From 3a878b65af82d706c6685cacb5fd52606556b0c9 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 5 Jul 2021 10:43:12 +0200
Subject: [PATCH] t2g.py: fix indentation
---
src/.docker_modules/kb/0.26.0/t2g.py | 36 +++++++++++++++++++++-------
1 file changed, 27 insertions(+), 9 deletions(-)
diff --git a/src/.docker_modules/kb/0.26.0/t2g.py b/src/.docker_modules/kb/0.26.0/t2g.py
index c9b23061..96421e4b 100755
--- a/src/.docker_modules/kb/0.26.0/t2g.py
+++ b/src/.docker_modules/kb/0.26.0/t2g.py
@@ -10,14 +10,32 @@ def validate_file(f):
raise argparse.ArgumentTypeError("{0} does not exist".format(f))
return f
+
if __name__ == "__main__":
- parser = argparse.ArgumentParser(description="create transcript to genes file from a gtf file.")
- parser.add_argument("-g", "--gtf", dest="gtf", required=True, type=validate_file,
- help="gtf file", metavar="FILE")
- args = parser.parse_args()
+ parser = argparse.ArgumentParser(
+ description="create transcript to genes file from a gtf file."
+ )
+ parser.add_argument(
+ "-g", "--gtf", dest="gtf", required=True, type=validate_file,
+ help="gtf file", metavar="FILE"
+ )
+ args = parser.parse_args()
- db = gffutils.create_db(args.gtf, dbfn = ":memory:", force = True, merge_strategy="merge", disable_infer_transcripts=True, disable_infer_genes=True)
- with open("t2g.txt", "w") as t2g:
- for gene in db.all_features():
- for transcript in db.children(gene, featuretype='transcript', order_by='start'):
- t2g.write(str(transcript["transcript_id"][0]) + "\t" + str(gene["gene_id"][0]) + "\n")
+ db = gffutils.create_db(
+ args.gtf,
+ dbfn=":memory:",
+ force=True,
+ merge_strategy="merge",
+ disable_infer_transcripts=True,
+ disable_infer_genes=True
+ )
+ with open("t2g.txt", "w") as t2g:
+ for gene in db.all_features():
+ for transcript in db.children(
+ gene, featuretype='transcript', order_by='start'):
+ t2g.write(
+ str(transcript["transcript_id"][0]) +
+ "\t" +
+ str(gene["gene_id"][0]) +
+ "\n"
+ )
--
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