write_fasta_from_gff.pl

[ktretina]

Hello,

I'd like to suggest that a check for a start and stop codon be added to this script (for both CDS and polypeptide sequences) for each sequence. Whether there is just a warning to STDOUT or to a log file does not matter so much to me, but this would be a very useful feature, particularly for an annotation project. I have recently found that such a check does not occur in WebApollo, and so this would be the most convenient place to add this check in our pipeline.

Thanks!

[jorvis]

I added this in the new python version here: https://github.com/jorvis/biocode/blob/master/gff/write_fasta_from_gff.py

The perl version will be removed in the near future.