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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/collect-seqs.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/collect-seqs.py')
| -rw-r--r-- | workflows/pangenome-generate/collect-seqs.py | 5 |
1 files changed, 4 insertions, 1 deletions
diff --git a/workflows/pangenome-generate/collect-seqs.py b/workflows/pangenome-generate/collect-seqs.py index af4a0dc..225a61f 100644 --- a/workflows/pangenome-generate/collect-seqs.py +++ b/workflows/pangenome-generate/collect-seqs.py @@ -36,11 +36,14 @@ if len(sys.argv) > 3: for item in validated: pdh = item["portable_data_hash"] + uuid = item["uuid"] with arvados.collection.CollectionReader(pdh, api_client=api, keep_client=keepclient) as col: with col.open("sequence.fasta", "rt") as fa: - subject = "http://collections.lugli.arvadosapi.com/c=%s/sequence.fasta" % pdh + subject = "http://covid19.genenetwork.org/resource/%s" % uuid label = fa.readline().strip() merged_metadata.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \"%s\" .\n" % (subject, label[1:].replace('"', '\\"'))) + merged_metadata.write("<%s> <http://biohackathon.org/bh20-seq-schema/collection_pdh> \"%s\" .\n" % (subject, pdh)) + merged_metadata.write("<%s> <http://biohackathon.org/bh20-seq-schema/collection_version> \"%s\" .\n" % (subject, item["version"])) skip = (subject in blacklist or label[1:] in blacklist) if skip: merged_metadata.write("<%s> <http://biohackathon.org/bh20-seq-schema/excluded_from_graph> \"true\"^^<http://www.w3.org/2001/XMLSchema#boolean> .\n" % subject) |