From 403ff4786e1a376dc061e2b32083ba22e87ee973 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Mon, 30 Apr 2018 13:59:43 +0200
Subject: [PATCH] Consider mCherry a protein_coding.

This is so that the small RNA annotation script does not miss mCherry.
---
 make_mCherry_transgene.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/make_mCherry_transgene.py b/make_mCherry_transgene.py
index 7cca330..165c3e9 100755
--- a/make_mCherry_transgene.py
+++ b/make_mCherry_transgene.py
@@ -50,7 +50,7 @@ def main():
         with fs.open("mCherry_transcript.fa", "w") as transcript_file:
             transcript_file.write(f">mCherry\n{mCherry_seq}\n")
         with fs.open("mCherry.gtf", "w") as transcript_gtf_file:
-            annotations = "gene_id \"mCherry\"; transcript_id \"mCherry\"; gene_biotype \"mCherry\";"
+            annotations = "gene_id \"mCherry\"; transcript_id \"mCherry\"; gene_biotype \"protein_coding\";"
             transcript_gtf_file.write("\t".join([
                 "mCherry", "local", "transcript", "1", str(len(mCherry_seq)),
                 "0", "+", ".", annotations]))
@@ -77,7 +77,7 @@ def main():
                             "mCherry_transgene", "local", "exon", str(start_in_transgene), str(end_in_transgene),
                             "0", "+", ".", annotations]))
                         transgene_gtf_file.write("\n")
-                        annotations = f"exon_id \"mCherry.e{exon_number}\"; exon_number \"{exon_number}\"; gene_id \"mCherry\"; transcript_id \"mCherry\"; gene_biotype \"mCherry\";"
+                        annotations = f"exon_id \"mCherry.e{exon_number}\"; exon_number \"{exon_number}\"; gene_id \"mCherry\"; transcript_id \"mCherry\"; gene_biotype \"protein_coding\";"
                         transcript_gtf_file.write("\t".join([
                             "mCherry", "local", "exon", str(start_in_transcript), str(end_in_transcript),
                             "0", "+", ".", annotations]))
-- 
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