polish: add more parameters

This commit is contained in:
kuoi 2023-09-13 20:57:13 +08:00
parent 5a7faee66e
commit ce2cc5a662

283
guoyi.run
View file

@ -1,47 +1,184 @@
log tnt.log;
macro=; taxname+1000; taxname=; mxram 10240; nstates 32; nstates NOGAPS;
macro=;
/*Arguments*/
if ( argnumber != 1 )
if ( (argnumber == 0) | (argnumber >=7) )
silent -console;
quote - /--------------------------------------------------\;
quote - | GUOYI TNT SCRIPT 2022-2023 MIT |;
quote - | You need to give your filename |;
quote - | shell> tnt run guoyi.tnt filename, (Linux & Mac) |;
quote - | shell> tnt run guoyi.run filename; (Windows) |;
quote - \--------------------------------------------------/;
quote - /----------------------------------------------------\;
quote - | GUOYI TNT SCRIPT 2022-2023 MIT |;
quote - | You need to give your filename |;
quote - | shell> tnt run guoyi.tnt filename, (Linux & Mac) |;
quote - | shell> tnt run guoyi.run filename(semicolon) (Win) |;
quote - | ============================== |;
quote - | === Parameters Details === |;
quote - | ============================== |;
quote - | filename datatype weight 0/K cons resample |;
quote - | - datatpye should be 32, dna, prot, num |;
quote - | num=number, dna=DNA, prot=protein |;
quote - | 32=max number allowed (default) |;
quote - | - weight should be iw, ew, eiw |;
quote - | iw=implied weight, ew=equal weight |;
quote - | eiw=extended implied weight (default) |;
quote - | N.B. ew must followed 0 |;
quote - | - cons should be str, mjr, hlf |;
quote - | mjr=majority rule, hlf=half |;
quote - | str=strict (default) |;
quote - | - resample should be sum of what you want |;
quote - | jak=1, boot=2, relative bremer=4 |;
quote - | i.e. jak+boot+bremer=7 (default) |;
quote - \----------------------------------------------------/;
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)
if (%4!=0)
quote Warning: equal weighting %4 should be fullfilled with 0;
end
end
end
if ((eqstring [ %3 iw ]) | (eqstring [ %3 eiw ]))
if (argnumber>=4)
piwe=%4;
else
piwe=12;
end
end
else
piwe=12;
end
/*Reopen tnt*/
procedure %1;
hold 10000;
/*Report what will be done*/
quote - /-----------------------------------------------\;
quote - | Implied weighting will be estimated. |;
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
end
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
end
if (eqstring [ %3 ew ])
quote - | Equal weighting will be used. |;
end
else
quote - | Ex-implied weighting will be used, K is 12. |;
end
if (ntax<=25)
quote - | Implicit enumeration will be performed. |;
end
if ((ntax>25) && (ntax < 75))
quote - | TBR Mult will be performed. |;
end
if (ntax>=75)
quote - | TBR Mult and Xmult will be performed. |;
end
if (argnumber>=5)
if (eqstring [ %5 mjr ])
quote - | Majority-rule consensus will be used. |;
end
if (eqstring [ %5 hlf ])
quote - | Half strict consensus will be used. |;
end
if(eqstring [ %5 str ])
quote - | Strict consensus will be used. |;
end
end
if (argnumber<5)
quote - | Strict consensus will be used. |;
end
if (argnumber>=6)
if (%6==1)
quote - | Jackknifing |;
end
if (%6==2)
quote - | Bootstrap |;
end
if (%6==3)
quote - | Jackknifing and bootstrap |;
end
if (%6==4)
quote - | Relative bremer support |;
end
if (%6==5)
quote - | Jackknifing and relative bremer support |;
end
if (%6==6)
quote - | Bootstrap and relative bremer support |;
end
if (%6==7)
quote - | Jackknifing, bootstrap and relative bremer |;
end
end
if (argnumber<6)
quote - | Jackknifing, bootstrap and relative bremer |;
end
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. |;
quote - \------------------------------------------------/;
/*Set K*/
piwe=12;
/*Reopen tnt*/
procedure %1;
hold 10000;
/*Implied weighting settings*/
xpiwe(*;
piwe&;
if(argnumber>2)
if (eqstring [ %3 iw ])
piwe&;
end
if (eqstring [ %3 eiw ])
xpiwe(*;
piwe&;
end
else
xpiwe(*;
piwe&;
end
/*Search trees*/
mult=replic 1000 tbr hold 1000;
bbreak=tbr fill;
sect: slack 1000;
xmult=hit 1000 noupdate replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
if(eqstring [ %3 ew ] | eqstring [ %3 iw ] )
if (ntax<=25)
ienum;
else
mult=replic 1000 tbr hold 1000;
bbreak=tbr fill;
if (ntax>74)
sect: slack 1000;
xmult=hit 1000 noupdate replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
end
end
else
mult=replic 1000 tbr hold 1000;
bbreak=tbr fill;
if (ntax>74)
sect: slack 1000;
xmult=hit 1000 noupdate replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
end
end
/*Export trees*/
export= trees.tre;
@ -52,7 +189,19 @@ tsave = trees.ctf;
tsave *= trees.tnt.tre;
/*Consensus tree*/
nelsen *;
if (argnumber<=4)
nelsen *;
else
if (eqstring [ %5 str ])
nelsen *;
end
if (eqstring [ %5 mjr ])
majority *;
end
if (eqstring [ %5 hlf ])
comcomp *;
end
end
/*Tree vault store*/
hold /+0;
@ -103,15 +252,40 @@ ttags-;
tchoose/;
ttags=;
ttags]; /*in one line*/
resample jak replications 1000 from 0;
resample boot replications 1000 from 0;
/* jak=1, boot=2, bremer=4, */
/* jak+boot=3, */
/* jak+brember=5, boot+bremer=6, */
/* jak+boot+bremer=7, */
sub 1; hold +1000; bbreak=fill;
sub 3; hold +3000; bbreak=fill;
sub 5; hold +5000; bbreak=fill;
sub 7; hold +7000; bbreak=fill;
bsupport[;
if (argnumber<=5)
/*jakknifing*/
resample jak replications 1000 from 0;
/*bootstrap*/
resample boot replications 1000 from 0;
/*relative bremer*/
sub 1; hold +1000; bbreak=fill;
sub 3; hold +3000; bbreak=fill;
sub 5; hold +5000; bbreak=fill;
sub 7; hold +7000; bbreak=fill;
bsupport[;
else
if((%6==1) | (%6==3) | (%6==5) | (%6==7))
resample jak replications 1000 from 0;
end
if((%6==2) | (%6==3) | (%6==6) | (%6==7))
resample boot replications 1000 from 0;
end
if((%6==4) | (%6==5) | (%6==6) | (%6==7))
sub 1; hold +1000; bbreak=fill;
sub 3; hold +3000; bbreak=fill;
sub 5; hold +5000; bbreak=fill;
sub 7; hold +7000; bbreak=fill;
bsupport[;
end
end
/*Export consensus tree with supports*/
ttags & resample.svg thickness 7 italics fontsize 15;
@ -151,9 +325,52 @@ quote - | only readable for TNT |;
quote - | The file `*.tnt.tre` contain |;
quote - | is the ctf file with taxname |;
quote - | The file `resample.svg` contain |;
if (argnumber>=5)
if(eqstring [ %5 mjr ])
quote - | majority rule consensus tree with |;
end
if(eqstring [ %5 hlf ])
quote - | half strict consensus tree with |;
end
if(eqstring [ %5 str ])
quote - | strict consensus tree with |;
quote - | relative jak, boot and bremer |;
quote - | support on the tree |;
end
else
quote - | strict consensus tree with |;
end
if (argnumber>=6)
if (%6==1)
quote - | jackknifing |;
end
if (%6==2)
quote - | bootstrap |;
end
if (%6==3)
quote - | jackknifing and bootstrap |;
end
if (%6==4)
quote - | relative bremer support |;
end
if (%6==5)
quote - | jackknifing and relative bremer |;
quote - | support |;
end
if (%6==6)
quote - | bootstrap and relative bremer |;
quote - | support |;
end
if (%6==7)
quote - | jackknifing, bootstrap and |;
quote - | relative bremer support |;
end
else
quote - | jackknifing, bootstrap and |;
quote - | relative bremer support |;
end
quote - | The file `apo.svg` contain the |;
quote - | tree with apomorphy mapping |;
quote - | The file `winclada.tre` can be |;