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| author | Peter Amstutz | 2020-10-19 21:04:19 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-11-09 16:45:33 -0500 |
| commit | 0b0fb1c8a68df989bb2e1f593d717ac62e31d952 (patch) | |
| tree | 0237427fed0c4919870c39a5026f5d3af52ed1e9 /workflows/pangenome-generate/from_sparql.py | |
| parent | b311e2ec0f1d02cf16152855dd8bdd760ed4578b (diff) | |
| download | bh20-seq-resource-0b0fb1c8a68df989bb2e1f593d717ac62e31d952.tar.gz bh20-seq-resource-0b0fb1c8a68df989bb2e1f593d717ac62e31d952.tar.lz bh20-seq-resource-0b0fb1c8a68df989bb2e1f593d717ac62e31d952.zip | |
Extract subset of the all-sequences fasta by running a sparql query.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/pangenome-generate/from_sparql.py')
| -rw-r--r-- | workflows/pangenome-generate/from_sparql.py | 8 |
1 files changed, 8 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/from_sparql.py b/workflows/pangenome-generate/from_sparql.py new file mode 100644 index 0000000..4610cad --- /dev/null +++ b/workflows/pangenome-generate/from_sparql.py @@ -0,0 +1,8 @@ +from rdflib import Graph +import sys +import subprocess +g = Graph() +g.parse(sys.argv[1], format="nt") +res = g.query(sys.argv[3]) +for r in res: + subprocess.run(["samtools", "faidx", sys.argv[2], r[0]]) |