I'm trying to download some protein sequences using Entrez through command line. However, altough 'esearch' command finds my proteins (searching by ID), the 'efetch' don't return anything. I've tried both gp and fasta formats.
Here are some example IDs:
GCB61038, GCB69151, GCC23899, GCC32047, MXQ86236
I have a list with 457 proteins that I can't download the sequences.
When using web API it looks like it automatically searches against ALL protein databases.
Can you download the GP this way?
Yes. Change the command to this:
Oh, you saved my life! If you allow me, one last question. Some of my proteins are encoded by a whole genome CDs. In the GP file it appears as "/coded_by="join(WAAD01021866.1:<231469..231602, etc ". When I download this file (fasta) using the efetch, I get the whole genome splitted in the proteins it codes, will this work in the way you thought me?