malacology
/
TNT_Script
1
0
Fork 0
Code Issues Pull Requests Projects Releases 12 Wiki Activity
TNT_Script/guoyi.run

701 lines
19 KiB
Plaintext
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

macro=;
log %7.tnt.log;
/*Arguments*/
if ( (argnumber == 0) || (argnumber >7) )
silent -console;
quote
/----------------------------------------------------\
| GUOYI TNT SCRIPT 2022-2023 MIT |
| You need to give your filename |
| shell> tnt run guoyi.tnt filename, (Linux & Mac) |
| shell> tnt run guoyi.run filename(semicolon) (Win) |
| ============================== |
| === Parameters Details === |
| ============================== |
| filename type weight K cons resamp prefix |
| - type should be 32, dna, prot, num |
| num=number, dna=DNA, prot=protein |
| 32=max number allowed (default) |
| - weight should be iw, ew, eiw |
| iw=implied weight, ew=equal weight |
| eiw=extended implied weight (default) |
| N.B. K of ew must followed 0 (=NA) |
| - K is 12 (default) following Goloboff |
| et al. 2017 (Cladistics 34: 407–437) |
| it must more than 0 |
| - cons should be str, mjr, hlf |
| mjr=majority rule, hlf=half |
| str=strict (default) |
| - resamp should be sum of what you want |
| jak=1, boot=2, sym=4 relative-bremer |
| (rbr)=0.1, bremer(br)=0.2 |
| i.e rbr+br+jak+boot+sym=7.3 (default) |
| - prefix can be empty, or a string |
| default is empty |
\----------------------------------------------------/;
proc/;
end
/*Basic settings*/
taxname+1000;
taxname=;
mxram 10240;
if(argnumber>=2)
nstates %2;
else
nstates 32;
end
nstates NOGAPS;
/*Set K*/
if(argnumber>2 )
if (eqstring [ %3 ew ])
quote Equal weighting is used;
if ((argnumber>=4) && (%4 != 0))
errmsg equal weighting %4 should be fullfilled with 0;
end
else
if ((eqstring [ %3 iw ]) || (eqstring [ %3 eiw ]))
if (argnumber>=4)
piwe=%4;
else
piwe=12;
end
else
errmsg %3 must be ew iw or eiw;
end end
else
piwe=12;
end
/*Reopen tnt*/
procedure %1;
hold 10000;
/*Report what will be done*/
quote
/-----------------------------------------------\;
if(argnumber>2)
if (eqstring [ %3 iw ])
if (argnumber>3)
quote
| Implied weighting will be used, K is %4. |;
else
quote
| Implied weighting will be used, K is 12. |;
end
else
if (eqstring [ %3 eiw ])
if (argnumber>3)
quote
| Ex-implied weighting will be used, K is %4. |;
else
quote
| Ex-implied weighting will be used, K is 12. |;
end
else
if (eqstring [ %3 ew ])
quote
| Equal weighting will be used. |;
else
errmsg %3 must be ew iw or eiw;
end end end
else
quote
| Ex-implied weighting will be used, K is 12. |;
end
if (ntax<=25)
quote
| Implicit enumeration will be performed. |;
else
if ((ntax>25) && (ntax < 75))
quote
| TBR Mult will be performed. |;
else
if (ntax>=75)
quote
| Xmult will be performed. |;
end end end
if (argnumber<=5)
quote
| Strict consensus will be used. |;
else
if (( %6 == 0.1 )||( %6 == 0.2 )||( %6 == 0.3 )||( %6==1.1 )||( %6 ==1.2 )||( %6 ==1.3 )||( %6 == 2.1 )||( %6 == 2.2 )||( %6 == 2.3 )||( %6 == 3.1 )||( %6 == 3.2 )||( %6 == 3.3 )||( %6 == 4.1 )||( %6 == 4.2 )||( %6 == 4.3 )||( %6 == 5.1 )||( %6 == 5.2 )||( %6 == 5.3 )||( %6 == 6.1 )||( %6 == 6.2 )||( %6 == 6.3 )||( %6 == 7.1 )||( %6 == 7.2 )||( %6 == 7.3 ))
if (!(eqstring [ %5 str ]))
errmsg Bremer support or relative bremer support must use strict consensus;
end
quote
| Strict consensus will be used. |;
else
if (eqstring [ %5 mjr ])
quote
| Majority-rule consensus will be used. |;
else
if (eqstring [ %5 hlf ])
quote
| Half strict consensus will be used. |;
else
if(eqstring [ %5 str ])
quote
| Strict consensus will be used. |;
else
errmsg %5 must be mjr hlf or str;
end end end
end end
if (argnumber>=6)
if ( (%6>0) && (%6<1) )
if (%6==0.1 || %6==0.3)
quote
| relative bremer support |;
else
if (%6==0.2 || %6==0.3)
quote
| bremer support |;
end end
else
if ((%6>=1) && (%6<2))
quote
| Jackknifing |;
if (%6==1.1 || %6==1.3)
quote
| relative bremer support |;
else
if (%6==1.2 || %6==1.3)
quote
| bremer support |;
end end
else
if ((%6>=2) && (%6<3))
quote
| Bootstrap |;
if (%6==2.1 || %6==2.3)
quote
| relative bremer support |;
else
if (%6==2.2 || %6==2.3)
quote
| bremer support |;
end end
else
if ((%6>=3) && (%6<4))
quote
| Jackknifing and bootstrap |;
if (%6==3.1 || %6==3.3)
quote
| relative bremer support |;
else
if (%6==3.2 || %6==3.3)
quote
| bremer support |;
end end
else
if ((%6>=4) && (%6<5))
quote
| Symmetric resampling |;
if (%6==4.1 || %6==4.3)
quote
| relative bremer support |;
else
if (%6==4.2 || %6==4.3)
quote
| bremer support |;
end end
else
if ((%6>=5) && (%6<6))
quote
| Jackknifing and symmetric resampling |;
if (%6==5.1 || %6==5.3)
quote
| relative bremer support |;
else
if (%6==5.2 || %6==5.3)
quote
| bremer support |;
end end
else
if ((%6>=6) && (%6<7))
quote
| Bootstrap and symmetric resampling |;
if (%6==6.1 || %6==6.3)
quote
| relative bremer support |;
else
if (%6==6.2 || %6==6.3)
quote
| bremer support |;
end end
else
if ((%6>=7) && (%6<8))
quote
| Jackknifing, bootstrap and symmetric |
| resampling |;
if (%6==7.1 || %6==7.3)
quote
| relative bremer support |;
else
if (%6==7.2 || %6==7.3)
quote
| bremer support |;
end end
else
errmsg Mistake %6 value;
end end end end end end end end
end
if (argnumber<6)
quote
| relative bremer support, bremer support |
| jackknifing, bootstrap, symmetric |
| resampling |;
end
quote
| will be shown on the resample.svg. |
| Apomorphic characters mapping will be shown |
| on the apo.svg and saved to apo*.tre. |
| TL, CI and RI will be calculated finally. |
\------------------------------------------------/;
/*Implied weighting settings*/
if(argnumber>2)
if (eqstring [ %3 iw ])
piwe&;
else
if (eqstring [ %3 eiw ])
xpiwe(*;
log %7.eiw.log;
piwe&;
log/;
log + %7.tnt.log;
else
if (eqstring [ %3 ew ])
else
errmsg %3 must be ew iw or eiw;
end end end
else
xpiwe(*;
log %7.eiw.log;
piwe&;
log/;
log+ %7.tnt.log;
end
/*Search trees*/
if(argnumber>2)
if(eqstring [ %3 ew ] || eqstring [ %3 iw ] )
if (ntax<=25)
ienum;
else
if (ntax<=74)
mult=replic 1000 tbr hold 10;
bbreak=tbr fill;
else
if (ntax>74)
sect: slack 40;
xmult=hit 50 replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
end end
end
else
if (ntax<=74)
mult=replic 1000 tbr hold 10;
bbreak=tbr fill;
else
sect: slack 40;
xmult=hit 50 replications 20 drift 20 ratchet 10 fuse 10 hold 1 keepall;
end
end
else
mult=replic 1000 tbr hold 10;
bbreak=tbr fill;
if (ntax>74)
sect: slack 40;
xmult=hit 50 replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
end
end
/*Export trees*/
export= %7.trees.tre;
taxname-;
export= %7.trees_no.tre;
tsave *= %7.trees.tnt.tre;
taxname=;
tsave = %7.trees.ctf;
/*Get npars number*/
var: npars;
set npars ntrees;
/*Get rbr/br/jak/boot/sym support and get consensus tree*/
ttags=;
ttags]; /*in one line*/
/* jak=1, boot=2, sym=4, */
/* jak+boot=3, */
/* jak+sym=5, boot+sym=6, */
/* jak+boot+sym=7, */
/* bremer=0.1, relative-bremer=0.2 */
/* bremer+relative-bremer=0.3 */
if (argnumber<=5)
/*set value of suboptimal from most parsimony tree */
sub: 0;
/*save strict consensus tree for bremer*/
hold+1;
nelsen * 0.'npars';
/*get the consensus tree number*/
var: contree;
set contree ntrees;
/*calculate relative bremer support*/
bs ]!! 0;
/*set the br value float*/
macfloat 1;
/*calculate bremer support*/
bsupport !! 0;
/*choose final tree*/
tchoose/;
/*adjust to zero following Pablo Goloboff*/
sub 0;
/*jakknifing*/
resample jak replications 1000 from 0; /*from 0 will orphan other trees*/
/*bootstrap*/
resample boot replications 1000 from 0;
/*symmetric resampling*/
resample sym replications 1000 from 0;
else
if(( %6 == 0.1 )||( %6 == 0.2 )||( %6 == 0.3 )||( %6==1.1 )||( %6 ==1.2 )||( %6 ==1.3 )||( %6 == 2.1 )||( %6 == 2.2 )||( %6 == 2.3 )||( %6 == 3.1 )||( %6 == 3.2 )||( %6 == 3.3 )||( %6 == 4.1 )||( %6 == 4.2 )||( %6 == 4.3 )||( %6 == 5.1 )||( %6 == 5.2 )||( %6 == 5.3 )||( %6 == 6.1 )||( %6 == 6.2 )||( %6 == 6.3 )||( %6 == 7.1 )||( %6 == 7.2 )||( %6 == 7.3 )) /*bremer support related can only use strict consensus*/
/*set value of suboptimal from most parsimony tree*/
sub: 0;
/*save strict consensus tree for bremer*/
hold+1;
nelsen * 0.'npars';
/*get the consensus tree number*/
var: contree;
set contree ntrees;
if(( %6 == 0.1 )||( %6 == 0.3 )||( %6==1.1 )||( %6 ==1.3 )||( %6 == 2.1 )||( %6 == 2.3 )||( %6 == 3.1 )||( %6 == 3.3 )||( %6 == 4.1 )||( %6 == 4.3 )||( %6 == 5.1 )||( %6 == 5.3 )||( %6 == 6.1 )||( %6 == 6.3 )||( %6 == 7.1 )||( %6 == 7.3 ))
/*calculate relative bremer support*/
bs ]!! 0;
end
if(( %6 == 0.2 )||( %6 == 0.3 )||( %6==1.2 )||( %6 ==1.3 )||( %6 == 2.2 )||( %6 == 2.3 )||( %6 == 3.2 )||( %6 == 3.3 )||( %6 == 4.2 )||( %6 == 4.3 )||( %6 == 5.2 )||( %6 == 5.3 )||( %6 == 6.2 )||( %6 == 6.3 )||( %6 == 7.2 )||( %6 == 7.3 ))
/*set the br value float*/
macfloat 1;
/*calculate bremer support*/
bsupport !! 0;
end
/*choose final tree*/
tchoose/;
/*adjust to zero following Pablo Goloboff*/
sub 0;
/*jackknifing*/
if((%6 == 1.1) || (%6 == 1.2) || (%6 == 1.3) || (%6 == 3.1) || (%6 == 3.2) || (%6 == 3.3) || (%6 == 5.1) || (%6 == 5.2) || (%6 == 5.3) || (%6 == 7.1) || (%6 == 7.2) || (%6 == 7.3))
resample jak replications 1000 from 0;
end
/*bootstrap*/
if((%6 == 2.1) || (%6 == 2.2) || (%6 == 2.3) || (%6 == 3.1) || (%6 == 3.2) || (%6 == 3.3) || (%6 == 6.1) || (%6 == 6.2) || (%6 == 6.3) || (%6 == 7.1) || (%6 == 7.2) || (%6 == 7.3))
resample boot replications 1000 from 0;
end
/*symmetric resampling*/
if((%6 == 4.1) || (%6 == 4.2) || (%6 == 4.3) || (%6 == 5.1) || (%6 == 5.2) || (%6 == 5.3) || (%6 == 6.1) || (%6 == 6.2) || (%6 == 6.3) || (%6 == 7.1) || (%6 == 7.2) || (%6 == 7.3))
resample sym replications 1000 from 0;
end
else /*non-bremer related should be consensus firstly*/
if (eqstring [ %5 str ])
nelsen * 0.'npars';
else
if (eqstring [ %5 mjr ])
majority * 0.'npars';
else
if (eqstring [ %5 hlf ])
comcomp * 0.'npars';
else
errmsg %5 must be mjr hlf or str;
end end end
/*choose the final tree: consenus tree*/
tchoose/;
/*jackkinfing*/
if((%6==1) || (%6==3) || (%6==5) || (%6==7))
resample jak replications 1000 from 0;
end
/*bootstrap*/
if((%6==2) || (%6==3) || (%6==6) || (%6==7))
resample boot replications 1000 from 0;
end
/*symmetric resampling*/
if((%6==4) || (%6==5) || (%6==6) || (%6==7))
resample sym replications 1000 from 0;
end
end
/*Tree vault store*/
hold /+0;
tvault >/;
end
/*Export consensus tree with supports*/
ttags & %7.resample.svg thickness 7 italics fontsize 15;
log %7.resample.log;
quote /-------------resample tags start---------------\;
ttags/;
quote \-------------resample tags stop----------------/;
log/;
log + %7.tnt.log;
export < %7.resample.tre;
taxname-;
export - %7.resample_no.tre;
ttags-;
taxname=;
/*Export consensus tree*/
tchoose /;
export - %7.original.tre;
taxname-;
export - %7.original_no.tre;
tsave = %7.original.ctf;
tsave *= %7.original.tnt.tre;
/*Apomorphic characters*/
export = %7.winclada.tre;
taxname =;
ttags=;
apo >0;
log %7.apo.log;
quote /-----------apomorphy tags start --------------\;
ttags/;
quote \-----------apomorphy tags stop ---------------/;
log/;
log + %7.tnt.log;
ttags & %7.apo.svg thickness 7 italics fontsize 15;
export < %7.apo.tre;
taxname-;
export - %7.apo_no.tre;
ttags-;
/*Character Analysis*/
log %7.homo.log;
chomo;
cscores;
log/;
log + %7.tnt.log;
/*Caulculate TL/CI/RI score*/
report-;
var: themin themax CI RI 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=;
/*Report CI/RI/TL */
log %7.report.log;
macfloat 3;
quote Consistency Index (CI) is 'CI';
quote Retention Index (RI) is 'RI';
quote Tree Length (TL) is 'TL';
log/;
log + %7.tnt.log;
/*Report*/
quote
/----------------------------------------------\
| The analysis has been finished. |
| The file `tnt.log` contains |
| K, TL, CI and RI |
| The file `trees*.tre` contain |
| trees found by mult and xmult |
| The file `original*.tre` contain |
| strict consensus tree without label |
| The file `resample*.tre` contain |
| consensus tree with support |
| The file `apo*.tre` contain |
| tree with apomorphic character |
| The file `*_no.tre` contain |
| tree with `taxname-` |
| The file `*.ctf` tree file is |
| only readable for TNT |
| The file `*.tnt.tre` contain |
| is the ctf file with taxname |
| The file `resample.svg` contain |;
if (argnumber<=5)
quote
| strict consensus tree with |;
else
if ( (argnumber >=6) && (( %6 == 0.1 )||( %6 == 0.2 )||( %6 == 0.3 )||( %6==1.1 )||( %6 ==1.2 )||( %6 ==1.3 )||( %6 == 2.1 )||( %6 == 2.2 )||( %6 == 2.3 )||( %6 == 3.1 )||( %6 == 3.2 )||( %6 == 3.3 )||( %6 == 4.1 )||( %6 == 4.2 )||( %6 == 4.3 )||( %6 == 5.1 )||( %6 == 5.2 )||( %6 == 5.3 )||( %6 == 6.1 )||( %6 == 6.2 )||( %6 == 6.3 )||( %6 == 7.1 )||( %6 == 7.2 )||( %6 == 7.3 )) )
quote
| strict consensus tree with |;
else
if (eqstring [ %5 mjr ])
quote
| majority-rule consensus tree with |;
else
if (eqstring [ %5 hlf ])
quote
| half strict consensus tree with |;
else
if(eqstring [ %5 str ])
quote
| strict consensus tree with |;
else
errmsg %5 must be mjr hlf or str;
errmsg Bremer support or relative bremer support must use strict consensus;
end end end
end end
if (argnumber>=6)
if ( (%6>0) && (%6<1) )
if (%6==0.1 || %6==0.3)
quote
| relative bremer support |;
else
if (%6==0.2 || %6==0.3)
quote
| bremer support |;
end end
else
if ((%6>=1) && (%6<2))
if (%6==1.1 || %6==1.3)
quote
| relative bremer support |;
else
if (%6==1.2 || %6==1.3)
quote
| bremer support |;
end end
quote
| jackknifing |;
else
if ((%6>=2) && (%6<3))
if (%6==2.1 || %6==2.3)
quote
| relative bremer support |;
else
if (%6==2.2 || %6==2.3)
quote
| bremer support |;
end end
quote
| bootstrap |;
else
if ((%6>=3) && (%6<4))
if (%6==3.1 || %6==3.3)
quote
| relative bremer support |;
else
if (%6==3.2 || %6==3.3)
quote
| bremer support |;
end end
quote
| jackknifing, bootstrap |;
else
if ((%6>=4) && (%6<5))
if (%6==4.1 || %6==4.3)
quote
| relative bremer support |;
else
if (%6==4.2 || %6==4.3)
quote
| bremer support |;
end end
quote
| symmetric resampling |;
else
if ((%6>=5) && (%6<6))
if (%6==5.1 || %6==5.3)
quote
| relative bremer support |;
else
if (%6==5.2 || %6==5.3)
quote
| bremer support |;
end end
quote
| jackknifing, symmetric resampling |;
else
if ((%6>=6) && (%6<7))
if (%6==6.1 || %6==6.3)
quote
| relative bremer support |;
else
if (%6==6.2 || %6==6.3)
quote
| bremer support |;
end end
quote
| bootstrap, symmetric resampling |;
else
if ((%6>=7) && (%6<8))
if (%6==7.1 || %6==7.3)
quote
| relative bremer support |;
else
if (%6==7.2 || %6==7.3)
quote
| bremer support |;
end end
quote
| jackknifing, bootstrap, symmetric |
| resampling |;
else
errmsg Mistake %6 value;
end end end end end end end end
else
quote
| relative bremer support, bremer |
| support, jackknifing, bootstrap, |
| symmetric resampling |;
end
quote
| The file `apo.svg` contains the |
| tree with apomorphy mapping |
| The file `report.log` contains the |
| CI RI TL publish-needed info |
| The file `resample/apo.log` contain the |
| tree tags in text |
| The file `homo.log` contain the report |
| of character homoplasy |
| The file `eiw.log` contain the report |
| of character concavities |
| The file `winclada.tre` can be |
| converted by tnt2winclada |
\----------------------------------------------/;
/*Quit*/
zzz;
Reference in New Issue View Git Blame Copy Permalink