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| author | Peter Amstutz | 2020-08-19 15:19:07 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-08-19 16:31:38 -0400 |
| commit | b3d2ccf951903ac0b7d717357fb1cccca26fbd15 (patch) | |
| tree | 92adcacbd208546bf3f063e6c25765e660972244 /workflows/pangenome-generate/dups2metadata.py | |
| parent | 592c921a3223c03d8a22f7a852641ac5d753fb31 (diff) | |
| download | bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.tar.gz bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.tar.lz bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.zip | |
Consolidate steps to scale graph generation workflow
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 | 17 |
1 files changed, 17 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/dups2metadata.py b/workflows/pangenome-generate/dups2metadata.py new file mode 100644 index 0000000..9bda10a --- /dev/null +++ b/workflows/pangenome-generate/dups2metadata.py @@ -0,0 +1,17 @@ +import sys + +md = open(sys.argv[1], "rt") +for d in md: + print(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())) |