diff options
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]]) |