I downloaded .fna, .gff and .ptt from RefSeq and hoped to show where genes are compared to other data. The other data is blast results (using given .fna) so you could say I'd like to know if my sequence is in a gene.
Problem is that both .gff and .ptt give much shorter regions than the .fna wordcount gives. I guess it would be okay if it were cut off from the end but is it really?
Question: Do the gene coordinates from ptt/gff match with .fna positions starting from the beginning?
//edit:
Problem was the way I was getting the genome length - I used wc which apparently also counted new lines giving me genome length + new line count.