Fishing nucleotide sequences from genome files given aligned protein FASTA files using biopython

Question

[mirali1025]

Hello everyone:

I have written a script using biopython to try and fish out nucleotide sequences of aligned proteins (within FASTA files). My task is to use local genbank files of particular strains and try to extract the nucleotide sequences based on the aligned FASTA files. I'm having some trouble finishing the script, however, but I think it is almost complete:

Biopython script

[h.mon]

One has to request permission to view your script and, sorry, I do not want use my personal email account, nor create a phony account just to try to help someone at a forum. Why don't you use a github gist?

If you make your alignment output gff or bed, you can then use bedtools to obtain the underlying sequence.