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| author | Pjotr Prins | 2021-01-05 09:34:26 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2021-01-05 09:34:26 +0000 |
| commit | 9d75ce088e6388bf23ae077fd06b2a3f51be1bda (patch) | |
| tree | 81a4491ca0dd37b458025cc7aa3e553a77b0fb30 /workflows | |
| parent | 3c09a92423408d01b64e1b842c6b96778939d098 (diff) | |
| download | bh20-seq-resource-9d75ce088e6388bf23ae077fd06b2a3f51be1bda.tar.gz bh20-seq-resource-9d75ce088e6388bf23ae077fd06b2a3f51be1bda.tar.lz bh20-seq-resource-9d75ce088e6388bf23ae077fd06b2a3f51be1bda.zip | |
API: fix returned record to include original metadata
Diffstat (limited to 'workflows')
| -rw-r--r-- | workflows/pull-data/genbank/README.md | 12 | ||||
| -rwxr-xr-x | workflows/tools/pubseq-fetch-ids | 2 |
2 files changed, 11 insertions, 3 deletions
diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md index 5464d1d..188ff6f 100644 --- a/workflows/pull-data/genbank/README.md +++ b/workflows/pull-data/genbank/README.md @@ -11,7 +11,8 @@ The following workflow sends GenBank data into PubSeq ```sh # --- get list of IDs already in PubSeq -../../tools/sparql-fetch-ids > pubseq_ids.txt +../../tools/pubseq-fetch-ids > pubseq_ids.txt + # --- get list of missing genbank IDs python3 genbank-fetch-ids.py --skip pubseq_ids.txt > genbank_ids.txt @@ -26,6 +27,13 @@ python3 ../../workflows/tools/normalize-yamlfa.py -s ~/tmp/yamlfa/state.json --s ``` +## Validate GenBank data + +To pull the data from PubSeq use the list of pubseq ids generated +above. + + + # TODO -- [ ] Add id for GenBank accession - i.e. how can we tell a record is from GenBank +- [X] Add id for GenBank accession - i.e. how can we tell a record is from GenBank diff --git a/workflows/tools/pubseq-fetch-ids b/workflows/tools/pubseq-fetch-ids index 19b2d82..f5920ec 100755 --- a/workflows/tools/pubseq-fetch-ids +++ b/workflows/tools/pubseq-fetch-ids @@ -2,7 +2,7 @@ # # Use a SPARQL query to fetch all IDs in the PubSeq database # -# sparql-fetch-ids > pubseq_ids.txt +# pubseq-fetch-ids > pubseq_ids.txt # # Note: requires Ruby 3.x. Older Ruby gives a syntax error |