biopipen 0.32.0__py3-none-any.whl → 0.32.1__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.32.0"
+__version__ = "0.32.1"

biopipen/reports/scrna/TopExpressingGenes.svelte

@@ -2,7 +2,7 @@
 {% from "utils/gsea.liq" import enrichr_report -%}
 <script>
     import { Image, DataTable, Descr } from "$libs";
-    import { Accordion, AccordionItem, Tabs, Tab, TabContent } from "$ccs";
+    import { Accordion, AccordionItem, Tabs, Tab, TabContent, InlineNotification } from "$ccs";
 </script>
 
 

biopipen/scripts/scrna/ScFGSEA.R

@@ -180,7 +180,7 @@ do_case <- function(name, case) {
     case$rest$maxSize <- case$maxsize
     case$rest$eps <- case$eps
     case$rest$nproc <- case$ncores
-    runFGSEA(ranks, gmtfile, case$top, info$casedir, case$rest)
+    runFGSEA(ranks, case$gmtfile, case$top, info$casedir, case$rest)
 
     add_report(
         list(kind = "fgsea", dir = info$casedir),

biopipen/scripts/scrna/SeuratClusterStats-features.R

@@ -414,7 +414,7 @@ do_one_features = function(name) {
             p = p + eval(parse(text = pls))
         }
     }
-    figfile = file.path(odir, paste0(slugify(name), ".", slugify(case$kind), ".png"))
+    figfile = file.path(odir, paste0(slugify(name), ".", slugify(kind), ".png"))
     png(figfile, width=devpars$width, height=devpars$height, res=devpars$res)
     tryCatch({
         print(p)

biopipen/scripts/scrna/SeuratPreparing-common.R

@@ -35,10 +35,10 @@ rename_files = function(e, sample, path) {
 perform_cell_qc <- function(sobj, per_sample = FALSE) {
     log_prefix <- ifelse(per_sample, "  ", "- ")
     log_info("{log_prefix}Adding metadata for QC ...")
-    sobj$percent.mt <- PercentageFeatureSet(sobj, pattern = "^MT-")
-    sobj$percent.ribo <- PercentageFeatureSet(sobj, pattern = "^RP[SL]")
-    sobj$percent.hb <- PercentageFeatureSet(sobj, pattern = "^HB[^(P)]")
-    sobj$percent.plat <- PercentageFeatureSet(sobj, pattern = "PECAM1|PF4")
+    sobj$percent.mt <- PercentageFeatureSet(sobj, pattern = "^MT-|^Mt-|^mt-")
+    sobj$percent.ribo <- PercentageFeatureSet(sobj, pattern = "^RP[SL]|^Rp[sl]")
+    sobj$percent.hb <- PercentageFeatureSet(sobj, pattern = "^HB[^P]|^Hb[^p]")
+    sobj$percent.plat <- PercentageFeatureSet(sobj, pattern = "PECAM1|PF4|Pecam1|Pf4")
 
     if (is.null(envs$cell_qc) || length(envs$cell_qc) == 0) {
         log_warn("{log_prefix}No cell QC criteria is provided. All cells will be kept.")
@@ -210,7 +210,7 @@ load_sample = function(sample) {
 
     if (isTRUE(envs$cell_qc_per_sample)) {
         log_info("- Perform cell QC for sample: {sample} ...")
-        obj = perform_cell_qc(obj, TRUE)
+        obj = perform_cell_qc(obj, per_sample = TRUE)
     }
 
     if (isTRUE(envs$use_sct)) {
@@ -287,7 +287,7 @@ run_cell_qc <- function(sobj) {
 
         if (!envs$cell_qc_per_sample) {
             log_info("Performing cell QC ...")
-            sobj = perform_cell_qc(sobj)
+            sobj = perform_cell_qc(sobj, per_sample = FALSE)
         }
 
         cached$data <- list(sobj = sobj, cell_qc_df = cell_qc_df)

{biopipen-0.32.0.dist-info → biopipen-0.32.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.32.0
+Version: 0.32.1
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang
@@ -12,6 +12,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Provides-Extra: runinfo
 Requires-Dist: datar[pandas] (>=0.15.6,<0.16.0)
 Requires-Dist: pipen-board[report] (>=0.16,<0.17)

{biopipen-0.32.0.dist-info → biopipen-0.32.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=s1FApnNsg-mmWP3shY6ep6EAjZrNFXHlyBXWcP2KV6Q,23
+biopipen/__init__.py,sha256=31GIxCk9aH78VuRzCVgISUIgmg2AZWeGccuxRLBiXe8,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=7IXvviRicZ2D1h6x3BVgbLJ96nsh-ikvZ0sVlQepqFE,1944
@@ -56,7 +56,7 @@ biopipen/reports/scrna/ScFGSEA.svelte,sha256=Gqt-XjqsB3XgdR3XukvphwyMExZpScwqgEo
 biopipen/reports/scrna/SeuratClusterStats.svelte,sha256=rTsoOCiVm7lEyBYgu2ZVcKNGi4g6PynYoOSx0DHdTHo,429
 biopipen/reports/scrna/SeuratMap2Ref.svelte,sha256=1g-FEmvR2YMn0OF66qESNBWmGdHQY3u8QuG4M-T7Y4E,659
 biopipen/reports/scrna/SeuratPreparing.svelte,sha256=CCQ3qodjfoQeMZhSZp7irvSqBt10m7urzcWEOHsZa8M,365
-biopipen/reports/scrna/TopExpressingGenes.svelte,sha256=h2Or2cKCzuY2cypq1PKrqiHFVMZmFUgFOXoQumvfGSk,471
+biopipen/reports/scrna/TopExpressingGenes.svelte,sha256=tt5_Vjym4coFT8Bvz0s6ZcCioTOIwCj83jdCGqPCmUw,491
 biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=4M8V6jDv1_ZviTsRdoYNQixoTnKiD06oPHzVabUTq6k,978
 biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.svelte,sha256=7FohWYR2BEqo77W4FuGsuwEEvG7j_Mc2ohXG8TSgODg,907
 biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte,sha256=bbPWDEXTi-A377Vo2VaEyh_VoxGmFj-P3WX8g_y_-9k,3416
@@ -161,12 +161,12 @@ biopipen/scripts/scrna/MetaMarkers.R,sha256=opw5RyHpNnYXXnw0HQvFSaptw3IDaTiArwT1
 biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=QJ_E6qjRC8GazoopcxZfT5cKxlubf4dK-V7KLBB-yRE,4210
 biopipen/scripts/scrna/RadarPlots.R,sha256=4zs0hAm7yq1Ls62f_29koPLqAKCeKbYiztNM-HR7j3U,13041
 biopipen/scripts/scrna/SCImpute.R,sha256=dSJOHhmJ3x_72LBRXT72dbCti5oiB85CJ-OjWtqONbk,2958
-biopipen/scripts/scrna/ScFGSEA.R,sha256=MFoJ3i3LFBfsPCxwLPnTh141ZJyrzwnrTuCZIFwvYjU,6318
+biopipen/scripts/scrna/ScFGSEA.R,sha256=LxFxd46qGt2OlvpO-4YqcEiZhFoVdFpJ1AmhUdpaIUo,6323
 biopipen/scripts/scrna/ScSimulation.R,sha256=b2LtL68ucxLoI57tSEDD0hOSbVHUA_x88Y96eK07N-s,1712
 biopipen/scripts/scrna/Seurat2AnnData.R,sha256=zXkdHEqv6H8RCw1bEPStvYHVpu5oRnioWxz164MgHxQ,276
 biopipen/scripts/scrna/SeuratClusterStats-clustree.R,sha256=FkbniQMHiZGrFAIuS8nUfPVJKFofSL-ZnpxTqIhTa54,3058
 biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=NEdlJHNXnJZfF7YkefYVWTPO8Z_KAppRAs9rNvB8TXs,2360
-biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=DeGo7AkBRq0V3Y3JDaifId6rrr5dwawTzcSAJ3W1lxE,15614
+biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=ae3hdEPzC3bO11ot2-xH6AT3-v8GWCxAxcm05xH4TBI,15609
 biopipen/scripts/scrna/SeuratClusterStats-hists.R,sha256=PXyDKww8HcloCU8r4IqRwRrm6Ly0cpmpvRcP30xxBa4,5038
 biopipen/scripts/scrna/SeuratClusterStats-ngenes.R,sha256=ihZLB27iEhgICKj-ZTnxTvRAYIgg9rzWr9Oyh1YmOYM,2160
 biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=jufs99zxNyUaTCDiWzO0yt76ncc73Yn_SpPa5igbJyA,9120
@@ -177,7 +177,7 @@ biopipen/scripts/scrna/SeuratFilter.R,sha256=BrYK0MLdaTtQvInMaQsmOt7oH_hlks0M1zy
 biopipen/scripts/scrna/SeuratLoading.R,sha256=ekWKnHIqtQb3kHVQiVymAHXXqiUxs6KKefjZKjaykmk,900
 biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=MP6ttYv8bK5kzWNoP3DXEad06snotVOqCqdvBHsOasc,12776
 biopipen/scripts/scrna/SeuratMetadataMutater.R,sha256=PMwG0Xvl_EEVKkicfrIi4arEqpY948PkYLkb59kTAXI,1135
-biopipen/scripts/scrna/SeuratPreparing-common.R,sha256=WuD7lGS17eAUQWSiIdAoV0EIeqS3Tnkkx-7PbP6Q3tc,16279
+biopipen/scripts/scrna/SeuratPreparing-common.R,sha256=zLZ8nhSJK7otrc8e-2FswGc45WRYTE6tdHzKZSFVV2s,16347
 biopipen/scripts/scrna/SeuratPreparing-doublet_detection.R,sha256=TNN2lfFjpnnO0rguMsG38JYCP1nFUhcPLJ1LqGj-Sc8,6674
 biopipen/scripts/scrna/SeuratPreparing.R,sha256=CZL6h3mLS5C34ooMa4GcwvSPn4l46Lx7-sRi9FmWvJI,3827
 biopipen/scripts/scrna/SeuratSplit.R,sha256=vdK11V39_Uo_NaOh76QWCtxObGaEr5Ynxqq0hTiSvsU,754
@@ -290,7 +290,7 @@ biopipen/utils/reference.py,sha256=oi5evicLwHxF0KAIPNZohBeHJLJQNWFJH0cr2y5pgcg,5
 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=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.32.0.dist-info/METADATA,sha256=1kWhdtPEVLqTrBh-9eK1I-Fb7KVCycmWJTA4_HXQLlw,882
-biopipen-0.32.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-biopipen-0.32.0.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
-biopipen-0.32.0.dist-info/RECORD,,
+biopipen-0.32.1.dist-info/METADATA,sha256=vaxY3m7PF1adjEsggWE8SmU2rPHtRS0-t-23r7xkgUo,933
+biopipen-0.32.1.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
+biopipen-0.32.1.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
+biopipen-0.32.1.dist-info/RECORD,,

{biopipen-0.32.0.dist-info → biopipen-0.32.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.0
+Generator: poetry-core 1.9.1
 Root-Is-Purelib: true
 Tag: py3-none-any