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View Code? Open in Web Editor NEWA python script to identify four-fold degenerate sites from a CDS fasta
A python script to identify four-fold degenerate sites from a CDS fasta
Just at the title, bedtools getfasta can't recognize the plus or minus strand for CDS region. So the CDS sequence of minus strand genes are wrong, so the next analysis is also not right. How to fix it?
Hi,
Thanks for sharing this tool. Unfortunately I'm not able to obtain the necessary input fasta; not even from the B73_RefGen_v4 Zea mays annotation files. I've tried with three different ones but neither has field separators matching yours. I've tried to infer which information is needed to build the fasta but I'm not 100% sure.
So would you mind sharing a bit of extra information? Even just printing the result from awk '($3=="CDS") {print}' [genes.gff] | head
would already be very helpful to allow me to understand which information from the annotation file is expected to be retrieved.
Thanks in advance. Best,
Daniel.
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