Option to run on all transcripts (#10)

* Option to run the script on all transcripts
zavolanlab · Jun 17, 2021 · 9345a3c · 9345a3c
1 parent 6078e47
commit 9345a3c
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/scripts/gtf2bed12 b/scripts/gtf2bed12
@@ -34,7 +34,7 @@ def main():
     parser.add_argument(
         "--transcript_type",
         dest="transcript_type",
-        help="Transcript type [Default: protein_coding]",
+        help="Transcript type [Default: protein_coding]. Please specify `all` for all transcripts.",
         required=False,
         default="protein_coding"
     )

diff --git a/setup.py b/setup.py
@@ -10,7 +10,7 @@
 
 setup(
     name='zgtf',
-    version='0.1.1',
+    version='0.1.2',
     description="gtf conversion utility.",
     author="Foivos Gypas",
     author_email='[email protected]',

diff --git a/zgtf/zgtf.py b/zgtf/zgtf.py
@@ -24,8 +24,9 @@ def gtf_to_transcript_exons(gtf, transcript_type):
                 sys.stderr.write(f"Problem with: {gtf_line}. Exiting.{os.linesep}")
                 sys.exit(1)
 
-            if tr_type != transcript_type:
-                continue
+            if transcript_type != "all":
+                if tr_type != transcript_type:
+                    continue
 
             if tr_id not in transcripts:
                 transcripts[tr_id] = [gtf_line]