From 14de29a9b46a47214050b3afba9a72e98507f175 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 9 Jul 2021 09:26:14 +0200
Subject: [PATCH] t2g.py: fool proof output format
---
src/.docker_modules/kb/0.26.0/t2g.py | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/src/.docker_modules/kb/0.26.0/t2g.py b/src/.docker_modules/kb/0.26.0/t2g.py
index c27cdfa9..f9f0b45d 100755
--- a/src/.docker_modules/kb/0.26.0/t2g.py
+++ b/src/.docker_modules/kb/0.26.0/t2g.py
@@ -3,6 +3,7 @@ import os
import gffutils
import argparse
+
def validate_file(f):
if not os.path.exists(f):
# Argparse uses the ArgumentTypeError to give a rejection message like:
@@ -32,10 +33,15 @@ if __name__ == "__main__":
with open("t2g.txt", "w") as t2g:
for gene in db.all_features():
for transcript in db.children(
- gene, featuretype='transcript', order_by='start'):
+ gene, featuretype='transcript', order_by='start'
+ ):
+ t2g_line = str(transcript["transcript_id"][0]) + \
+ "\t" + \
+ str(gene["gene_id"][0])
+ t2g_line = t2g_line.split("\t")
t2g.write(
- str(transcript["transcript_id"][0]) +
+ str(t2g_line[0].split(".")[0]) +
"\t" +
- str(gene["gene_id"][0]) +
+ str(t2g_line[1].split(".")[0]) +
"\n"
)
--
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