diff options
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 |