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| author | Pjotr Prins | 2021-01-04 10:25:36 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-04 10:25:36 +0000 |
| commit | f9f27a787fef0ad58c1ae465d8ba1ee4634083ae (patch) | |
| tree | 64bba4b6c496c9aa63aeb651bcc8252256a905bf /workflows/pull-data/genbank | |
| parent | bf8f13af6f083d382b4a3900566ef5e329084cbf (diff) | |
| download | bh20-seq-resource-f9f27a787fef0ad58c1ae465d8ba1ee4634083ae.tar.gz bh20-seq-resource-f9f27a787fef0ad58c1ae465d8ba1ee4634083ae.tar.lz bh20-seq-resource-f9f27a787fef0ad58c1ae465d8ba1ee4634083ae.zip | |
mapping: no longer requires specimen file for genbank output
Diffstat (limited to 'workflows/pull-data/genbank')
| -rw-r--r-- | workflows/pull-data/genbank/README.md | 10 |
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 |