From d455a58414eb45453ac31aa6ff47096e3226d9d5 Mon Sep 17 00:00:00 2001
From: e-sollier <etienne.sollier@gmail.com>
Date: Fri, 15 Nov 2024 09:36:49 +0100
Subject: [PATCH] gtf: use gene_id or gene if gene_name is missing

---
 figeno/cli/cli.py            | 2 +-
 figeno/genes.py              | 6 ++++++
 figeno/gui/package-lock.json | 4 ++--
 figeno/gui/package.json      | 2 +-
 pyproject.toml               | 2 +-
 5 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/figeno/cli/cli.py b/figeno/cli/cli.py
index 56ad18b..c7b79f7 100644
--- a/figeno/cli/cli.py
+++ b/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)
diff --git a/figeno/genes.py b/figeno/genes.py
index e2275d9..a6df458 100644
--- a/figeno/genes.py
+++ b/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
diff --git a/figeno/gui/package-lock.json b/figeno/gui/package-lock.json
index c36f9bb..6e0f93c 100644
--- a/figeno/gui/package-lock.json
+++ b/figeno/gui/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "figeno",
-  "version": "1.5.1",
+  "version": "1.6.2",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "figeno",
-      "version": "1.5.1",
+      "version": "1.6.2",
       "dependencies": {
         "@dnd-kit/core": "^6.1.0",
         "@dnd-kit/sortable": "^8.0.0",
diff --git a/figeno/gui/package.json b/figeno/gui/package.json
index ea2f89e..aa291c5 100644
--- a/figeno/gui/package.json
+++ b/figeno/gui/package.json
@@ -1,6 +1,6 @@
 {
   "name": "figeno",
-  "version": "1.6.2",
+  "version": "1.6.3",
   "private": true,
   "homepage": "./",
   "dependencies": {
diff --git a/pyproject.toml b/pyproject.toml
index a1e96f9..81f4f00 100644
--- a/pyproject.toml
+++ b/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 = [