milot-mirdita
commented
1 year ago You need to specify the numeric NCBI taxon identifier for this to work. You can look up the numeric values on the NCBI taxonomy browser: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2&lvl=3&srchmode=1&keep=1&unlock
Tried the following commands:
foldseek easy-search --taxon-list "Bacteria" 1rqf.cif pdb foldseek_testrun/bacterial_test tmp foldseek easy-search --taxon-list Bacteria 1rqf.cif pdb foldseek_testrun/bacterial_test tmp foldseek easy-search --taxon-list "txid2" 1rqf.cif pdb foldseek_testrun/bacterial_test tmp foldseek easy-search --taxon-list txid2 1rqf.cif pdb foldseek_testrun/bacterial_test tmp
None of them gave me а filtered output with only bacterial proteins. Am I missing something in the command? There is no available documentation on how to apply taxonomic filters in the command line. I can see that this is an option in the web version of foldseek and want to use it with my search settings.