biopipen 0.34.4__py3-none-any.whl → 0.34.6__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.34.4"
+__version__ = "0.34.6"

biopipen/ns/tcr.py

@@ -1682,6 +1682,10 @@ class ScRepLoading(Proc):
         type (choice): The type of the data to load.
             - TCR: T cell receptor data
             - BCR: B cell receptor data
+            - auto: Automatically detect the type from the metadata.
+                If `auto` is selected, the type will be determined by the presence of
+                `TCRData` or `BCRData` columns in the metadata. If both columns are
+                present, `TCR` will be selected by default.
         combineTCR (type=json): The extra arguments for `scRepertoire::combineTCR`
             function.
             See also <https://www.borch.dev/uploads/screpertoire/reference/combinetcr>
@@ -1721,13 +1725,12 @@ class ScRepLoading(Proc):
     output = "outfile:file:{{in.metafile | stem}}.scRep.qs"
     lang = config.lang.rscript
     envs = {
-        "type": "TCR",  # or BCR
+        "type": "auto",  # or TCR/BCR
         "combineTCR": {"samples": True},
         "combineBCR": {"samples": True},
         "exclude": ["BCRData", "TCRData", "RNAData"],
         "format": None,
         "tmpdir": config.path.tmpdir,
-
     }
     script = "file://../scripts/tcr/ScRepLoading.R"
 
@@ -1750,7 +1753,7 @@ class ScRepCombiningExpression(Proc):
     Output:
         outfile: The `Seurat` object with the TCR/BCR data combined
             In addition to the meta columns added by
-            `scRepertoire::combineExpression()`, a new column `TCR_Presence` will be
+            `scRepertoire::combineExpression()`, a new column `VDJ_Presence` will be
             added to the metadata. It indicates whether the cell has a TCR/BCR
             sequence or not. The value is `TRUE` if the cell has a TCR/BCR sequence,
             and `FALSE` otherwise.

biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R

@@ -111,7 +111,7 @@ if (file.exists(celltypist_outfile) &&
         command <- paste(command, "-v")
     }
     log$info("Running celltypist:")
-    log$debug("- {command}")
+    print("- {command}")
     rc <- system(command)
     if (rc != 0) {
         stop("Failed to run celltypist. Check the job.stderr file to see the error message.")

biopipen/scripts/scrna/SeuratClusterStats-features.R

@@ -148,7 +148,7 @@ do_one_features <- function(name) {
     if (!is.null(case$comparisons)) {
         default_descr <- paste0(
             default_descr,
-            "Statistical comparisons were performed between groups using '{case$pairwise_method %||% 'wilcox.test'}' method."
+            glue("Statistical comparisons were performed between groups using \"{case$pairwise_method %||% 'wilcox.test'}\" method.")
         )
     }
     reporter$add2(

biopipen/scripts/scrna/SeuratClusterStats-stats.R

@@ -47,7 +47,7 @@ do_one_stats <- function(name) {
     if (!is.null(case$comparisons)) {
         default_descr <- paste0(
             default_descr,
-            "Statistical comparisons were performed between groups using '{case$pairwise_method %||% 'wilcox.test'}' method."
+            glue("Statistical comparisons were performed between groups using \"{case$pairwise_method %||% 'wilcox.test'}\" method.")
         )
     }
     if (save_data) {

biopipen/scripts/tcr/ScRepCombiningExpression.R

@@ -34,7 +34,7 @@ obj <- combineExpression(
     cloneSize = unlist(cloneSize),
     addLabel = addLabel
 )
-obj$TCR_Presence <- !is.na(obj$CTaa)
+obj$VDJ_Presence <- !is.na(obj$CTaa)
 
 log$info("Saving combined object ...")
 save_obj(obj, outfile)

biopipen/scripts/tcr/ScRepLoading.R

@@ -21,6 +21,18 @@ log <- get_logger()
 
 log$info("Loading metadata ...")
 metadata <- read.table(metafile, header = TRUE, sep = "\t", row.names = NULL, check.names = FALSE)
+if (type == "AUTO") {
+    if ("TCRData" %in% colnames(metadata) && "BCRData" %in% colnames(metadata)) {
+        log$warn("Both TCRData and BCRData columns found in metadata. Defaulting to TCR.")
+        type <- "TCR"
+    } else if ("TCRData" %in% colnames(metadata)) {
+        type <- "TCR"
+    } else if ("BCRData" %in% colnames(metadata)) {
+        type <- "BCR"
+    } else {
+        stop("Error: Neither TCRData nor BCRData column found in metadata.")
+    }
+}
 
 data_column <- ifelse(type == "TCR", "TCRData", "BCRData")
 combine_fn <- ifelse(type == "TCR", combineTCR, combineBCR)

{biopipen-0.34.4.dist-info → biopipen-0.34.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: biopipen
-Version: 0.34.4
+Version: 0.34.6
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.34.4.dist-info → biopipen-0.34.6.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=ABU6VLs8eGZmSsX5g58N78lvccWAQvf1yHxS1ESlkG4,23
+biopipen/__init__.py,sha256=QHGuacl6zpfoE0OOXgLhITO4iY3VuSxXyJ6Kvvrpg-E,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
@@ -27,7 +27,7 @@ biopipen/ns/scrna_metabolic_landscape.py,sha256=EwLMrsj_pTqvyAgtHLoishjQxCg_j8n5
 biopipen/ns/snp.py,sha256=iXWrw7Lmhf4_ct57HGT7JGTClCXUD4sZ2FzOgsC2pTg,28123
 biopipen/ns/stats.py,sha256=DlPyK5Vsg6ZEkV9SDS3aAw21eXzvOHgqeZDkXPhg7go,20509
 biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
-biopipen/ns/tcr.py,sha256=urx0RomtzhyEtE0V8r3mpNUEMSZCXJ8T6C_I1TSShSY,99373
+biopipen/ns/tcr.py,sha256=XvhbZcVzdJYCjGe61G_EitdRpZyDnyDsaMNPlyH5590,99676
 biopipen/ns/vcf.py,sha256=zjOH2qiSJsHACLmBqV-Tew-mn-peZgvYLAWjTLh7uTI,23823
 biopipen/ns/web.py,sha256=8VY4Xsb8UrzS4IkGUX_84GQP1JG6NcTZrV7f9tA1tUI,5458
 biopipen/reports/bam/CNAClinic.svelte,sha256=D4IxQcgDCPQZMbXog-aZP5iJEQTK2N4i0C60e_iXyfs,213
@@ -142,7 +142,7 @@ biopipen/scripts/scrna/AnnData2Seurat.R,sha256=wc5PDbK9TkuJtoXXxF4W1ODylWhyfKWd3
 biopipen/scripts/scrna/CCPlotR-patch.R,sha256=KpB8fwacBaWaUNjIidcLUkMShLjS4Gq9UY8LUgIITB0,8369
 biopipen/scripts/scrna/CellCellCommunication.py,sha256=Wg0uFSo0Yt0wq6UT1TBodyK8GtWQXGv7hXRfM665paU,4354
 biopipen/scripts/scrna/CellCellCommunicationPlots.R,sha256=4l2EJVd1y94Nfry8fuRL9OSF6AhS8PGBekimpRUu3s8,1919
-biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R,sha256=AlNx0vBKqvpQ83yfNUbU4taJ8CUyz63iXzumZcw-PBc,6968
+biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R,sha256=CwYR8WWQMf8r7V2CTalG4kxdKnYMtyhpJBe9zP2sQWA,6964
 biopipen/scripts/scrna/CellTypeAnnotation-direct.R,sha256=w3CKRUA9NZfC3TFbU8I35L4XJ6MtVaWX-VnV7ScZlBI,2196
 biopipen/scripts/scrna/CellTypeAnnotation-hitype.R,sha256=vvjhxin4aoA9heecey0dpr6ofirybygY3ApjgtQW89Y,2094
 biopipen/scripts/scrna/CellTypeAnnotation-sccatch.R,sha256=xxB4K1MzBSNQnDxa44s5ExeU67MbncOBf8lGFr7RvwQ,1870
@@ -167,9 +167,9 @@ biopipen/scripts/scrna/ScVelo.py,sha256=SPUZFgZW1Zhw-bnjJo98RK0vpuNFODQ8Q3eTguNc
 biopipen/scripts/scrna/Seurat2AnnData.R,sha256=F8g5n2CqX4-KBggxd8ittz8TejYuqqNLMudAHdFt1QM,184
 biopipen/scripts/scrna/SeuratClusterStats-clustree.R,sha256=K2pRNe3qFjTJY3VL4EQFxoU1Lzp5DUavhcfx6HZk2J8,3954
 biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=2YNUxPz1xwND9yrOtBZ75u-wwnmkJUkoUyeBlJvBWKQ,1541
-biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=s_NjsK9YNF-POnzIiavG3RrKd9dihxR9ic8kVOSSZfI,7312
+biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=G-4wNGGZPCEXup1u9dQwSQ6P-oZVRU_faFMoXfAn6i8,7320
 biopipen/scripts/scrna/SeuratClusterStats-ngenes.R,sha256=BN8HSl1HoZp8ibESaCVEJPCBWzmu1AFLMgW5ZeZphS0,3077
-biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=iRzuv6s_jD4vmheTSEsqp1Q8OQanmxvQoCkrnHQ0hfg,3590
+biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=xu256GS80jV8kZePn7qFncK58dYSHzaQY3_SDnuxv6E,3598
 biopipen/scripts/scrna/SeuratClusterStats.R,sha256=ITFqh7p1ggtDXzVxbBEO2TcdOw4dA6oGhL5m7hFAQmU,1838
 biopipen/scripts/scrna/SeuratClustering.R,sha256=W9HI3Fk3u8MVNycffip8LYRnGg7pW07io7YbtfSk2Pw,979
 biopipen/scripts/scrna/SeuratFilter.R,sha256=BrYK0MLdaTtQvInMaQsmOt7oH_hlks0M1zykkJtg2lM,509
@@ -234,8 +234,8 @@ biopipen/scripts/tcr/ImmunarchFilter.R,sha256=-en-zi0ZB1JjuqhPlaEAN8YvHrELZNJ1V7
 biopipen/scripts/tcr/ImmunarchLoading.R,sha256=u3o2aag_7cZ17HA8RxpN58wvrII0Uh-q6FY6dA8MWeQ,5756
 biopipen/scripts/tcr/ImmunarchSplitIdents.R,sha256=FGCeGV0uSmFU91lKkldUAeV4A2m3hHw5X4GNi8ffGzI,1873
 biopipen/scripts/tcr/SampleDiversity.R,sha256=oipN4-2nQZe8bYjI0lZ0SvZ7T8GZ_FWkpkobi1cwmWE,2664
-biopipen/scripts/tcr/ScRepCombiningExpression.R,sha256=TwnlUWG9isSl7H1VqhFLbWlVSdDwFRVSszqbnShH_E0,1011
-biopipen/scripts/tcr/ScRepLoading.R,sha256=FORXYfeTitFr9EtfJrv2A-2GeWG-WKDBBANeeT9ejds,5269
+biopipen/scripts/tcr/ScRepCombiningExpression.R,sha256=sYn6BEUB53Z3pF7IAjYpewGYBvVBwzJqoAOPpcAxzQo,1011
+biopipen/scripts/tcr/ScRepLoading.R,sha256=COdY7KotlYemq4LDJT3d08NlzOzRwrDUTrNUdt4P66A,5732
 biopipen/scripts/tcr/TCRClusterStats.R,sha256=ns3S95DVDBuhSe1YgTZ1OksbfBgREO2Tnp1d4QzbTw0,13530
 biopipen/scripts/tcr/TCRClustering.R,sha256=K01qYLNhXrMmPb3TJE504lpRXnfizUNZ5q75nL7dxBg,9152
 biopipen/scripts/tcr/TCRDock.py,sha256=Oyw27k6vr0pnJ0w1-lrk5b6sZ_IOf6TmbhSxQae-3Q8,3148
@@ -284,7 +284,7 @@ biopipen/utils/misc.py,sha256=pDZ-INWVNqHuXYvcjmu8KqNAigkh2lsHy0BxX44CPvc,4048
 biopipen/utils/reference.py,sha256=Oc6IlA1giLxymAuI7DO-IQLHQ7-DbsWzOQE86oTDfMU,5955
 biopipen/utils/reporter.py,sha256=VwLl6xyVDWnGY7NEXyqBlkW8expKJoNQ5iTyZSELf5c,4922
 biopipen/utils/vcf.py,sha256=MmMbAtLUcKPp02jUdk9TzuET2gWSeoWn7xgoOXFysK0,9393
-biopipen-0.34.4.dist-info/METADATA,sha256=j8gy7m8azCVgfmruZ37tT-r_MjdSK5tiJdEOvQ7k62E,975
-biopipen-0.34.4.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-biopipen-0.34.4.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
-biopipen-0.34.4.dist-info/RECORD,,
+biopipen-0.34.6.dist-info/METADATA,sha256=xjkZ-4jHx3uZyZwVYbfc0vlPlatZ927dHLpxm6y9ys0,975
+biopipen-0.34.6.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+biopipen-0.34.6.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
+biopipen-0.34.6.dist-info/RECORD,,