1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
|
import sys
import arvados
import json
import shutil
import logging
import subprocess
import arvados.collection
import ruamel.yaml
import schema_salad.schema
import schema_salad.jsonld_context
from schema_salad.sourceline import add_lc_filename
api = arvados.api()
keepclient = arvados.keep.KeepClient(api_client=api)
validated = arvados.util.list_all(api.collections().list, filters=[
["owner_uuid", "=", sys.argv[1]],
["properties.status", "=", "validated"]])
validated.sort(key=lambda v: v["portable_data_hash"])
relabeled_fasta = open("relabeledSeqs.fasta", "wt")
merged_metadata = open("mergedMetadata.ttl", "wt")
metadataSchema = sys.argv[2]
blacklist = set()
if len(sys.argv) > 3:
with open(sys.argv[3]) as bl:
for l in bl:
blacklist.add(l.strip())
(document_loader,
avsc_names,
schema_metadata,
metaschema_loader) = schema_salad.schema.load_schema(metadataSchema)
for item in validated:
pdh = item["portable_data_hash"]
uuid = item["uuid"]
try:
subject = "http://covid19.genenetwork.org/resource/%s" % uuid
with arvados.collection.CollectionReader(pdh, api_client=api, keep_client=keepclient) as col:
with col.open("metadata.yaml", "rt") as md:
metadata_content = ruamel.yaml.round_trip_load(md)
metadata_content["id"] = subject
add_lc_filename(metadata_content, metadata_content["id"])
doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadata_content, False, False)
g = schema_salad.jsonld_context.makerdf(subject, doc, document_loader.ctx)
with col.open("sequence.fasta", "rt") as fa:
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)
if not skip:
relabeled_fasta.write(">"+subject+"\n")
data = fa.read(8096)
while data:
if not skip:
relabeled_fasta.write(data)
endswithnewline = data.endswith("\n")
data = fa.read(8096)
if not skip and not endswithnewline:
relabeled_fasta.write("\n")
merged_metadata.write(g.serialize(format="ntriples").decode("utf-8"))
except Exception as e:
logging.exception("Error processing collection %s" % uuid)
subprocess.run(["samtools", "faidx", "relabeledSeqs.fasta"])
shutil.rmtree(".cache")
|
