fix unexpected exon_id issue with gtf file.

Author: ygidtu

AppImageBuilder.yml

@@ -11,7 +11,7 @@ AppDir:
   app_info:
     id: org.appimage-crafters.trackplot
     name: trackplot
-    version: 0.3.4
+    version: 0.3.5
     # Set the python executable as entry point
     exec: "bin/python3"
     # Set the application main script path as argument. Use '$@' to forward CLI parameters

example/density_list.tsv

@@ -6,3 +6,4 @@ example/bams/3.bam bam  3bam    blue
 example/bams/sc.bam bam sc	red	frf	1000000
 example/bams/sc.bam bam sc1	blue	frf	1000000
 example/depth.bgz   depth   depth
+example/bedgraph/ENCFF260QGF_lung_filter.bedgraph.gz bedgraph bedgraph

example/example.png

@@ -8,4 +8,5 @@ example/bws/1.bw    bw  bw  YlOrBr
 example/bws/2.bw    bw  bw  YlOrBr
 example/bws/3.bw    bw  bw  YlOrBr
 example/bws/4.bw    bw  bw  YlOrBr
-example/bws/0.bw    bw  bw  YlOrBr
+example/bws/0.bw    bw  bw  YlOrBr
+example/bedgraph/ENCFF260QGF_lung_filter.bedgraph.gz bedgraph bedgraph

example/example.sorted.gtf.gz

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "trackplot"
-version = "0.3.4"
+version = "0.3.5"
 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"

example/heatmap_list.tsv

@@ -385,12 +385,23 @@ def __load_gtf__(self):
                 if rec.transcript_id not in exons.keys():
                     exons[rec.transcript_id] = []
 
+                # fix exon_id error
+                exon_id = ""
+                if "exon_id" in rec.keys():
+                    exon_id = rec.exon_id
+                elif "ID" in rec.keys():
+                    exon_id = rec["ID"]
+                elif "id" in rec.keys():
+                    exon_id = rec["id"]
+                elif "_id" in rec.keys():
+                    exon_id = rec["_id"]
+
                 exons[rec.transcript_id].append(
                     GenomicLoci(
                         chromosome=rec.contig,
                         start=start, end=end,
                         strand=rec.strand,
-                        name=rec.exon_id
+                        name=exon_id
                     )
                 )
 

pyproject.toml

@@ -30,7 +30,7 @@
 faulthandler.enable()
 
 
-__version__ = "0.3.4"
+__version__ = "0.3.5"
 __author__ = "ygidtu & Ran Zhou"
 __email__ = "ygidtu@gmail.com"
 

trackplot/file/Annotation.py

@@ -1,7 +1,7 @@
 {
   "name": "trackplot",
   "private": true,
-  "version": "0.3.4",
+  "version": "0.3.5",
   "type": "module",
   "scripts": {
     "dev": "vite",