TNT_Script/guoyi.run

macro=;

log %7.tnt.log;

/*Arguments*/
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(semicolon) (Win) |;
  quote -   |        ==============================              |;
  quote -   |        === Parameters     Details ===              |;
  quote -   |        ==============================              |;
  quote -   |        filename type weight K cons resamp prefix   |;
  quote -   |          - type 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. K of ew must followed 0 (=NA)      |;
  quote -   |          - K is 12 (default) following Goloboff    |;
  quote -   |            et al. 2017 (Cladistics 34: 407–437)    |;
  quote -   |            it must more than 0                     |;
  quote -   |          - cons should be str, mjr, hlf            |;
  quote -   |            mjr=majority rule, hlf=half             |;
  quote -   |            str=strict (default)                    |;
  quote -   |          - resamp should be sum of what you want   |;
  quote -   |            jak=1, boot=2, bremer=4 sym=8           |;
  quote -   |            i.e. jak+boot+sym+bremer=15 (default)   |;
  quote -   |          - prefix can be empty, or a string        |;
  quote -   |            default is empty                        |;
  quote -   \----------------------------------------------------/;
  proc/; 
end

/*Basic settings*/
taxname+1000;
taxname=;
mxram 500;
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 -   /-----------------------------------------------\;
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 -   |    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 bremer support              |;
  end
  if (%6==6)
quote -   |    Bootstrap and bremer support                |;
  end
  if (%6==7)
quote -   |    Jackknifing, bootstrap and bremer support   |;
  end
  if (%6==8)
quote -   |    Symmetric resampling                        |;
  end
  if (%6==9)
quote -   |    Jackknifing and symmetric resampling        |;
  end
  if (%6==10)
quote -   |    Bootstrap and symmetric resampling          |;
  end
  if (%6==11)
quote -   |    Jackknifing, bootstrap and symmetric        |;
quote -   |        resampling                              |;
  end
  if (%6==12)
quote -   |    Symmetric resampling and bremer support     |;
  end
  if (%6==13)
quote -   |    Jackknifing, symmetric resampling and       |;
quote -   |        bremer support                          |;
  end
  if (%6==14)
quote -   |    Bootstrap, symmetric resampling and         |;
quote -   |        bremer support                          |;
  end
  if (%6==15)
quote -   |    Jackknifing, bootstrap, symmetric           |;
quote -   |        resampling and bremer support           |;
  end
end
if (argnumber<6)
quote -   |    Jackknifing, bootstrap, symmetric           |;
quote -   |        resampling and bremer support           |;
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 -   \------------------------------------------------/;

/*Implied weighting settings*/
if(argnumber>2)
  if (eqstring [ %3 iw ])
    piwe&;
  end
  if (eqstring [ %3 eiw ])
    xpiwe(*;
    piwe&;
  end
else
  xpiwe(*;
  piwe&;
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 1000;
        bbreak=tbr fill;
      end
      if (ntax>74)
        sect: slack 40; 
        xmult=hit 50 replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
      end
    end
  else
    if (ntax<=74)
      mult=replic 1000 tbr hold 1000;
      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 1000;
  bbreak=tbr fill;
  if (ntax>74)
    sect: slack 1000;
    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;
taxname=;
tsave = %7.trees.ctf;
tsave *= %7.trees.tnt.tre;

/*Consensus tree*/
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;
tvault >/;

/*Export consensus tree*/
tchoose /;
export - %7.original.tre;
taxname-;
export - %7.original_no.tre;
tsave = %7.original.ctf;
tsave *= %7.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*/
export = %7.winclada.tre;
taxname =;
ttags=;
apo >0;
quote -         /----------------------------------------------\;
quote -                     apomorphy tags start                ;
ttags/;
quote -                     apomorphy tags stop                 ;
quote -         \----------------------------------------------/;
ttags & %7.apo.svg thickness 7 italics fontsize 15;
export < %7.apo.tre;
taxname-;
export - %7.apo_no.tre;
ttags-;

/*Get jak/boot/bremer support*/
tchoose/;
ttags=;
ttags]; /*in one line*/

/*    jak=1,		boot=2,		bremer=4,	*/
/*    jak+boot=3,					*/
/*    jak+brember=5,	boot+bremer=6,			*/
/*    jak+boot+bremer=7,  				*/
/*    sym=8,						*/
/*    jak+sym=9,	boot+sym=10,	bremer+sym=12   */
/*    jak+boot+sym=11,	jak+bremer+sym=13,		*/
/*    boot+bremer+sym=14,				*/
/*    jak+sym+boot+bremer=15				*/

if (argnumber<=5)
  /*jakknifing*/
  resample jak replications 1000 from 0;
  /*bootstrap*/
  resample boot replications 1000 from 0;
  /*symmetric resampling*/
  resample sym replications 1000 from 0;
  /*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!!0;
else
  if((%6==1) | (%6==3) | (%6==5) | (%6==7) | (%6==9) | (%6==11) | (%6==13) | (%6==15))
    resample jak replications 1000 from 0;
  end
  
  if((%6==2) | (%6==3) | (%6==6) | (%6==7) | (%6==10) | (%6==11) | (%6==14) | (%6==15))
    resample boot replications 1000 from 0;
  end

  if((%6==8) | (%6==9) | (%6==10) | (%6==11) | (%6==12) | (%6==13) | (%6==14) | (%6==15))
    resample sym replications 1000 from 0;
  end

  if((%6==4) | (%6==5) | (%6==6) | (%6==7) | (%6==12) | (%6==13) | (%6==14) | (%6==15))
    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!!0;
  end
end

/*Export consensus tree with supports*/
ttags & %7.resample.svg thickness 7 italics fontsize 15;
quote -         /----------------------------------------------\;
quote -                       resample tags start               ;
ttags/;
quote -                       resample tags stop                ;
quote -         \----------------------------------------------/;
export < %7.resample.tre;
taxname-;
export - %7.resample_no.tre;
ttags-;

/*Report CI/RI/TL */
macfloat 3;
quote Consistency Index (CI) is 'CI';
quote Retention Index (RI) is 'RI';
quote Tree Length (TL) is 'TL';

/*Report*/
quote -         /----------------------------------------------\;
quote -         |      The analysis has been finished.         |;
quote -         |      The file `tnt.log` contains             |;
quote -         |          K, TL, CI and RI                    |;
quote -         |      The file `trees*.tre` contain           |;
quote -         |          trees found by mult and xmult       |;
quote -         |      The file `original*.tre` contain        |;
quote -         |          strict consensus tree without label |;
quote -         |      The file `resample*.tre` contain        |;
quote -         |          consensus tree with support         |;
quote -         |      The file `apo*.tre` contain             |;
quote -         |          tree with apomorphic character      |;
quote -         |      The file `*_no.tre` contain             |;
quote -         |          tree with `taxname-`                |;
quote -         |      The file `*.ctf` tree file is           |;
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          |;
  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 -         |          bremer support                      |;
  end
  if (%6==5)
quote -         |          jackknifing and bremer support      |;
  end
  if (%6==6)
quote -         |          bootstrap and bremer support        |;
  end
  if (%6==7)
quote -         |          jackknifing, bootstrap and          |;
quote -         |          bremer support                      |;
  end
  if (%6==8)
quote -         |          symmetric resampling                |;
  end
  if (%6==9)
quote -         |          Jackknifing and symmetric resample  |;
  end
  if (%6==10)
quote -         |          Bootstrap and symmetric resample    |;
  end
  if (%6==11)
quote -         |          jackknifing, bootstrap and          |;
quote -         |          symmetric resample                  |;
  end
  if (%6==12)
quote -         |          bremer support and symmetric        |;
quote -         |          resample                            |;
  end
  if (%6==13)
quote -         |          Jackknifing, symmetric resample and |;
quote -         |          bremer support                      |;
  end
  if (%6==14)
quote -         |          bootstrap, symmetric resmaple and   |;
quote -         |          bremer support                      |;
  end
  if (%6==15)
quote -         |          jackknifing, bootstrap, symmetric   |;
quote -         |          resample and bremer support         |;
  end
else
quote -         |          jackknifing, bootstrap, symmetric   |;
quote -         |          resample and bremer support         |;
end

quote -         |      The file `apo.svg` contain the          |;
quote -         |          tree with apomorphy mapping         |;
quote -         |      The file `winclada.tre` can be          |;
quote -         |          converted by tnt2winclada           |;
quote -         \----------------------------------------------/;

/*Quit*/
zzz;