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genomeannotation / annie

annie = ANNotation Information Extractor
MIT License
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index out of range #9

Open Gon1976 opened 2 years ago

Gon1976 commented 2 years ago

Hi, I am trying to run annie but I have this error: python annie.py -b blast_aaJJvsnr -g augustus.gff -db ../../nr/nr.fasta -o annie.gff Traceback (most recent call last): File "annie.py", line 122, in main(sys.argv) File "annie.py", line 78, in main annotations.extend(read_sprot(blast_file, gff_file, fasta_file)) File "src/sprot.py", line 8, in read_sprot fasta_info = get_fasta_info(fasta_file) File "src/sprot.py", line 45, in get_fasta_info while words[i].find("OS=") == -1: IndexError: list index out of range

Could be a problem of the fasta file? The fasta file correspond to the nr.fasta of proteins download from ncbi, which I use to make the blast. thanks Gonzalo

Juke34 commented 2 years ago

On fasta file other than uniprot it will be difficult to make it work. It uses specific attributes in the fasta header that are probably missing in nr.

Gon1976 commented 2 years ago

so, it will work if I use a database generated with uniprot fasta? I will missing some annotations. Do you know another alternative? thanks

Juke34 commented 2 years ago

so, it will work if I use a database generated with uniprot fasta?

yes