fix: resample score doesn't map to the tre
This commit is contained in:
parent
d4c7afd20c
commit
5a7faee66e
1 changed files with 47 additions and 49 deletions
90
guoyi.run
90
guoyi.run
|
|
@ -1,19 +1,15 @@
|
|||
log tnt.log;
|
||||
macro=;
|
||||
taxname+1000;
|
||||
taxname=;
|
||||
mxram 10240;
|
||||
nstates 32;
|
||||
nstates NOGAPS;
|
||||
macro=; taxname+1000; taxname=; mxram 10240; nstates 32; nstates NOGAPS;
|
||||
|
||||
/*Arguments*/
|
||||
if ( argnumber != 1 )
|
||||
silent -console;
|
||||
quote - /-----------------------------------------------\;
|
||||
quote - /--------------------------------------------------\;
|
||||
quote - | GUOYI TNT SCRIPT 2022-2023 MIT |;
|
||||
quote - | You need to give your filename |;
|
||||
quote - | tnt*> guoyi filename |;
|
||||
quote - \-----------------------------------------------/;
|
||||
quote - | shell> tnt run guoyi.tnt filename, (Linux & Mac) |;
|
||||
quote - | shell> tnt run guoyi.run filename; (Windows) |;
|
||||
quote - \--------------------------------------------------/;
|
||||
proc/;
|
||||
end
|
||||
|
||||
|
|
@ -22,8 +18,8 @@ quote - /-----------------------------------------------\;
|
|||
quote - | Implied weighting will be estimated. |;
|
||||
quote - | TBR Mult and Xmult will be performed. |;
|
||||
quote - | Strict consensus will be used. |;
|
||||
quote - | Relative bremer support, jackknifing and |;
|
||||
quote - | boot will be shown on the resample.svg. |;
|
||||
quote - | Jackknifing, bootstrap and relative bremer |;
|
||||
quote - | will be shown on the resample.svg. |;
|
||||
quote - | Apomorphic characters mapping will be shown |;
|
||||
quote - | on the apo.svg and saved to apo*.tre. |;
|
||||
quote - | TL, CI and RI will be calculated finally. |;
|
||||
|
|
@ -37,13 +33,15 @@ piwe=12;
|
|||
procedure %1;
|
||||
hold 10000;
|
||||
|
||||
/*Search trees*/
|
||||
/*Implied weighting settings*/
|
||||
xpiwe(*;
|
||||
piwe&;
|
||||
|
||||
/*Search trees*/
|
||||
mult=replic 1000 tbr hold 1000;
|
||||
bbreak=tbr;
|
||||
bbreak=tbr fill;
|
||||
sect: slack 1000;
|
||||
xmult=hit 1000 noupdate replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
|
||||
piwe&;
|
||||
|
||||
/*Export trees*/
|
||||
export= trees.tre;
|
||||
|
|
@ -56,6 +54,10 @@ tsave *= trees.tnt.tre;
|
|||
/*Consensus tree*/
|
||||
nelsen *;
|
||||
|
||||
/*Tree vault store*/
|
||||
hold /+0;
|
||||
tvault >/;
|
||||
|
||||
/*Export consensus tree*/
|
||||
tchoose /;
|
||||
export - original.tre;
|
||||
|
|
@ -64,8 +66,24 @@ export - original_no.tre;
|
|||
tsave = original.ctf;
|
||||
tsave *= original.tnt.tre;
|
||||
|
||||
/*Caulculate TL/CI/RI score*/
|
||||
report-;
|
||||
var-;
|
||||
var =
|
||||
0 themin
|
||||
1 themax
|
||||
2 CI
|
||||
3 RI
|
||||
4 TL
|
||||
;
|
||||
set themin minsteps;
|
||||
set themax maxsteps;
|
||||
set TL length[0];
|
||||
set CI 'themin'/'TL'; /*CI=1 means no homoplasy*/
|
||||
set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
|
||||
report=;
|
||||
|
||||
/*Apomorphic characters*/
|
||||
tchoose/;
|
||||
export = winclada.tre;
|
||||
taxname =;
|
||||
ttags=;
|
||||
|
|
@ -81,20 +99,19 @@ taxname-;
|
|||
export - apo_no.tre;
|
||||
ttags-;
|
||||
|
||||
/*Get Bremer/jak/boot support*/
|
||||
/*Get jak/boot/relative-bremer support*/
|
||||
tchoose/;
|
||||
ttags=;
|
||||
ttags]; /*in one line*/
|
||||
resample jak replications 1000 from 0;
|
||||
|
||||
resample boot replications 1000 from 0;
|
||||
|
||||
sub 1; hold +1000; bbreak=fill;
|
||||
sub 2; hold +2000; bbreak=fill;
|
||||
sub 3; hold +3000; bbreak=fill;
|
||||
sub 4; hold +4000; bbreak=fill;
|
||||
sub 5; hold +5000; bbreak=fill;
|
||||
sub 6; hold +6000; bbreak=fill;
|
||||
sub 7; hold +7000; bbreak=fill;
|
||||
sub 8; hold +8000; bbreak=fill;
|
||||
bsupport[;
|
||||
resample jak replications 1000;
|
||||
resample boot replications 1000;
|
||||
|
||||
/*Export consensus tree with supports*/
|
||||
ttags & resample.svg thickness 7 italics fontsize 15;
|
||||
|
|
@ -108,30 +125,11 @@ taxname-;
|
|||
export - resample_no.tre;
|
||||
ttags-;
|
||||
|
||||
/*Caulculate TL/CI/RI score*/
|
||||
length *;
|
||||
report-;
|
||||
var-;
|
||||
var =
|
||||
0 themin
|
||||
1 themax
|
||||
+ CIs [ ( ntrees + 1 ) ]
|
||||
+ RIs [ ( ntrees + 1 ) ]
|
||||
+ this
|
||||
;
|
||||
set themin minsteps;
|
||||
set themax maxsteps;
|
||||
loop 0 ntrees
|
||||
progress #1 (ntrees+1) Calculating indices...;
|
||||
set this length[#1];
|
||||
set CIs[#1] 'themin'/'this'; /*CI=1 means no homoplasy*/
|
||||
set RIs[#1] ('themax'-'this')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
|
||||
stop
|
||||
progress/;
|
||||
report=;
|
||||
/*Report CI/RI/TL */
|
||||
macfloat 3;
|
||||
maketable CIs Consistency index;
|
||||
maketable RIs Retention index;
|
||||
quote Consistency Index (CI) is 'CI';
|
||||
quote Retention Index (RI) is 'RI';
|
||||
quote Tree Length (TL) is 'TL';
|
||||
|
||||
/*Report*/
|
||||
quote - /----------------------------------------------\;
|
||||
|
|
@ -154,7 +152,7 @@ quote - | The file `*.tnt.tre` contain |;
|
|||
quote - | is the ctf file with taxname |;
|
||||
quote - | The file `resample.svg` contain |;
|
||||
quote - | strict consensus tree with |;
|
||||
quote - | relative bremer, jak and boot |;
|
||||
quote - | relative jak, boot and bremer |;
|
||||
quote - | support on the tree |;
|
||||
quote - | The file `apo.svg` contain the |;
|
||||
quote - | tree with apomorphy mapping |;
|
||||
|
|
|
|||
Loading…
Reference in a new issue