From 7a115a1a092463b892906753d61cdf03a3699220 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 22 Jul 2021 15:08:25 +0200
Subject: [PATCH] kb: t2g tools work and gz and plain file
---
src/.docker_modules/kb/0.26.0/fix_t2g.py | 17 ++++++++++++-----
src/.docker_modules/kb/0.26.0/t2g.py | 15 +++++++++++----
2 files changed, 23 insertions(+), 9 deletions(-)
diff --git a/src/.docker_modules/kb/0.26.0/fix_t2g.py b/src/.docker_modules/kb/0.26.0/fix_t2g.py
index 6535758b..a6b4619b 100644
--- a/src/.docker_modules/kb/0.26.0/fix_t2g.py
+++ b/src/.docker_modules/kb/0.26.0/fix_t2g.py
@@ -1,6 +1,7 @@
#!/usr/local/bin/python
import os
import re
+import gzip
import argparse
@@ -30,7 +31,7 @@ def get_t2g_line(line, t2g_re):
def write_t2g_line(t2g, line, t2g_re):
- results = t2g_line(line, t2g_re)
+ results = get_t2g_line(line, t2g_re)
if results['transcript_id']:
t2g.write(
t2g_line(
@@ -51,7 +52,13 @@ if __name__ == "__main__":
args = parser.parse_args()
t2g_re = build_t2g_re()
- with open(args.t2g, "r") as gtf:
- with open("fix_t2g.txt", "w") as t2g:
- for line in gtf:
- write_t2g_line(t2g, str(line), t2g_re)
+ try:
+ with gzip.open(args.t2g, "rb") as gtf:
+ with open("fix_t2g.txt", "w") as t2g:
+ for line in gtf:
+ write_t2g_line(t2g, str(line), t2g_re)
+ except gzip.BadGzipFile:
+ with open(args.t2g, "r") as gtf:
+ with open("fix_t2g.txt", "w") as t2g:
+ for line in gtf:
+ write_t2g_line(t2g, str(line), t2g_re)
diff --git a/src/.docker_modules/kb/0.26.0/t2g.py b/src/.docker_modules/kb/0.26.0/t2g.py
index 02a4c30d..b99e74e6 100755
--- a/src/.docker_modules/kb/0.26.0/t2g.py
+++ b/src/.docker_modules/kb/0.26.0/t2g.py
@@ -62,7 +62,14 @@ if __name__ == "__main__":
gene_re = build_gene_re()
transcript_re = build_transcript_re()
- with gzip.open(args.gtf, "rb") as gtf:
- with open("t2g_dup.txt", "w") as t2g:
- for line in gtf:
- write_t2g_line(t2g, str(line), transcript_re, gene_re)
\ No newline at end of file
+ try:
+ with gzip.open(args.gtf, "rb") as gtf:
+ with open("t2g_dup.txt", "w") as t2g:
+ for line in gtf:
+ write_t2g_line(t2g, str(line), transcript_re, gene_re)
+ except gzip.BadGzipFile:
+ with open(args.gtf, "r") as gtf:
+ with open("t2g_dup.txt", "w") as t2g:
+ for line in gtf:
+ write_t2g_line(t2g, str(line), transcript_re, gene_re)
+
--
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