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| author | lltommy | 2020-11-11 09:56:12 +0100 |
|---|---|---|
| committer | lltommy | 2020-11-11 09:56:12 +0100 |
| commit | d6aa323b6fc7a82e45cc1df51fc72c2d547146eb (patch) | |
| tree | 6e8b77bde4dc34fab3fa8804906f3cb821f61dae /workflows/pangenome-generate/from_sparql.py | |
| parent | c5fe5de7e4c77bfb48b1ae2f662c2d9cc120c06e (diff) | |
| parent | c872248e43c1c66e5fed8ef341f7b4ac21d63e6f (diff) | |
| download | bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.tar.gz bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.tar.lz bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.zip | |
Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
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]]) |