biopipen 0.31.2__tar.gz → 0.31.3__tar.gz

{biopipen-0.31.2 → biopipen-0.31.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.31.2
+Version: 0.31.3
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

biopipen-0.31.3/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.31.3"

{biopipen-0.31.2 → biopipen-0.31.3}/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-0.31.3}/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-0.31.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.31.2"
+version = "0.31.3"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"

{biopipen-0.31.2 → biopipen-0.31.3}/setup.py

@@ -82,7 +82,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.31.2',
+    'version': '0.31.3',
     '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"