Best programming language for pathways and genomics?

Question

[tim.gallengor]

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.

[samuelmiver]

I would suggest you to start programming with python (cleaner and easier to understand than perl) and have always in mind R/Bioconductor that will give you a lot of statistical functions widely used in genomics.

In addition, never forget the power of grep/sed/awk in text processing and file manipulation.

[tim.gallengor]

Thank you, I think I am going to go with python. Also, it seems like a good general language as well.