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| author | Peter Amstutz | 2020-08-19 15:15:57 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-08-19 16:31:38 -0400 |
| commit | d1e8809a15ae74d0b847abb80f9f63f53078e1d6 (patch) | |
| tree | 77a62801b9e8928889d85dadccf1ffce85b2e0cb /workflows/pangenome-generate/dups2metadata.py | |
| parent | b3d2ccf951903ac0b7d717357fb1cccca26fbd15 (diff) | |
| download | bh20-seq-resource-d1e8809a15ae74d0b847abb80f9f63f53078e1d6.tar.gz bh20-seq-resource-d1e8809a15ae74d0b847abb80f9f63f53078e1d6.tar.lz bh20-seq-resource-d1e8809a15ae74d0b847abb80f9f63f53078e1d6.zip | |
Scaling pangenome generation
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/pangenome-generate/dups2metadata.py')
| -rw-r--r-- | workflows/pangenome-generate/dups2metadata.py | 7 |
1 files changed, 3 insertions, 4 deletions
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> <http://biohackathon.org/bh20-seq-schema/has_duplicate_sequence> <%s> ." % (n.strip(), sp[0].strip())) + sys.stdout.write("<%s> <http://biohackathon.org/bh20-seq-schema/has_duplicate_sequence> <%s> .\n" % (n.strip(), sp[0].strip())) |