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polish: add handle arg vars

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kuoi 2023-10-10 00:25:05 +08:00
parent 0c0cd350e9
commit b0ea8a801e
1 changed files with 273 additions and 459 deletions
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@ -2,7 +2,7 @@ macro=;
log %7.tnt.log;
/*Arguments*/
/*primary notification*/
if ( (argnumber == 0) || (argnumber >7) )
silent -console;
quote
@ -38,6 +38,146 @@ if ( (argnumber == 0) || (argnumber >7) )
proc/;
end
/*Var for handling args*/
var:
dojak doboot dosym dobrs dorbrs rsmp dobremer
dostr domjr dohlf
doew doiw doeiw dowt wttype
kvalue
search;
set dojak 0; set doboot 0; set dosym 0; set dobrs 0; set dorbrs 0; set rsmp 0; set dobremer 0;
set dostr 0; set domjr 0; set dohlf 0;
set doew 0; set doiw 0; set doeiw 0; set dowt 0; set wttype 0;
set kvalue 12;
set search 0;
/*handle weighting type*/
if (argnumber>=3)
if (eqstring [ %3 ew ])
set doew 1;
set wttype 1;
else
if (eqstring [ %3 iw ])
set doiw 1;
set wttype 2;
else
if (eqstring [ %3 eiw ])
set doeiw 1;
set wttype 3;
else
errmsg Weighting type must be ew, iw or eiw;
end end end
else
set doeiw 1;
set wttype 3;
end
if ('doiw' || 'doeiw')
set dowt 1;
end
/*handle k value*/
if (argnumber>=4)
set kvalue %4;
if ( 'doew' && ('kvalue' != 0))
errmsg Equal weighting (ew) must be followed with 0 instead of 'kvalue';
end
end
/*handle resmaple type*/
if (argnumber<6)
set dojak 1; set doboot 1; set dosym 1; set dorbrs 1;
else
set rsmp %6;
loop 1 5
if ('rsmp' >= 4)
set dosym 1;
set rsmp 'rsmp'-4;
else
if ('rsmp' >= 2)
set doboot 1;
set rsmp 'rsmp'-2;
else
if ('rsmp' >= 1)
set dojak 1;
set rsmp 'rsmp'-1;
else
if ('rsmp' >=0.2)
set dobrs 1;
set rsmp 'rsmp'-0.2;
else
if ('rsmp' >=0.1)
set dorbrs 1;
set rsmp 'rsmp'-0.1;
end end end end end
stop
end
if ('rsmp' != 0)
errmsg Input %6 is illegal;
end
if ('dobrs' || 'dorbrs')
set dobremer 1;
end
/*handle consensus type*/
if (argnumber>=6)
if ('dobremer')
set dostr 1;
if (eqstring [ %5 str ])
else
if (eqstring [ %5 mjr ])
errmsg Bremer support or any bremer support variations must use strict consensus;
else
if (eqstring [ %5 hlf ])
errmsg Bremer support or any bremer support variations must use strict consensus;
else
errmsg Consensus type must be str mjr or hlf;
end end end
else
if (eqstring [ %5 str ])
set dostr 1;
else
if (eqstring [ %5 mjr ])
set domjr 1;
else
if (eqstring [ %5 hlf ])
set dohlf 1;
else
errmsg Consensus type must be str mjr or hlf;
end end end
end
else
if (argnumber==5)
if ((eqstring [ %5 mjr ]) || (eqstring [ %5 hlf ]))
errmsg Bremer support or any bremer support variations must use strict consensus;
else
if (eqstring [ %5 str ])
set dostr 1;
else
errmsg Consensus type must be str mjr or hlf;
end end
else
set dostr 1;
end end
/*handle search*/
if (ntax<=25)
if ('doeiw')
search=2;
else
search=1;
end
else
if (ntax<75)
search=2
else
search=3
end
end
/*Basic settings*/
taxname+1000;
taxname=;
@ -50,24 +190,8 @@ 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;
if ('dowt')
piwe='kvalue';
end
/*Reopen tnt*/
@ -77,180 +201,65 @@ 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
if ('wttype'==1)
quote
| Ex-implied weighting will be used, K is 12. |;
end
if (ntax<=25)
| Equal weighting will be used. |;
else
if ('wttype'==2)
quote
| Implied weighting will be used, K is 'kvalue'. |;
else
if ('wttype'==3)
quote
| Ex-implied weighting will be used, K is 'kvalue'. |;
end end end
if ('search'==1)
quote
| Implicit enumeration will be performed. |;
else
if ((ntax>25) && (ntax < 75))
if ('search'==2)
quote
| TBR Mult will be performed. |;
else
if (ntax>=75)
if ('search'==3)
quote
| Xmult will be performed. |;
end end end
if (argnumber<=5)
if ('dostr')
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
if ('domjr')
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)
else
if ('dohlf')
quote
| relative bremer support, bremer support |
| jackknifing, bootstrap, symmetric |
| resampling |;
end
| Half strict consensus will be used. |;
end end end
if ('dorbrs')
quote
| relative bremer support |;
else
if ('dobrs')
quote
| bremer support |;
else
if ('dojak')
quote
| jackknifing |;
else
if ('doboot')
quote
| bootstrap |;
else
if ('dosym')
| symmetric resampling |;
end end end end end
quote
| will be shown on the resample.svg. |
| Apomorphic characters mapping will be shown |
@ -259,61 +268,29 @@ quote
\------------------------------------------------/;
/*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
if ('doiw')
piwe&;
else
if ('doeiw')
xpiwe(*;
log %7.eiw.log;
piwe&;
log/;
log+ %7.tnt.log;
end
log + %7.tnt.log;
end 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
if ('search'==1)
ienum;
else
if ('search'==2)
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
else
if ('search'==3)
sect: slack 40;
xmult=hit 50 replications 20 drift 10 ratchet 10 fuse 10 hold 1 keepall;
end end end
/*Export trees*/
export= %7.trees.tre;
@ -327,6 +304,21 @@ tsave = %7.trees.ctf;
var: npars;
set npars ntrees;
/*Get consensus tree*/
if ('dostr')
nelsen * 0.'npars';
else
if ('domjr')
majority * 0.'npars';
else
if ('dohlf')
comcomp * 0.'npars';
end end end
/*Get the consensus tree number*/
var: contree;
set contree ntrees;
/*Get rbr/br/jak/boot/sym support and get consensus tree*/
ttags=;
ttags]; /*in one line*/
@ -336,133 +328,52 @@ ttags]; /*in one line*/
/* jak+sym=5, boot+sym=6, */
/* jak+boot+sym=7, */
/* bremer=0.1, relative-bremer=0.2 */
/* relative-bremer=0.1, bremer=0.2 */
/* bremer+relative-bremer=0.3 */
if (argnumber<=5)
if ('dobremer')
/*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*/
if ('dorbrs')
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 >/;
/*calculate bremer support*/
if ('dobrs')
macfloat 1; /*set the br value float*/
bsupport !! 0;
end
end
/*choose final tree*/
tchoose/;
/*adjust to zero following Pablo Goloboff*/
sub 0;
/*jakknifing*/
if ('dojak')
resample jak replications 1000 from 0; /*from 0 will orphan other trees*/
end
/*bootstrap*/
if ('doboot')
resample boot replications 1000 from 0;
end
/*symmetric resampling*/
if ('dosym')
resample sym replications 1000 from 0;
end
/*Tree vault store*/
hold /+0;
tvault >/;
/*Export consensus tree with supports*/
ttags & %7.resample.svg thickness 7 italics fontsize 15;
log %7.resample.log;
@ -550,136 +461,39 @@ quote
| is the ctf file with taxname |
| The file `resample.svg` contain |;
if (argnumber<=5)
if ('dostr')
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 )) )
if ('domjr')
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
if ('dohlf')
quote
| half strict consensus tree with |;
end end end
if ('dorbrs')
quote
| relative bremer support |;
else
if ('dobrs')
quote
| bremer support |;
else
if ('dojak')
quote
| jackknifing |;
else
if ('doboot')
quote
| bootstrap |;
else
if ('dosym')
quote
| relative bremer support, bremer |
| support, jackknifing, bootstrap, |
| symmetric resampling |;
end
end end end end end
quote
| The file `apo.svg` contains the |