My colleagues and I have recently published a toolbox of command-line utilities that are modeled after GNU Textutils (e.g. grep, cut, tr, uniq) called FAST: Fast Analysis of Sequences (cite).
To install FAST you can use:
perl -MCPAN -e 'install FAST'
Or install the current development version from github. The FAST install comes with a cookbook, sample dataset and all utilities have
man pages. The cookbook is also available on the github wiki.
To convert the features annotated in a genbank file to fastA sequences you can use
gbfcut. Below are examples of using
To convert all annotated features of a genbank file to fastA format:
Output only tRNA features:
gbfcut -k tRNA genbank-file
Output all feature sequences with a "note" qualifier containing "telomere":
gbfcut -q note=telomere genebank-file