I have imported a genome annotation using the chado gff bulk loader. The bulk loader has assigned
automatic names to all polypeptides (e.g. 'polypeptide-auto767716').
Is there any existing SQL or other code fragment that shows how to accomplish bulk-renaming of protein sequences
in chado from a mapping file?
I would like to assign the correct gene ID and predicted AA sequence to the auto generated
polypeptides from a fasta file with gene-to-transcript-to-polypeptide mappings in the fasta header.
I can also generate a 3 column
mapping table like:
GeneID TranscriptID ProteinID
(but not a column containing the auto-IDs)