I am new to bioinformatics and programming. My background is in physiology, and I am looking to learn a programming language that can easily work with pathway and genomic data. Working with BioPAX XMLs and NGS VCFs seems to be the direction I am going in. What would be the best programming language to easily work with this type of data (analyze, annotate, create, edit, compare, run functions, etc..)?
I have read good things about Perl and Python, but Java also seems very powerful.
Any advice would be greatly appreciated. Thanks in advance.
P.S. I have been using cytoscape and its function doesn't cover what I need.