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authorPjotr Prins2021-01-04 10:25:36 +0000
committerPjotr Prins2021-01-04 10:25:36 +0000
commitf9f27a787fef0ad58c1ae465d8ba1ee4634083ae (patch)
tree64bba4b6c496c9aa63aeb651bcc8252256a905bf /workflows/pull-data
parentbf8f13af6f083d382b4a3900566ef5e329084cbf (diff)
downloadbh20-seq-resource-f9f27a787fef0ad58c1ae465d8ba1ee4634083ae.tar.gz
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mapping: no longer requires specimen file for genbank output
Diffstat (limited to 'workflows/pull-data')
-rw-r--r--workflows/pull-data/genbank/README.md10
1 files changed, 7 insertions, 3 deletions
diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md
index d7cc15f..5464d1d 100644
--- a/workflows/pull-data/genbank/README.md
+++ b/workflows/pull-data/genbank/README.md
@@ -13,13 +13,17 @@ The following workflow sends GenBank data into PubSeq
# --- get list of IDs already in PubSeq
../../tools/sparql-fetch-ids > pubseq_ids.txt
# --- get list of missing genbank IDs
-./genbank-fetch-ids.py --skip pubseq_ids.txt > genbank_ids.txt
+python3 genbank-fetch-ids.py --skip pubseq_ids.txt > genbank_ids.txt
+
# --- fetch XML
python3 update-from-genbank.py --ids genbank_ids.txt --out ~/tmp/genbank
+
# --- Transform to YAML/JSON and FASTA
python3 transform-genbank-xml2yamlfa.py --out ~/tmp/pubseq file(s)
-# --- Normalize data
-../../tools/normalize-yamlfa.py --in ~/tmp/pubseq/state.json file(s)
+
+# --- Normalize data (validation mode)
+python3 ../../workflows/tools/normalize-yamlfa.py -s ~/tmp/yamlfa/state.json --species ncbi_host_species.csv --specimen specimen.csv --validate
+
```
# TODO