From 1e428e53fa7fac5262a35cea67330bbd13c58084 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 13 Oct 2020 09:55:36 +0200 Subject: [PATCH] remove stop_err --- tools/sr_assembly/velveth_wrapper.py | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/tools/sr_assembly/velveth_wrapper.py b/tools/sr_assembly/velveth_wrapper.py index bccf8f2e11c..22257a47b59 100644 --- a/tools/sr_assembly/velveth_wrapper.py +++ b/tools/sr_assembly/velveth_wrapper.py @@ -10,11 +10,6 @@ import sys assert sys.version_info[:2] >= (2, 4) -def stop_err(msg): - sys.stderr.write("%s\n" % msg) - sys.exit() - - def __main__(): # Parse command line html_file = sys.argv[1] @@ -22,7 +17,8 @@ def __main__(): try: # for test - needs this done os.makedirs(working_dir) except Exception as e: - stop_err('Error running velveth ' + str(e)) + sys.exit('Error running velveth ' + str(e)) + hash_length = sys.argv[3] inputs = ' '.join(sys.argv[4:]) cmdline = 'velveth %s %s %s > /dev/null' % (working_dir, hash_length, inputs) @@ -42,7 +38,8 @@ def __main__(): if returncode != 0: raise Exception(stderr) except Exception as e: - stop_err('Error running velveth ' + str(e)) + sys.exit('Error running velveth ' + str(e)) + sequences_path = os.path.join(working_dir, 'Sequences') roadmaps_path = os.path.join(working_dir, 'Roadmaps') rval = ['Velvet Galaxy Composite Dataset

']