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debbiemarkslab / EVcouplings

Evolutionary couplings from protein and RNA sequence alignments
http://evcouplings.org
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Add 'checkpoint_domtbl' option to alignment stage #219

Closed njrollins closed 5 years ago

njrollins commented 5 years ago

Currently there is no option to save the .domtbl files generated during alignment stage. Alongside the checkpoint_ali option, would be useful for checking the integrity of the alignment process

thomashopf commented 5 years ago

Yes would be very useful but unfortunately I am not aware of a jackhmmer command line flag that would allow to do this (unlike --chkali for alignment and --chkhmm HMM).

The only way to get a domtbl after each iteration would be to manually create a jackhmmer-like protocol using phmmer + hmmsearch and saving the output after each stage, but that means creating a new protocol and quite a bit of work... so closing for now but whenever someone embarks on that mission please feel free to reopen.