add --format-output for both html and table

[rothita]

(Not a bug, just asking for a new feature :) )

Hi, I started using the tool, which looks very useful and efficient! thanks for all the hard work It will be very useful for me if I could have more than one output format in one run; To be more specific: the pretty HTML format + the output table (mode 0/4) so I could choose the columns.

If it isn't not much of a bother, could you add this option? thanks :) Itai

[hmms117]

Hi With the neat addition of the pdb-output --format-mode 5 (thanks!), it would be useful to be able to define multiple output formats for the same search. E.g getting both TSV, HTML as well as a list of superimposed PDBs.

Would it be trivial to allow multiple outputs like --format-mode 1,3,5 ? If not, repeating searches will also work.

(oh and thanks for v4!)

[milot-mirdita]

That would require some amount of work on our part. But if you the normal search workflow instead of easy-search you can avoid repeating the slow search:

foldseek createdb [inputs...] qdb
foldseek search qdb targetdb res tmp
foldseek convertalis qdb targetdb res res.m8
foldseek convertalis qdb targetdb res res.html --format-output 3
foldseek convertalis qdb targetdb res res.pdb --format-output 5