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TNT_Script
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add: prefix

This commit is contained in:
kuoi 2023-09-14 00:08:43 +08:00
parent 05ba3e3fc4
commit b2fbe72823
2 changed files with 38 additions and 25 deletions
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14
README.md
View File

@ -18,7 +18,7 @@ The TNT script follows MIT and part of script is from setk.run belonging to Salv
- Perform Strict consensus / Majority-rule consensus / Half strict consensus.
- Calculate Relative Bremer support, jackknifing (1,000 times), and bootstrap (1,000 times).
- Calculate jackknifing (1,000 times), bootstrap (1,000 times) and Relative Bremer support.
- Map apomorphic characters on the consensus tree.
@ -29,13 +29,13 @@ The TNT script follows MIT and part of script is from setk.run belonging to Salv
For Windows users
```
tnt run guoyi.run filename datatype weight 0/K cons resample;
tnt run guoyi.run filename datatype weight 0/K cons resample prefix;
```
For Linux and Mac users
```
tnt run guoyi.run filename datatype weight 0/K cons resample,
tnt run guoyi.run filename datatype weight K cons resample prefix,
```
- datatpye should be `32`, `dna`, `prot`, `num`
@ -46,6 +46,10 @@ tnt run guoyi.run filename datatype weight 0/K cons resample,
- iw=implied weight, ew=equal weight, eiw=extended implied weight (default) N.B. ew must followed 0 (the K value position for ew iw and eiw)
- 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)
@ -54,6 +58,10 @@ tnt run guoyi.run filename datatype weight 0/K cons resample,
- jak=1, boot=2, relative bremer=4 i.e. jak+boot+bremer=7 (default)
- prefix can be empty or a string
- default is empty
## Results
- Results instructions are at the end of `tnt.log`.

49
guoyi.run
View File

@ -1,9 +1,9 @@
log tnt.log;
macro=;
log %7.tnt.log;
/*Arguments*/
if ( (argnumber == 0) | (argnumber >=7) )
if ( (argnumber == 0) | (argnumber >7) )
silent -console;
quote - /----------------------------------------------------\;
quote - | GUOYI TNT SCRIPT 2022-2023 MIT |;
@ -13,20 +13,25 @@ if ( (argnumber == 0) | (argnumber >=7) )
quote - | ============================== |;
quote - | === Parameters Details === |;
quote - | ============================== |;
quote - | filename datatype weight 0/K cons resample |;
quote - | - datatpye should be 32, dna, prot, num |;
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. ew must followed 0 |;
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 - | - resample should be sum of what you want |;
quote - | - resamp should be sum of what you want |;
quote - | jak=1, boot=2, relative bremer=4 |;
quote - | i.e. jak+boot+bremer=7 (default) |;
quote - | - prefix can be empty, or a string |;
quote - | default is empty |;
quote - \----------------------------------------------------/;
proc/;
end
@ -181,12 +186,12 @@ else
end
/*Export trees*/
export= trees.tre;
export= %7.trees.tre;
taxname-;
export= trees_no.tre;
export= %7.trees_no.tre;
taxname=;
tsave = trees.ctf;
tsave *= trees.tnt.tre;
tsave = %7.trees.ctf;
tsave *= %7.trees.tnt.tre;
/*Consensus tree*/
if (argnumber<=4)
@ -209,11 +214,11 @@ tvault >/;
/*Export consensus tree*/
tchoose /;
export - original.tre;
export - %7.original.tre;
taxname-;
export - original_no.tre;
tsave = original.ctf;
tsave *= original.tnt.tre;
export - %7.original_no.tre;
tsave = %7.original.ctf;
tsave *= %7.original.tnt.tre;
/*Caulculate TL/CI/RI score*/
report-;
@ -233,7 +238,7 @@ set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
report=;
/*Apomorphic characters*/
export = winclada.tre;
export = %7.winclada.tre;
taxname =;
ttags=;
apo >0;
@ -242,10 +247,10 @@ quote - apomorphy tags start ;
ttags/;
quote - apomorphy tags stop ;
quote - \----------------------------------------------/;
ttags & apo.svg thickness 7 italics fontsize 15;
export < apo.tre;
ttags & %7.apo.svg thickness 7 italics fontsize 15;
export < %7.apo.tre;
taxname-;
export - apo_no.tre;
export - %7.apo_no.tre;
ttags-;
/*Get jak/boot/relative-bremer support*/
@ -288,15 +293,15 @@ else
end
/*Export consensus tree with supports*/
ttags & resample.svg thickness 7 italics fontsize 15;
ttags & %7.resample.svg thickness 7 italics fontsize 15;
quote - /----------------------------------------------\;
quote - resample tags start ;
ttags/;
quote - resample tags stop ;
quote - \----------------------------------------------/;
export < resample.tre;
export < %7.resample.tre;
taxname-;
export - resample_no.tre;
export - %7.resample_no.tre;
ttags-;
/*Report CI/RI/TL */