fix transcript_id and transcript_name issues

Author: ygidtu

AppImageBuilder.yml

@@ -11,7 +11,7 @@ AppDir:
   app_info:
     id: org.appimage-crafters.trackplot
     name: trackplot
-    version: 0.5.1
+    version: 0.5.2
     # Set the python executable as entry point
     exec: "bin/python3"
     # Set the application main script path as argument. Use '$@' to forward CLI parameters

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "trackplot"
-version = "0.5.1"
+version = "0.5.2"
 description = "The trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. https://sashimi.readthedocs.io/"
 authors = ["ygidtu <ygidtu@gmail.com>"]
 license = "BSD-3"
@@ -23,9 +23,9 @@ hicmatrix = "^17"
 loguru = "^0.6.0"
 matplotlib = "^3.6.3"
 numpy = "^1.24.1"
-pandas = { version = "^1.5.3", allow-prereleases = true }
+pandas = "^1.5.3"
 pybigwig = "^0.3.18"
-pysam = { version = "^0.21.0", allow-prereleases = true }
+pysam = "^0.21.0"
 requests = "^2.28.2"
 scipy = "^1.10.0"
 seaborn = "^0.12.2"

trackplot/cli.py

@@ -8,7 +8,7 @@
 import os
 import sys
 from multiprocessing import cpu_count
-from typing import Optional, Dict, Set, Tuple
+from typing import Optional
 
 import click
 from click_option_group import optgroup

trackplot/file/Bam.py

@@ -161,8 +161,7 @@ def load(self,
         spanned_junctions = kwargs.get("junctions", {})
         included_junctions = kwargs.get("included_junctions", {})
         remove_duplicate_umi = kwargs.get("remove_duplicate_umi", False)
-        spanned_junctions_plus = dict()
-        spanned_junctions_minus = dict()
+        spanned_junctions_plus, spanned_junctions_minus = {}, {}
         plus, minus = np.zeros(len(region), dtype=np.int32), np.zeros(len(region), dtype=np.int32)
         site_plus, site_minus = np.zeros(len(region), dtype=np.int32), np.zeros(len(region), dtype=np.int32)
 

trackplot/plot.py

@@ -30,7 +30,7 @@
 faulthandler.enable()
 
 
-__version__ = "0.5.1"
+__version__ = "0.5.2"
 __author__ = "ygidtu & Ran Zhou"
 __email__ = "ygidtu@gmail.com"
 

trackplot/plot_func.py

@@ -436,7 +436,13 @@ def plot_annotation(
     for transcript in data:
         strand = transcript.strand
         # @2018.12.20 add transcript id, based on fixed coordinates
-        if transcript.transcript:
+        # @2025.02.04 add warnings for transcript name and id check
+        if transcript.transcript or transcript.transcript_id:
+            show_text = transcript.transcript
+            if not transcript.transcript:
+                logger.warning(f"there is not transcript_name, using transcript_id instead")
+                show_text = transcript.transcript_id
+            
             if show_gene and transcript.gene and transcript.gene_id != transcript.transcript_id:
                 if show_id:
                     ax.text(x=-.01 * max(graph_coords), y=y_loc + 0.25,
@@ -445,9 +451,11 @@ def plot_annotation(
                             s=transcript.transcript_id, fontsize=font_size, ha="right")
                 else:
                     ax.text(x=-.01 * max(graph_coords), y=y_loc,
-                            s=transcript.gene + " | " + transcript.transcript, fontsize=font_size, ha="right")
+                            s=transcript.gene + " | " + show_text, fontsize=font_size, ha="right")
             else:
-                ax.text(x=-1, y=y_loc - 0.1, s=transcript.transcript, fontsize=font_size, ha="right")
+                ax.text(x=-1, y=y_loc - 0.1, s=show_text, fontsize=font_size, ha="right")
+        else:
+            logger.warning(f"there is no transcript_name and transcript_id")
 
         # @2018.12.19
         # s and e is the start and end site of single exon

web/package.json

@@ -1,7 +1,7 @@
 {
   "name": "trackplot",
   "private": true,
-  "version": "0.5.1",
+  "version": "0.5.2",
   "type": "module",
   "scripts": {
     "dev": "vite",
@@ -22,9 +22,9 @@
     "vue-router": "^4.5.0"
   },
   "devDependencies": {
-    "@vitejs/plugin-vue": "^3.2.0",
+    "@vitejs/plugin-vue": "^5.2.1",
     "unplugin-auto-import": "^0.11.5",
     "unplugin-vue-components": "^0.22.12",
-    "vite": "^3.2.11"
+    "vite": "^6.0.11"
   }
 }