/usr/share/proftmb/options is in proftmb 1.1.12-7.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | ;Options file created by: [proftmb];
;----------------------------------;
-d "/usr/share/proftmb"
; root path where files (options
; -s,-r,-l,-a,-e,-t,-u,-z,-n) reside
; -d == --directory-root
-a "StateRedux4" ; state reduction for decoding
; -a == --reduction-state-decode
-b "ReduxDecode4" ; state reduction for reporting
; -b == --reduction-state-report
-m "StrandStates" ; list of membrane strand states
; -m == --membrane-strand-states
-z "Swiss_Zcurve"
; file containing means and sd's at integral length
; values
; -z == --z-curve-file
-x "ZCalibration"
; file mapping coverage and accuracy values to z-scores
; -x == --z-calibration-curve
-n "bact.comp" ; background frequency file
; -n == --null-frequency
-c 4
; minimum z-score for per-residue prediction
; -c == --minimum-score-cutoff
-o "proftmb" ; output file prefix
; -o == --outfile-prefix
-s "Swiss8.arch"
; data representing the model architecture
; -s == --static-model-data
-t "Swiss8.params"
; params representing the encoded training data
; -t == --trained-params
|