5.8 years ago by
I have been trying these utilities in the last few days. They work nice, but the documentation is very obscure! There is not even an --help flag implemented, and you have to go back to the web page every time.
Anyway, here are a few examples, not covered in the in the documentation:
Given a Gene ID, download the aminoacid sequences of the corresponding Proteins, keeping only the reviewed entries (e.g. no putative, predicted sequences):
esearch -db gene -query "1234[id]" | elink -target protein | efilter -query "REVIEWED[FILTER]"| efetch -format fasta
Given a file containing a list of Gene IDs (one per line), download all the entries in tabular format:
esearch -db gene -query $(paste -s -d ',' mygenes.ids) | efetch -format tabular > mygenes.details.txt
Please add more examples!