This iis not a bug with virsorter but I thought it might help to document this somewhere. So here I am.
The tool virsorter_to_anvio.py uses the output of anvi-export-gene-calls (among other files) to import virsorter annotation into anvio dbs (see post here). The script relies on the output columns to be in a particular order. That order has changed at some point in anvio's recent past.
It should be
gene_callers_id contig start stop direction partial source version but is now gene_callers_id contig direction partial source start stop version aa_sequence,
so the columns need to be rearranged or the script changed. I wish I could offer I script fix :) but I just used awk.
simroux
commented
4 years ago
This iis not a bug with
virsorterbut I thought it might help to document this somewhere. So here I am.The tool
virsorter_to_anvio.pyuses the output ofanvi-export-gene-calls(among other files) to import virsorter annotation into anvio dbs (see post here). The script relies on the output columns to be in a particular order. That order has changed at some point in anvio's recent past.It should be
gene_callers_id contig start stop direction partial source versionbut is nowgene_callers_id contig direction partial source start stop version aa_sequence,so the columns need to be rearranged or the script changed. I wish I could offer I script fix :) but I just used
awk.awk 'BEGIN {FS="\t"; OFS="\t"} {print $1, $2, $6, $7, $3, $4, $5, $8}' all_gene_calls_TEMP.txt > all_gene_calls.txtThis rearranges and eliminates the
aa_sequencecolumn which as far as I can tell is not needed.