From 17a98ceb666178bd645807c21c482540627bb74e Mon Sep 17 00:00:00 2001
From: LauraU123 <laura.urbanska@stud.unibas.ch>
Date: Fri, 28 Oct 2022 10:57:57 +0200
Subject: [PATCH] added script to write gtf output
---
scripts/writegtf.py | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
create mode 100644 scripts/writegtf.py
diff --git a/scripts/writegtf.py b/scripts/writegtf.py
new file mode 100644
index 0000000..426f3f4
--- /dev/null
+++ b/scripts/writegtf.py
@@ -0,0 +1,21 @@
+'''
+This function writes keeps the representative transcripts from the original input file (gtf)
+and writes them to an output.
+(The representative transcripts being listed in a csv file)
+'''
+
+def gtf_representative_transcripts(original_gtf, transcripts):
+ transcript = pd.read_csv(transcripts)
+ representative_transcripts = []
+
+ with open (original_gtf, 'r') as file:
+ for id in transcript['id']:
+ for line in file:
+ if id in line:
+ representative_transcripts.append(line)
+
+
+ with open ('output.gtf', 'w') as outputfile:
+ outputfile.write(representative_transcripts)
+
+
--
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