3tnt.sh

@@ -1,54 +0,0 @@
-#!/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

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

README.md

@@ -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, which can be read by figtree after processing by tnt2figtree.
+- `resample.tre` is the consensus tree with support.
 
-- `trees*.tre` contains he MPTs, which can be read by figtree after processing by tnt2figtree.
+- `trees*.tre` contains he MPTs.
 
 - `resample/apo.log` contains the tree tags.
 
@@ -100,6 +100,58 @@ 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.
 
-# Further information
+# TNT2WinClada
 
-To make tnt exported trees can be readable by WinClada (Nixon, 2021) and FigTree, please check tnt2winclada and tnt2figtree in this repository.
+```
+~|~|\ |~|~  ~)  |    |o._ |~| _  _| _ 
+ | | \| |   /_   \/\/ || ||_|(_|(_|(_|
+
+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>
+```

src_tnt2figtree/CMakeLists.txt

@@ -1,14 +0,0 @@
-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

@@ -1,55 +0,0 @@
-# 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

@@ -1,197 +0,0 @@
-#include <fstream>
-#include <iostream>
-#include <regex>
-
-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

@@ -1,14 +0,0 @@
-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

@@ -1,55 +0,0 @@
-# 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>
-```