33.1.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+biopipen-0.33.1.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
+biopipen-0.33.1.dist-info/RECORD,,