Fetch sequences from db

A simple script to grab bioseqs by accession.

This just wraps the BioRuby fetch functionality in a friendly commandline interface. In brief, it can accept accession ids on the commandline or from a piped file (one accession per line) and save the corresponding sequences from the db. Sequences may be downloaded via the bioruby or EBI servers. The file format is Genbank but could easily be hacked to something else.

It would be polite to limit requests to a reasoanable number, say 500 in one go.


Call as:

fetchdbseqs.rb [options] [ID1 ID2 ...]

where the available options are:

-h, --help Display this screen
--server NAME Which server to query
--read-stdin Read sequence ids from standard input
-o, --overwrite
 Overwrite pre-existing files


  • Ruby
  • BioRuby