aboutsummaryrefslogtreecommitdiff
path: root/workflows/pull-data/genbank/README.md
diff options
context:
space:
mode:
authorPjotr Prins2021-01-01 10:59:56 -0600
committerPjotr Prins2021-01-01 10:59:56 -0600
commita029c2329e748874bee88317e44d3f47547f71d8 (patch)
tree2ef6d412ff5ba3aae61c74898e7b2738ba4e6bc3 /workflows/pull-data/genbank/README.md
parent3f059ebde6fe6888e62f4fc232d05fb3a322b011 (diff)
downloadbh20-seq-resource-a029c2329e748874bee88317e44d3f47547f71d8.tar.gz
bh20-seq-resource-a029c2329e748874bee88317e44d3f47547f71d8.tar.lz
bh20-seq-resource-a029c2329e748874bee88317e44d3f47547f71d8.zip
genbank: minor fixes
Diffstat (limited to 'workflows/pull-data/genbank/README.md')
-rw-r--r--workflows/pull-data/genbank/README.md6
1 files changed, 3 insertions, 3 deletions
diff --git a/workflows/pull-data/genbank/README.md b/workflows/pull-data/genbank/README.md
index 479ddc9..5597234 100644
--- a/workflows/pull-data/genbank/README.md
+++ b/workflows/pull-data/genbank/README.md
@@ -2,11 +2,11 @@
```sh
# --- get list of IDs already in PubSeq
-sparql-fetch-ids > pubseq_ids.txt
+./sparql-fetch-ids > pubseq_ids.txt
# --- get list of missing genbank IDs
-genbank-fetch-ids.py --skip pubseq_ids.txt > genbank_ids.txt
+./genbank-fetch-ids.py --skip pubseq_ids.txt > genbank_ids.txt
# --- fetch XML
-update-from-genbank.py --ids genbank_ids.txt --out ~/tmp/genbank
+python3 update-from-genbank.py --ids genbank_ids.txt --out ~/tmp/genbank
# --- Transform to YAML and FASTA
transform-genbank-xml2yamlfa --dir ~/tmp/genbank id --outdir ~/tmp/pubseq
```