Converting GenBank files to Chaos-XML

About

One of the main applications for Bio-Chaos is to turn a GenBank file into a Chaos-XML file or Datastore. This is done using the

cx-genbank2chaos.pl

script, which comes as part of the Bio-Chaos distribution.

This is not a simple matter of file conversion - the genbank format (both flat file and XML) can be both ambiguous and lossy. The gory details of recovering standardised, chado and SO compliant feature graphs is handled using a part of BioPerl called the Unflattener.

Use

You do not need to know the gory details if all you want is a Chaos-XML file or a Chaos Datastore - you can just run the script, like this:


cx-genbank2chaos.pl -islands t/data/NT_010755.gbk

The above will generate a datastore (one file per gene) from the genbank file (this file can be found in the Bio-Chaos distribution at the above location). Each gene will have been transformed from its location on the sequence above onto a "gene island" contig. This facilitates processing using libraries such as CGL

You can get help at any time by using the

-h

option. Or you can look at the CPAN Documentation page for this script