diff options
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 1a0807c..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://covid19.genenetwork.org/resource/%s" % 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) |