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| author | Pjotr Prins | 2021-01-01 12:24:44 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-01 12:24:44 +0000 |
| commit | 2c6181c7eb86c0285928a434a37401d6680f9f79 (patch) | |
| tree | 90606b0276edf4a929ef639c5117e3afd2e094d4 /workflows/pull-data/genbank | |
| parent | dd9c8df418040093f2116de6592fc6add0c6a2ce (diff) | |
| download | bh20-seq-resource-2c6181c7eb86c0285928a434a37401d6680f9f79.tar.gz bh20-seq-resource-2c6181c7eb86c0285928a434a37401d6680f9f79.tar.lz bh20-seq-resource-2c6181c7eb86c0285928a434a37401d6680f9f79.zip | |
genbank-fetch-ids
Diffstat (limited to 'workflows/pull-data/genbank')
| -rw-r--r-- | workflows/pull-data/genbank/README.md | 4 | ||||
| -rwxr-xr-x | workflows/pull-data/genbank/genbank-fetch-ids.py (renamed from workflows/pull-data/genbank/update-from-genbank.py) | 0 |
2 files changed, 3 insertions, 1 deletions
diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md index c235be7..f442b5d 100644 --- a/workflows/pull-data/genbank/README.md +++ b/workflows/pull-data/genbank/README.md @@ -3,8 +3,10 @@ ```sh # --- get list of IDs already in PubSeq sparql-fetch-ids > pubseq_ids.txt +# --- get list of missing genbank IDs +genbank-fetch-ids --skip pubseq_ids.txt > genbank_ids.txt # --- fetch XML -update-from-genbank.py --skip pubseq_ids.txt --outdir ~/tmp/genbank +update-from-genbank.py --ids genbank_ids.txt --outdir ~/tmp/genbank # --- Transform to YAML and FASTA transform-genbank-xml2yamlfa --dir ~/tmp/genbank id --outdir ~/tmp/pubseq ``` diff --git a/workflows/pull-data/genbank/update-from-genbank.py b/workflows/pull-data/genbank/genbank-fetch-ids.py index e62a611..e62a611 100755 --- a/workflows/pull-data/genbank/update-from-genbank.py +++ b/workflows/pull-data/genbank/genbank-fetch-ids.py |