Any good parser with Python??

Question

[lessismore]

Hello people,

i am trying to find a good parser with python. Basically i would like to fetch fasta sequences from a genome fasta file using coordinates from gff file. Any suggestion is really welcomed. Thanks

[st.ph.n]

If you can't write a python script to do this, or at least start one and if you get errors, post the code and error so someone can assist you, why are you asking for Python? I think @badribio's answer is a very good starting point for you for a CLI option.

Answer 1

[badribio]

Have you looked at this

http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html