[Bioperl-l] best way to edit sequence features

[Carnë Draug]

Hi

I've been planning on writing a free (as in freedom) tool to edit
sequences and make plamids maps. The idea is to build the command line
tool first and maybe later work on a GUI for it.

The problem I foresee at the moment while designing it, is how to
change a feature of the sequence. I'm not familiar with all sequence
formats (only fasta, ensembl and genbank) but I can't see how to
specify from the command line what feature to edit since I can't see
any unique identifiers for them. Is there a file format that makes
this easier? Any tips would be most appreciated.

Thank in advance,
Carnë Draug