This project is to develop python tools for generating official gene set (OGS) by integrating manually curated and predicted gene annotations (GFF3 format). There are two phases involved: (1) QC phase and (2) Merge phase.
Translator method in the current version of gff3_to_fasta (v0.0.1) only considers standard codons and universal stop codons for generating peptide sequences. However, the genetic codes used for translation might be different for different species. Therefore, as suggested by @childers, it will be great if the translator method in this program can further consider to incorporate multiple codon tables for multiple species.
NCBI has compiled related information for codon tables for different species on April 30, 2013 (The Genetic Codes). These suggested codon tables can be incorporated into this program in the future.
Two tools with translation function having options for choosing genetic codes are recommended:
ExPASy โ Translate tool (ExPASy, University of Geneva, Switzerland). This site useful if users have a gene which begins with an alternative start codon.
Translate Nucleic Acid Sequence Tool (University of Massachusetts Medical School, U.S.A.) which permits choice of reading frame(s) and genetic code.