diff options
Diffstat (limited to 'workflows/pangenome-generate/merge-metadata.py')
| -rw-r--r-- | workflows/pangenome-generate/merge-metadata.py | 40 |
1 files changed, 36 insertions, 4 deletions
diff --git a/workflows/pangenome-generate/merge-metadata.py b/workflows/pangenome-generate/merge-metadata.py index 64275b1..65d08a6 100644 --- a/workflows/pangenome-generate/merge-metadata.py +++ b/workflows/pangenome-generate/merge-metadata.py @@ -1,9 +1,28 @@ +import re import schema_salad.schema import schema_salad.jsonld_context +import json +import sys +import os +import logging -metadataSchema = '$(inputs.metadataSchema.path)' -metadata = $(inputs.metadata) -subjects = $(inputs.subjects) +metadataSchema = sys.argv[1] +originalLabels = sys.argv[2] +dups = None +if len(sys.argv) == 4: + dups = sys.argv[3] + +def readitems(stem): + items = [] + b = 1 + while os.path.exists("%s%i" % (stem, b)): + with open("%s%i" % (stem, b)) as f: + items.extend(json.load(f)) + b += 1 + return items + +metadata = readitems("block") +subjects = readitems("subs") (document_loader, avsc_names, @@ -11,7 +30,20 @@ subjects = $(inputs.subjects) metaschema_loader) = schema_salad.schema.load_schema(metadataSchema) for i, m in enumerate(metadata): - doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, m["path"], True) + doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, m["path"], False, False) doc["id"] = subjects[i] g = schema_salad.jsonld_context.makerdf(subjects[i], doc, document_loader.ctx) print(g.serialize(format="ntriples").decode("utf-8")) + +if dups: + sameseqs = open(dups, "rt") + for d in sameseqs: + logging.warn(d) + g = re.match(r"\d+\t(.*)", d) + logging.warn("%s", g.group(1)) + sp = g.group(1).split(",") + for n in sp[1:]: + print("<%s> <http://biohackathon.org/bh20-seq-schema/has_duplicate_sequence> <%s> ." % (n.strip(), sp[0].strip())) + +orig = open(originalLabels, "rt") +print(orig.read()) |