biopipen 0.16.5__py3-none-any.whl → 0.16.7__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.16.5"
+__version__ = "0.16.7"

biopipen/ns/scrna.py

@@ -353,7 +353,7 @@ class CellsDistribution(Proc):
             * `subset`: An expression to subset the cells, will be passed to `dplyr::filter()`. Default is `TRUE` (no filtering).
             * `id`: The column name in metadata for the group ids (i.e. `CDR3.aa`)
             * `compare`: Either a (numeric) column name (i.e. `Clones`) in metadata to compare between groups, or `.n` to compare the number of cells in each group.
-            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df %>% mutate(expanded = expanded(...))`.
+            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df |> mutate(expanded = expanded(...))`.
             * `order`: The order of the returned ids. It could be `sum` or `diff`, which is the sum or diff of the `compare` between idents.
                 Two kinds of modifiers can be added, including `desc` and `abs`.
                 For example, `sum,desc` means the sum of `compare` between idents in descending order.
@@ -442,7 +442,7 @@ class SeuratMetadataMutater(Proc):
             * `subset`: An expression to subset the cells, will be passed to `dplyr::filter()`. Default is `TRUE` (no filtering).
             * `id`: The column name in metadata for the group ids (i.e. `CDR3.aa`)
             * `compare`: Either a (numeric) column name (i.e. `Clones`) in metadata to compare between groups, or `.n` to compare the number of cells in each group.
-            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df %>% mutate(expanded = expanded(...))`.
+            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df |> mutate(expanded = expanded(...))`.
             * `order`: The order of the returned ids. It could be `sum` or `diff`, which is the sum or diff of the `compare` between idents.
                 Two kinds of modifiers can be added, including `desc` and `abs`.
                 For example, `sum,desc` means the sum of `compare` between idents in descending order.
@@ -458,7 +458,7 @@ class SeuratMetadataMutater(Proc):
         r-dplyr:
             - check: {{proc.lang}} <(echo "library(dplyr)")
     """  # noqa: E501
-    input = "srtobj:file, metafile:file, mutaters:var"
+    input = "srtobj:file, metafile:file"
     output = "rdsfile:file:{{in.srtobj | stem}}.RDS"
     lang = config.lang.rscript
     envs = {"mutaters": {}}
@@ -580,7 +580,7 @@ class MarkersFinder(Proc):
             * `subset`: An expression to subset the cells, will be passed to `dplyr::filter()`. Default is `TRUE` (no filtering).
             * `id`: The column name in metadata for the group ids (i.e. `CDR3.aa`)
             * `compare`: Either a (numeric) column name (i.e. `Clones`) in metadata to compare between groups, or `.n` to compare the number of cells in each group.
-            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df %>% mutate(expanded = expanded(...))`.
+            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df |> mutate(expanded = expanded(...))`.
             * `order`: The order of the returned ids. It could be `sum` or `diff`, which is the sum or diff of the `compare` between idents.
                 Two kinds of modifiers can be added, including `desc` and `abs`.
                 For example, `sum,desc` means the sum of `compare` between idents in descending order.
@@ -994,7 +994,7 @@ class ScFGSEA(Proc):
             * `subset`: An expression to subset the cells, will be passed to `dplyr::filter()`. Default is `TRUE` (no filtering).
             * `id`: The column name in metadata for the group ids (i.e. `CDR3.aa`)
             * `compare`: Either a (numeric) column name (i.e. `Clones`) in metadata to compare between groups, or `.n` to compare the number of cells in each group.
-            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df %>% mutate(expanded = expanded(...))`.
+            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df |> mutate(expanded = expanded(...))`.
             * `order`: The order of the returned ids. It could be `sum` or `diff`, which is the sum or diff of the `compare` between idents.
                 Two kinds of modifiers can be added, including `desc` and `abs`.
                 For example, `sum,desc` means the sum of `compare` between idents in descending order.
@@ -1341,7 +1341,7 @@ class MetaMarkers(Proc):
             * `subset`: An expression to subset the cells, will be passed to `dplyr::filter()`. Default is `TRUE` (no filtering).
             * `id`: The column name in metadata for the group ids (i.e. `CDR3.aa`)
             * `compare`: Either a (numeric) column name (i.e. `Clones`) in metadata to compare between groups, or `.n` to compare the number of cells in each group.
-            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df %>% mutate(expanded = expanded(...))`.
+            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df |> mutate(expanded = expanded(...))`.
             * `order`: The order of the returned ids. It could be `sum` or `diff`, which is the sum or diff of the `compare` between idents.
                 Two kinds of modifiers can be added, including `desc` and `abs`.
                 For example, `sum,desc` means the sum of `compare` between idents in descending order.

{biopipen-0.16.5.dist-info → biopipen-0.16.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.16.5
+Version: 0.16.7
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.16.5.dist-info → biopipen-0.16.7.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=r0anPjT1FU7ZF59Wu8yrTS7JfVcf5Cbwqs29-uSLGyo,23
+biopipen/__init__.py,sha256=d1jssHDng02ej4s_3Yzl--DPqN1B-xx2byinKhvGh94,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=JALO2S7TfmV3gIRPJ0cLTFWncPXXheQJS3vYQlyX6wQ,1600
@@ -19,7 +19,7 @@ biopipen/ns/gsea.py,sha256=EsNRAPYsagaV2KYgr4Jv0KCnZGqayM209v4yOGGTIOI,7423
 biopipen/ns/misc.py,sha256=fzn0pXvdghMkQhu-e3MMapPNMyO6IAJbtTzVU3GbFa0,3246
 biopipen/ns/plot.py,sha256=yguxmErUOH-hOM10JfuI_sXw2p49XF8yGR_gXfbd5yQ,4066
 biopipen/ns/rnaseq.py,sha256=l4vFeRasGhkexopGTM_VfSyIFewOxg-9L5niFzhWUNA,565
-biopipen/ns/scrna.py,sha256=tO14g27oR5dL4ErGQE6kIxfSLk4vmIUi3pqOKbHfX5M,71206
+biopipen/ns/scrna.py,sha256=bLgIHJfbJtAQLhUz3sub3sb0cvO3HOYWdi3YjxZ0fFA,71187
 biopipen/ns/scrna_basic.py,sha256=os00_hhEaCVRspSCnHvOoItS11OU_aFKgMqbocVyZQU,8538
 biopipen/ns/scrna_metabolic_landscape.py,sha256=AW36EOH-5AJNcMK4j7_LPgJYpyXASH3jj99g_m15SaA,26056
 biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
@@ -192,7 +192,7 @@ biopipen/utils/plot.R,sha256=pzl37PomNeUZPxohHZ2w93j3Fc4T0Qrc62FF-9MTKdw,4417
 biopipen/utils/reference.py,sha256=6bPSwQa-GiDfr7xLR9a5T64Ey40y24yn3QfQ5wDFZkU,4420
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.16.5.dist-info/METADATA,sha256=q7Kzos97srcjdvs5q72VAWnRxVNMfhHtTn6bSdX3mfc,863
-biopipen-0.16.5.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
-biopipen-0.16.5.dist-info/entry_points.txt,sha256=K9wUvJm9uFSpzqwG-6jRIcEXBg6jqNgYjdi_BL4Uf8o,523
-biopipen-0.16.5.dist-info/RECORD,,
+biopipen-0.16.7.dist-info/METADATA,sha256=og2HcHqumGOAJCZ4D0Ld0AAlY5rBtnYHD0datVioPHk,863
+biopipen-0.16.7.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
+biopipen-0.16.7.dist-info/entry_points.txt,sha256=K9wUvJm9uFSpzqwG-6jRIcEXBg6jqNgYjdi_BL4Uf8o,523
+biopipen-0.16.7.dist-info/RECORD,,