fix: typo

3tnt.sh

@@ -0,0 +1,54 @@
+#!/bin/bash
+
+# Found TNT
+
+if [ -z "tnt" ]; then
+    echo "TNT not found"
+    exit 1
+fi
+
+# Define input data
+
+input_file=$1
+
+if [ -z "$input_file" ]; then
+    echo "Usage: $0 <input_file> <guoyi.run>"
+    exit 1
+fi
+
+# Define tnt script
+
+script_file=$2
+
+if [ -z "$script_file" ]; then
+    echo "Usage: $0 <input_file> <guoyi.run>"
+    echo "Warning: guoyi.run will be set as /usr/share/tnt/tnt_scripts/guoyi.run"
+    script_file="/usr/share/tnt/tnt_scripts/guoyi.run"
+fi
+
+
+# Define three weighting functions
+task1() {
+    echo "Equal Weighting started"
+    tnt run $script_file $input_file 3 ew 0 str 5 EW,
+    echo "Equal Weighting completed"
+}
+
+task2() {
+    echo "Implied Weighting started"
+    tnt run $script_file $input_file 3 iw 12 str 5 IW,
+    echo "Implied Weighting completed"
+}
+
+task3() {
+    echo "Extended Implied Weighting started"
+    tnt run $script_file $input_file 3 eiw 12 str 5 EIW,
+    echo "Extended Implied Weighting completed"
+}
+
+task1 
+task2
+task3 
+
+echo "All tasks completed"
+

CMakeLists.txt

@@ -1,15 +1,13 @@
 cmake_minimum_required(VERSION 3.0)
 
-project(tnt2winclada)
+project(tnt_script)
 SET( CMAKE_EXPORT_COMPILE_COMMANDS ON )
 
 set(CMAKE_CXX_STANDARD 11)
 
-add_executable(tnt2winclada tnt2winclada.cpp)
+add_subdirectory(src_tnt2winclada)
+add_subdirectory(src_tnt2figtree)
 
-target_compile_options(tnt2winclada PRIVATE -Wall -Wextra -pedantic)
-
-install(TARGETS tnt2winclada DESTINATION /usr/bin)
 install(FILES guoyi.run DESTINATION /usr/share/tnt/tnt_scripts)
-install(FILES LICENSE DESTINATION /usr/share/licenses/tnt2winclada)
-install(FILES README.md DESTINATION /usr/share/doc/tnt2winclada)
+install(FILES LICENSE DESTINATION /usr/share/licenses/tnt-guoyi-script)
+install(FILES README.md DESTINATION /usr/share/doc/tnt-guoyi-script)

README.md

@@ -1,7 +1,5 @@
 # guoyi.run
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8428198.svg)](https://doi.org/10.5281/zenodo.8428198)
-
 TNT Script for Maximum Parsimony Analysis (Phylogeny)
 
 ## Usage
@@ -58,7 +56,9 @@ tnt run guoyi.run filename datatype weight 0/K cons resample prefix,
 
 - resample should be sum of what you want
 
-  -  relative bremer support (rbrs)=0.1, bremer support (brs)=0.2, jackknifing (jak)=1, bootstrap (boot)=2, symmetric resampling (sym)=4 i.e. rbrs+jak+boot+sym=7.1 (default)       
+  -  relative bremer support (rbrs)=0.1, bremer support (brs)=0.2, jackknifing (jak)=1, bootstrap (boot)=2, symmetric resampling (sym)=4 i.e. jak+boot+sym=7 (default) 
+
+  -  Notice: Bremer related support would change the tree topology, so it should be used with caution.
 
 - prefix can  be empty or a string
 
@@ -80,9 +80,9 @@ tnt run guoyi.run filename datatype weight 0/K cons resample prefix,
 
 - `apo.tre` is the apomorphic character mapping tree.
 
-- `resample.tre` is the consensus tree with support.
+- `resample.tre` is the consensus tree with support, which can be read by figtree after processing by tnt2figtree.
 
-- `trees*.tre` contains he MPTs.
+- `trees*.tre` contains he MPTs, which can be read by figtree after processing by tnt2figtree.
 
 - `resample/apo.log` contains the tree tags.
 
@@ -100,58 +100,8 @@ tnt run guoyi.run filename datatype weight 0/K cons resample prefix,
 
 Cite this script is mandatory, list me (Guoyi Zhang) in your Acknowledgements is recommended. This script follows MIT License.
 
-# TNT2WinClada
+# Further information
 
-```
-~|~|\ |~|~  ~)  |    |o._ |~| _  _| _ 
- | | \| |   /_   \/\/ || ||_|(_|(_|(_|
+To make tnt exported trees can be readable by WinClada (Nixon, 2021) and FigTree, please check tnt2winclada and tnt2figtree in this repository.
 
-MIT, Guoyi Zhang, 2023
-```
-
-## Function
-
-Convert TNT output tree file without tags and taxname, e.g. `winclada.tre` produced by TNT script, to WinClada acceptable format tree.
-
-## Compile
-
-### Linux & Unix
-
-```
-mkdir -p build && cd build
-cmake ..
-make && make install
-```
-
-### Windows
-
-```
-cl /EHsc tnt2winclada.cpp
-```
-
-## Usage
-
-```
-tnt2winclada -i ${input_file} -o ${output_file}
-```
-
-Interactive commands are also available.
-
-```
-tnt2winclada
-
-~|~|\ |~|~  ~)  |    |o._ |~| _  _| _ 
- | | \| |   /_   \/\/ || ||_|(_|(_|(_|
-TNT2WinClada
-MIT, Guoyi Zhang, 2023
-please type help to see more commands
-
-tnt2winclada> help
-help			show interactive commands help
-input <filename>	input a TNT output tree from the specified file
-output <filename>	output a winclada accessible tree file
-quit			quit the program
-exit			exit the program
-
-tnt2winclada>
-```
+runwincladtree.run can handle [wincladtree script](https://www.lillo.org.ar/phylogeny/tnt/scripts/wincladtree.run) with input file which must be $(PREFIX).winclada.ss or winclada.tree.

guoyi.run

@@ -111,7 +111,7 @@ end
 
 /*handle resmaple type*/
 if (argnumber<6)
-  set dojak 1; set doboot 1; set dosym 1; set dorbrs 1;
+  set dojak 1; set doboot 1; set dosym 1; set dorbrs 0;
 else
   set rsmp %6;
   loop 1 5
@@ -356,7 +356,6 @@ set contree ntrees;
 /*Store consensus tree to tree vault*/
 hold /+0; 
 tv>/;
-tchoose 0.'npars';
 
 /*Get rbr/br/jak/boot/sym support and get consensus tree*/
 ttags=;
@@ -377,20 +376,21 @@ if ('dobremer')
 
   /*calculate relative bremer support*/
   if ('dorbrs')
-  bs ]!! 0;
+  bs ]!! 0.'npars';
   end
 
   /*calculate bremer support*/
   if ('dobrs')
   macfloat 1; /*set the br value float*/
-  bsupport !! 0;
+  bsupport !! 0.'npars';
   end
 
 end
-  
+
 /*Choose final tree*/
+tchoose 0.'npars';
 tv<;
-tchoose/;
+tchoose /;
 
 /*adjust to zero following Pablo Goloboff*/
 sub 0;
@@ -426,6 +426,10 @@ taxname=;
 
 /*Export consensus tree*/
 tchoose /;
+ttags=;
+tp/;
+ttags & %7.original.svg thickness 7 italics fontsize 15;
+ttags-;
 export - %7.original.tre;
 taxname-;
 export - %7.original_no.tre;
@@ -463,13 +467,21 @@ 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*/
+if ('themax' != 'themin')
+	set RI ('themax'-'TL')/('themax'-'themin'); /*RI=1 character fits perfetcly*/
+else
+	set RI 999;
+end
 
 /*Report CI/RI/TL */
 log %7.report.log;
 macfloat 3;
 quote Consistency Index (CI) is 'CI';
-quote Retention Index (RI) is 'RI';
+if ('RI' == 999)
+	quote Retention Index (RI) is NA;
+else
+	quote Retention Index (RI) is 'RI';
+end
 quote Tree Length (TL) is 'TL';
 log/;
 
@@ -537,7 +549,11 @@ if ('dohlf')
   quote
 |          half strict consensus tree with     |;
 end end end
-
+if ('dobremer')
+  quote
+|          WARNING: bremer-related will        |
+|          WARNING: change the polytomy        |;
+end
 if ('dorbrs')
   quote
 |          relative bremer support             |;

runwincladtree.run

@@ -0,0 +1,7 @@
+macro=;
+taxname+5000;
+p %1;
+ttags=;
+apo>0;
+wincladtree %1.wincladtree.svg noalign shade rotate squaresize 15 taxangle 0;
+zzz;

src_tnt2figtree/CMakeLists.txt

@@ -0,0 +1,14 @@
+cmake_minimum_required(VERSION 3.0)
+
+project(tnt2figtree)
+SET( CMAKE_EXPORT_COMPILE_COMMANDS ON )
+
+set(CMAKE_CXX_STANDARD 11)
+
+add_executable(tnt2figtree tnt2figtree.cpp)
+
+target_compile_options(tnt2figtree PRIVATE -Wall -Wextra -pedantic)
+
+install(TARGETS tnt2figtree DESTINATION /usr/bin)
+install(FILES ../LICENSE DESTINATION /usr/share/licenses/tnt2figtree)
+install(FILES README.md DESTINATION /usr/share/doc/tnt2figtree)

src_tnt2figtree/README.md

@@ -0,0 +1,55 @@
+# TNT2FigTree
+
+```
+~|~|\ |~|~~)|~o(~|~|~._ _ _
+ | | \| | /_|~| _| | | }_}_
+
+MIT, Guoyi Zhang, 2024
+```
+
+## Function
+
+Convert TNT output tree file with resample tags, e.g. `resample.tre` produced by TNT script `guoyi.run`, to complete nexus format tree.
+
+## Compile
+
+### Linux & Unix
+
+```
+mkdir -p build && cd build
+cmake ..
+make && make install
+```
+
+### Windows
+
+```
+cl /EHsc tnt2figtree.cpp
+```
+
+## Usage
+
+```
+tnt2figtree ${input_file} ${output_file}
+```
+
+Interactive commands are also available.
+
+```
+tnt2figtree
+
+~|~|\ |~|~~)|~o(~|~|~._ _ _
+ | | \| | /_|~| _| | | }_}_
+TNT2FigTree
+MIT, Guoyi Zhang, 2024
+please type help to see more commands
+
+tnt2figtree> help
+help			show interactive commands help
+import <filename>	import a TNT output nexus format tree by TNT export command
+export <filename>	export a nexus format tree file
+quit			quit the program
+exit			exit the program
+
+tnt2figree>
+```

src_tnt2figtree/tnt2figtree.cpp

@@ -0,0 +1,198 @@
+#include <fstream>
+#include <iostream>
+#include <regex>
+#include <sstream>
+
+std::string remove_useless(std::string input_str1)
+{
+	std::string result_str1 =
+	    std::regex_replace(input_str1, std::regex(" /*"), " ");
+	result_str1 = std::regex_replace(result_str1, std::regex("\\["), "{");
+	result_str1 = std::regex_replace(result_str1, std::regex("\\]"), "}");
+	return result_str1;
+}
+
+std::string add_support(std::string input_str2)
+{
+	std::string result_str2 = "";
+	size_t i = 0;
+	while (i < input_str2.length()) {
+		if (input_str2[i] == ')') {
+			result_str2 += input_str2[i];
+			i++;
+			std::string support_str = "";
+			while (i < input_str2.length() &&
+			       std::regex_match(std::string(1, input_str2[i]),
+						std::regex("[/0-9{}?]"))) {
+				support_str += input_str2[i];
+				i++;
+			}
+			result_str2 += "[&support=\"" + support_str + "\"]";
+		}
+		else {
+			result_str2 += input_str2[i];
+			i++;
+		}
+	}
+	return result_str2;
+}
+
+std::string add_blen(std::string input_str3)
+{
+	std::string result_str3 = "";
+	int i = 0;
+	for (char c : input_str3) {
+		if (c == '(') {
+			i++;
+			result_str3 += c;
+		}
+		else if (c == ')') {
+			result_str3 += ":" + std::to_string(i) + c;
+			i--;
+		}
+		else if (c == ',') {
+			result_str3 += ":" + std::to_string(i) + c;
+		}
+		else {
+			result_str3 += c;
+		}
+	}
+	return result_str3;
+}
+
+std::string remove_slash(std::string input_str4)
+{
+	std::string result_str4 = std::regex_replace(
+	    input_str4, std::regex("\\[&support=\"[\\/\\s]*\"\\]"), "");
+	return result_str4;
+}
+
+std::vector<std::string> get_lines(std::string filename)
+{
+	std::ifstream file(filename);
+	if (!file.is_open()) {
+		std::cout << "Failed to open the input file." << std::endl;
+	}
+
+	std::vector<std::string> lines;
+	std::string line;
+	while (std::getline(file, line)) {
+		lines.push_back(line);
+	}
+	file.close();
+	return lines;
+}
+
+std::vector<std::string> process_line(std::vector<std::string> lines,
+				      size_t lineNum)
+{
+	std::string line = remove_useless(lines[lineNum]);
+	line = add_blen(line);
+	line = add_support(line);
+
+	lines[lineNum] = remove_slash(line);
+	return lines;
+}
+
+void write_lines(const std::vector<std::string>& lines,
+		 const std::string& filename)
+{
+	std::ofstream outfile(filename);
+
+	if (!outfile.is_open()) {
+		std::cout << "Failed to open the output file." << std::endl;
+	}
+
+	for (const std::string& line : lines) {
+		outfile << line << std::endl;
+	}
+
+	outfile.close();
+}
+
+void interactive_commands(std::vector<std::string> lines)
+{
+	std::string command, filename1, filename2;
+	std::cout
+	    << "~|~|\\ |~|~~)|~o(~|~|~._ _ _\n | | \\| | /_|~| _| | | }_}_"
+	    << std::endl;
+	std::cout << "TNT2FigTree\nMIT, Guoyi Zhang, 2024\nplease type help "
+		     "to see more commands"
+		  << std::endl;
+	while (true) {
+		std::cout << "tnt2figtree> ";
+		getline(std::cin, command);
+		if (command == "help") {
+			std::cout << "help\t\t\tshow interactive commands "
+				     "help\nimport <filename>\timport a TNT "
+				     "output nexus format tree by TNT export "
+				     "command\nexport <filename>\texport a "
+				     "nexus format tree file\nquit\t\t\tquit "
+				     "the program\nexit\t\t\texit the program"
+				  << std::endl;
+		}
+		else if (command.find("import ") == 0) {
+			std::stringstream ss(command.substr(7));
+			ss >> filename1;
+			if (filename1.empty()) {
+				std::cout << "tnt2figtree> please specify a "
+					     "filename."
+					  << std::endl;
+			}
+			else {
+				lines = get_lines(filename1);
+			}
+		}
+		else if (command.find("export ") == 0) {
+			std::stringstream ss(command.substr(7));
+			ss >> filename2;
+			if (filename2.empty()) {
+				std::cout << "tnt2figtree> please specify a "
+					     "filename."
+					  << std::endl;
+			}
+			else {
+				for (size_t i = 0; i < lines.size(); i++) {
+					if (lines[i][0] == '(') {
+						lines = process_line(lines, i);
+					}
+				}
+				write_lines(lines, filename2);
+			}
+		}
+		else if (command == "quit" || command == "exit") {
+			break;
+		}
+		else {
+			std::cout << "tnt2figtree> unrecognized command. Type "
+				     "'help' for "
+				     "a list of commands."
+				  << std::endl;
+		}
+	}
+}
+
+int main(int argc, char* argv[])
+{
+	std::vector<std::string> lines;
+	if (argc == 1) {
+		interactive_commands(lines);
+		return 0;
+	}
+	else if (argc == 3) {
+		lines = get_lines(argv[1]);
+		for (size_t i = 0; i < lines.size(); i++) {
+			if (lines[i][0] == '(') {
+				lines = process_line(lines, i);
+			}
+		}
+		write_lines(lines, argv[2]);
+	}
+	else {
+		std::cout << "Usage: " << argv[0]
+			  << " <input_tnt_treefile> <output_nexus_treefile>"
+			  << std::endl;
+	}
+	return 0;
+}
+

src_tnt2winclada/CMakeLists.txt

@@ -0,0 +1,14 @@
+cmake_minimum_required(VERSION 3.0)
+
+project(tnt2winclada)
+SET( CMAKE_EXPORT_COMPILE_COMMANDS ON )
+
+set(CMAKE_CXX_STANDARD 11)
+
+add_executable(tnt2winclada tnt2winclada.cpp)
+
+target_compile_options(tnt2winclada PRIVATE -Wall -Wextra -pedantic)
+
+install(TARGETS tnt2winclada DESTINATION /usr/bin)
+install(FILES ../LICENSE DESTINATION /usr/share/licenses/tnt2winclada)
+install(FILES README.md DESTINATION /usr/share/doc/tnt2winclada)

src_tnt2winclada/README.md

@@ -0,0 +1,55 @@
+# TNT2WinClada
+
+```
+~|~|\ |~|~  ~)  |    |o._ |~| _  _| _ 
+ | | \| |   /_   \/\/ || ||_|(_|(_|(_|
+
+MIT, Guoyi Zhang, 2023
+```
+
+## Function
+
+Convert TNT output tree file without tags and taxname, e.g. `winclada.tre` produced by TNT script `guoyi.run`, to WinClada acceptable format tree.
+
+## Compile
+
+### Linux & Unix
+
+```
+mkdir -p build && cd build
+cmake ..
+make && make install
+```
+
+### Windows
+
+```
+cl /EHsc tnt2winclada.cpp
+```
+
+## Usage
+
+```
+tnt2winclada -i ${input_file} -o ${output_file}
+```
+
+Interactive commands are also available.
+
+```
+tnt2winclada
+
+~|~|\ |~|~  ~)  |    |o._ |~| _  _| _ 
+ | | \| |   /_   \/\/ || ||_|(_|(_|(_|
+TNT2WinClada
+MIT, Guoyi Zhang, 2023
+please type help to see more commands
+
+tnt2winclada> help
+help			show interactive commands help
+input <filename>	input a TNT output tree from the specified file
+output <filename>	output a winclada accessible tree file
+quit			quit the program
+exit			exit the program
+
+tnt2winclada>
+```