biopipen 0.31.2__tar.gz → 0.31.4__tar.gz

{biopipen-0.31.2 → biopipen-0.31.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.31.2
+Version: 0.31.4
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang
@@ -18,5 +18,5 @@ Requires-Dist: pipen-board[report] (>=0.16,<0.17)
 Requires-Dist: pipen-cli-run (>=0.14,<0.15)
 Requires-Dist: pipen-filters (>=0.14,<0.15)
 Requires-Dist: pipen-poplog (>=0.2.0,<0.3.0)
-Requires-Dist: pipen-runinfo (>=0.7,<0.8) ; extra == "runinfo"
+Requires-Dist: pipen-runinfo (>=0.8,<0.9) ; extra == "runinfo"
 Requires-Dist: pipen-verbose (>=0.12,<0.13)

biopipen-0.31.4/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.31.4"

{biopipen-0.31.2 → biopipen-0.31.4}/biopipen/ns/plot.py

@@ -35,7 +35,7 @@ class VennDiagram(Proc):
     envs = {
         "inopts": {"row.names": -1, "header": False},
         "intype": "raw",
-        "devpars": {"res": 100, "width": 1000, "height": 1000},
+        "devpars": {"res": 100, "width": 800, "height": 600},
         "args": {},
         "ggs": None,
     }

{biopipen-0.31.2 → biopipen-0.31.4}/biopipen/scripts/plot/VennDiagram.R

@@ -1,8 +1,6 @@
 {{ biopipen_dir | joinpaths: "utils", "io.R" | source_r }}
 {{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 
-library(dplyr)
-
 infile = {{in.infile | quote}}
 outfile = {{out.outfile | quote}}
 inopts = {{envs.inopts | r}}
@@ -18,9 +16,7 @@ if (intype == "raw") {
     indata = lapply(indata, function(x) unlist(strsplit(x, ",", fixed=TRUE)))
 } else { # computed
     elems = rownames(indata)
-    indata = indata %>%
-        mutate(across(everything(), function(x) elems[as.logical(x)])) %>%
-        as.list()
+    indata = apply(indata, 2, function(x) elems[as.logical(x)])
 }
 
 plotVenn(

{biopipen-0.31.2 → biopipen-0.31.4}/biopipen/scripts/scrna/SeuratMap2Ref.R

@@ -90,8 +90,8 @@ for (rname in names(mapquery_args$refdata)) {
     }
 }
 
-if (refnorm == "auto" && .is_sct(reference)) {
-    refnorm = "SCTransform"
+if (refnorm == "auto") {
+    refnorm = ifelse (.is_sct(reference), "SCTransform", "NormalizeData")
 }
 if (refnorm == "SCTransform") {
     # Check if the reference is SCTransform'ed
@@ -110,7 +110,7 @@ if (refnorm == "SCTransform") {
 } else if (refnorm == "NormalizeData") {
     findtransferanchors_args$normalization.method = "LogNormalize"
 } else {
-    stop("Unknown normalization method: {refnorm}")
+    stop(paste0("Unknown normalization method: ", refnorm))
 }
 
 # Load Seurat object

{biopipen-0.31.2 → biopipen-0.31.4}/biopipen/scripts/tcr/CDR3AAPhyschem.R

@@ -169,9 +169,12 @@ immdata = readRDS(immdatafile)
 
 merge_data = function(sam) {
     # Merge the data for one sample from immdata and metadata
-    out = immdata$data[[sam]] %>%
-        separate_rows(chain, CDR3.aa, V.name, J.name, sep = ";") %>%
-        filter(chain == "TRB") %>%
+    out = immdata$data[[sam]]
+    if ("chain" %in% colnames(out)) {
+        out = out %>% separate_rows(chain, CDR3.aa, V.name, J.name, sep = ";") %>%
+            filter(chain == "TRB")
+    }
+    out = out %>%
         mutate(
             Sample = sam,
             locus = "TCRB",

{biopipen-0.31.2 → biopipen-0.31.4}/biopipen/scripts/tcr/TCRClustering.R

@@ -35,12 +35,11 @@ if (is.null(prefix)) { prefix = "" }
 
 get_cdr3aa_df = function() {
     out = expand_immdata(immdata, cell_id = "Barcode") %>%
-        mutate(Barcode = glue(paste0(prefix, "{Barcode}"))) %>%
-        select(Barcode, CDR3.aa, chain)
+        mutate(Barcode = glue(paste0(prefix, "{Barcode}")))
 
     if (on_multi) {
         out$CDR3.aa = sub(";", "", out$CDR3.aa)
-    } else {
+    } else if ("chain" %in% colnames(out)) {
         out = out %>% separate_rows(chain, CDR3.aa, sep = ";") %>%
             filter(chain == "TRB")
     }
@@ -170,7 +169,7 @@ prepare_input = function() {
         sdata = seqdata[[sample]]
         if (on_multi) {
             sdata[[cdr3col]] = sub(";", "", sdata[[cdr3col]])
-        } else {
+        } else if ("chain" %in% colnames(sdata)) {
             sdata = sdata %>% separate_rows(chain, cdr3col, sep = ";") %>%
                 filter(chain == "TRB")
         }

{biopipen-0.31.2 → biopipen-0.31.4}/biopipen/utils/plot.R

@@ -10,7 +10,7 @@ plotVenn = function(
     # Extra ggplot components in string
     ggs = NULL,
     # Parameters for device (res, width, height) for `png()`
-    devpars = list(res=100, width=1000, height=1000),
+    devpars = list(res=100, width=800, height=600),
     # The output file. If NULL, will return the plot object
     outfile = NULL
 ) {

{biopipen-0.31.2 → biopipen-0.31.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.31.2"
+version = "0.31.4"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"
@@ -18,7 +18,7 @@ pipen-verbose = "^0.12"
 pipen-poplog = "^0.2.0"
 datar = { version = "^0.15.6", extras = ["pandas"] }
 pipen-board = { version = "^0.16", extras = ["report"] }
-pipen-runinfo = { version = "^0.7", optional = true }
+pipen-runinfo = { version = "^0.8", optional = true }
 
 [tool.poetry.extras]
 runinfo = ["pipen-runinfo"]

{biopipen-0.31.2 → biopipen-0.31.4}/setup.py

@@ -53,7 +53,7 @@ install_requires = \
  'pipen-verbose>=0.12,<0.13']
 
 extras_require = \
-{'runinfo': ['pipen-runinfo>=0.7,<0.8']}
+{'runinfo': ['pipen-runinfo>=0.8,<0.9']}
 
 entry_points = \
 {'pipen_cli_run': ['bam = biopipen.ns.bam',
@@ -82,7 +82,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.31.2',
+    'version': '0.31.4',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.31.2/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.31.2"