How to use coordinates in order to extract sequences in FASTA file?

[prs321]

I have obtained a .coords file from MUMmer after aligning my assembly to the reference genome.

I have been asked to write a script that outputs 2 fasta files,

1 which will contain the sequences that were aligned to the reference and 1 which will contain the sequences that were not aligned to the sequence.

I'm not sure how to go about this. How am I supposed to use the coordinates for the sequences that aligned in order to do this?

Also, won't there be parts of sequences that don't align? What/how do I go about collecting those pieces and putting it in the 2nd fasta file?

[crazyhottommy]

I wrote a blog about this some time ago, maybe helpful to you

http://crazyhottommy.blogspot.com/2013/04/batch-converting-coordinates-to.html