Extract protein sequences from a GBK(GenBank) file without scripting
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 gbfcut:

To convert all annotated features of a genbank file to fastA format:

gbfcut genbank-file


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