From d1e8809a15ae74d0b847abb80f9f63f53078e1d6 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 19 Aug 2020 15:15:57 -0400 Subject: Scaling pangenome generation Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- workflows/pangenome-generate/dups2metadata.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'workflows/pangenome-generate/dups2metadata.py') diff --git a/workflows/pangenome-generate/dups2metadata.py b/workflows/pangenome-generate/dups2metadata.py index 9bda10a..89e7236 100644 --- a/workflows/pangenome-generate/dups2metadata.py +++ b/workflows/pangenome-generate/dups2metadata.py @@ -1,17 +1,16 @@ import sys +import re md = open(sys.argv[1], "rt") for d in md: - print(d) + sys.stdout.write(d) if len(sys.argv) < 3: exit(0) sameseqs = open(sys.argv[2], "rt") for d in sameseqs: - logging.warn(d) g = re.match(r"\d+\t(.*)", d) - logging.warn("%s", g.group(1)) sp = g.group(1).split(",") for n in sp[1:]: - print("<%s> <%s> ." % (n.strip(), sp[0].strip())) + sys.stdout.write("<%s> <%s> .\n" % (n.strip(), sp[0].strip())) -- cgit v1.2.3