gtf: use gene_id or gene if gene_name is missing

figeno/cli/cli.py

@@ -2,7 +2,7 @@
 
 from figeno.cli import gui, init,make
 
-__version__ = "1.6.2"
+__version__ = "1.6.3"
 
 def main():
     parser = ArgumentParser("figeno",formatter_class=ArgumentDefaultsHelpFormatter)

figeno/genes.py

@@ -123,6 +123,9 @@ def read_genes_gtf(gtf_file,chr=None,start=None,end=None,gene_names=None,collaps
                 if x.lstrip(" ").startswith("gene_name"):
                     x = x[x.find("\"")+1:]
                     gene_name = x[:x.find("\"")]
+                elif (x.lstrip(" ").startswith("gene_id") or x.lstrip(" ").startswith("gene")) and gene_name=="":
+                    x = x[x.find("\"")+1:]
+                    gene_name = x[:x.find("\"")]
                 elif x.lstrip(" ").startswith("transcript_name"):
                     x = x[x.find("\"")+1:]
                     transcript_name = x[:x.find("\"")]
@@ -156,6 +159,9 @@ def read_genes_gtf(gtf_file,chr=None,start=None,end=None,gene_names=None,collaps
                 elif x.lstrip(" ").startswith("gene_name"):
                     x = x[x.find("\"")+1:]
                     gene_name = x[:x.find("\"")]
+                elif (x.lstrip(" ").startswith("gene_id") or x.lstrip(" ").startswith("gene")) and gene_name=="":
+                    x = x[x.find("\"")+1:]
+                    gene_name = x[:x.find("\"")]
 
             if (gene_names is not None) and (not gene_name.upper() in gene_names): continue
             if collapsed: name = gene_name

figeno/gui/package.json

@@ -1,6 +1,6 @@
 {
   "name": "figeno",
-  "version": "1.6.2",
+  "version": "1.6.3",
   "private": true,
   "homepage": "./",
   "dependencies": {

pyproject.toml

@@ -9,7 +9,7 @@ packages = ["figeno", "figeno.data", "figeno.cli", "figeno.gui"]
 
 [project]
 name = 'figeno'
-version = "1.6.2"
+version = "1.6.3"
 description = 'Package for generating genomics figures.'
 readme = 'README.md'
 authors = [