Hey, I am a newbie to COG software and I have no idea how to get the prot-id and genome-id for the preparation of the sequence universe. The readme page said that "Suppose you have a file GenThree.p2o.csv that lists all sequences involved in the project (format ",")."
I have protein sequences and their Accession number. I could get the information below on NCBI website, but I have no idea how to get the pro-id and genome-id to prepare the sequence universe.
Hello, it seems to me you have to simply define your proteins as a list. This means you choose the id's that you use for each one (accessions, GI's, your own numbering). The same goes for the genome-id - just use an identifier for the organism that the protein comes from. Have a look also at this answer to a similar question:
https://www.biostars.org/p/126011/#126241
Hope this clears things up a bit!
Ivan
Hi Bei and Ivan,
I am also having the same problem. According to your discussion and this discussion:https://www.biostars.org/p/126011/#126241
I tried to created the attached csv file. But getting error like:
command: COGmakehash -i=protein_id_falciparum.csv -o=./BLASTconv -s="," -n=1
output: Can't open output file ./BLASTconv/hash.csv
This error is consistent. What do you think my csv file that I am providing is good or bad?
Any suggestion will be warmly appreciated.
Best Regards
Zillur
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