Compare commits
No commits in common. "945ba6882b4da21ba0839581ae86d25b59a98c4c" and "d395c8720f0a1d22050c72a3d8e1b2c4be2f308f" have entirely different histories.
945ba6882b
...
d395c8720f
9 changed files with 63 additions and 398 deletions
54
3tnt.sh
54
3tnt.sh
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@ -1,54 +0,0 @@
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#!/bin/bash
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# Found TNT
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if [ -z "tnt" ]; then
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echo "TNT not found"
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exit 1
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fi
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# Define input data
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input_file=$1
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if [ -z "$input_file" ]; then
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echo "Usage: $0 <input_file> <guoyi.run>"
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exit 1
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fi
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# Define tnt script
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script_file=$2
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if [ -z "$script_file" ]; then
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echo "Usage: $0 <input_file> <guoyi.run>"
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echo "Warning: guoyi.run will be set as /usr/share/tnt/tnt_scripts/guoyi.run"
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script_file="/usr/share/tnt/tnt_scripts/guoyi.run"
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fi
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# Define three weighting functions
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task1() {
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echo "Equal Weighting started"
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tnt run $script_file $input_file 3 ew 0 str 5 EW,
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echo "Equal Weighting completed"
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}
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task2() {
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echo "Implied Weighting started"
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tnt run $script_file $input_file 3 iw 12 str 5 IW,
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echo "Implied Weighting completed"
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}
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task3() {
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echo "Extended Implied Weighting started"
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tnt run $script_file $input_file 3 eiw 12 str 5 EIW,
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echo "Extended Implied Weighting completed"
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}
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task1
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task2
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task3
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echo "All tasks completed"
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@ -1,13 +1,15 @@
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cmake_minimum_required(VERSION 3.0)
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project(tnt_script)
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project(tnt2winclada)
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SET( CMAKE_EXPORT_COMPILE_COMMANDS ON )
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set(CMAKE_CXX_STANDARD 11)
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add_subdirectory(src_tnt2winclada)
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add_subdirectory(src_tnt2figtree)
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add_executable(tnt2winclada tnt2winclada.cpp)
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target_compile_options(tnt2winclada PRIVATE -Wall -Wextra -pedantic)
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install(TARGETS tnt2winclada DESTINATION /usr/bin)
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install(FILES guoyi.run DESTINATION /usr/share/tnt/tnt_scripts)
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install(FILES LICENSE DESTINATION /usr/share/licenses/tnt-guoyi-script)
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install(FILES README.md DESTINATION /usr/share/doc/tnt-guoyi-script)
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install(FILES LICENSE DESTINATION /usr/share/licenses/tnt2winclada)
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install(FILES README.md DESTINATION /usr/share/doc/tnt2winclada)
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60
README.md
60
README.md
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@ -80,9 +80,9 @@ tnt run guoyi.run filename datatype weight 0/K cons resample prefix,
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- `apo.tre` is the apomorphic character mapping tree.
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- `resample.tre` is the consensus tree with support, which can be read by figtree after processing by tnt2figtree.
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- `resample.tre` is the consensus tree with support.
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- `trees*.tre` contains he MPTs, which can be read by figtree after processing by tnt2figtree.
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- `trees*.tre` contains he MPTs.
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- `resample/apo.log` contains the tree tags.
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@ -100,6 +100,58 @@ tnt run guoyi.run filename datatype weight 0/K cons resample prefix,
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Cite this script is mandatory, list me (Guoyi Zhang) in your Acknowledgements is recommended. This script follows MIT License.
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# Further information
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# TNT2WinClada
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To make tnt exported trees can be readable by WinClada (Nixon, 2021) and FigTree, please check tnt2winclada and tnt2figtree in this repository.
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```
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~|~|\ |~|~ ~) | |o._ |~| _ _| _
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MIT, Guoyi Zhang, 2023
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```
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## Function
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Convert TNT output tree file without tags and taxname, e.g. `winclada.tre` produced by TNT script, to WinClada acceptable format tree.
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## Compile
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### Linux & Unix
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```
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mkdir -p build && cd build
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cmake ..
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make && make install
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```
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### Windows
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```
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cl /EHsc tnt2winclada.cpp
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```
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## Usage
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```
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tnt2winclada -i ${input_file} -o ${output_file}
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```
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Interactive commands are also available.
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```
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tnt2winclada
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~|~|\ |~|~ ~) | |o._ |~| _ _| _
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| | \| | /_ \/\/ || ||_|(_|(_|(_|
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TNT2WinClada
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MIT, Guoyi Zhang, 2023
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please type help to see more commands
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tnt2winclada> help
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help show interactive commands help
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input <filename> input a TNT output tree from the specified file
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output <filename> output a winclada accessible tree file
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quit quit the program
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exit exit the program
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tnt2winclada>
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```
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@ -1,14 +0,0 @@
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cmake_minimum_required(VERSION 3.0)
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project(tnt2figtree)
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SET( CMAKE_EXPORT_COMPILE_COMMANDS ON )
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set(CMAKE_CXX_STANDARD 11)
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add_executable(tnt2figtree tnt2figtree.cpp)
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target_compile_options(tnt2figtree PRIVATE -Wall -Wextra -pedantic)
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install(TARGETS tnt2figtree DESTINATION /usr/bin)
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install(FILES ../LICENSE DESTINATION /usr/share/licenses/tnt2figtree)
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install(FILES README.md DESTINATION /usr/share/doc/tnt2figtree)
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@ -1,55 +0,0 @@
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# TNT2FigTree
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```
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~|~|\ |~|~~)|~o(~|~|~._ _ _
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| | \| | /_|~| _| | | }_}_
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MIT, Guoyi Zhang, 2024
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```
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## Function
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Convert TNT output tree file with resample tags, e.g. `resample.tre` produced by TNT script `guoyi.run`, to complete nexus format tree.
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## Compile
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### Linux & Unix
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```
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mkdir -p build && cd build
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cmake ..
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make && make install
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```
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### Windows
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```
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cl /EHsc tnt2figtree.cpp
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```
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## Usage
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```
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tnt2figtree ${input_file} ${output_file}
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```
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Interactive commands are also available.
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```
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tnt2figtree
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~|~|\ |~|~~)|~o(~|~|~._ _ _
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| | \| | /_|~| _| | | }_}_
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TNT2FigTree
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MIT, Guoyi Zhang, 2024
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please type help to see more commands
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tnt2figtree> help
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help show interactive commands help
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import <filename> import a TNT output nexus format tree by TNT export command
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export <filename> export a nexus format tree file
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quit quit the program
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exit exit the program
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tnt2figree>
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```
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@ -1,197 +0,0 @@
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#include <fstream>
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#include <iostream>
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#include <regex>
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std::string remove_useless(std::string input_str1)
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{
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std::string result_str1 =
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std::regex_replace(input_str1, std::regex(" /*"), " ");
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result_str1 = std::regex_replace(result_str1, std::regex("\\["), "{");
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result_str1 = std::regex_replace(result_str1, std::regex("\\]"), "}");
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return result_str1;
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}
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std::string add_support(std::string input_str2)
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{
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std::string result_str2 = "";
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size_t i = 0;
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while (i < input_str2.length()) {
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if (input_str2[i] == ')') {
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result_str2 += input_str2[i];
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i++;
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std::string support_str = "";
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while (i < input_str2.length() &&
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std::regex_match(std::string(1, input_str2[i]),
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std::regex("[/0-9{}?]"))) {
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support_str += input_str2[i];
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i++;
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}
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result_str2 += "[&support=\"" + support_str + "\"]";
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}
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else {
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result_str2 += input_str2[i];
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i++;
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}
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}
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return result_str2;
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}
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std::string add_blen(std::string input_str3)
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{
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std::string result_str3 = "";
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int i = 0;
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for (char c : input_str3) {
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if (c == '(') {
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i++;
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result_str3 += c;
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}
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else if (c == ')') {
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result_str3 += ":" + std::to_string(i) + c;
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i--;
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}
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else if (c == ',') {
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result_str3 += ":" + std::to_string(i) + c;
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}
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else {
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result_str3 += c;
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}
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}
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return result_str3;
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}
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std::string remove_slash(std::string input_str4)
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{
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std::string result_str4 = std::regex_replace(
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input_str4, std::regex("\\[&support=\"[\\/\\s]*\"\\]"), "");
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return result_str4;
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}
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std::vector<std::string> get_lines(std::string filename)
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{
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std::ifstream file(filename);
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if (!file.is_open()) {
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std::cout << "Failed to open the input file." << std::endl;
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}
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std::vector<std::string> lines;
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std::string line;
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while (std::getline(file, line)) {
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lines.push_back(line);
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}
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file.close();
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return lines;
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}
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std::vector<std::string> process_line(std::vector<std::string> lines,
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size_t lineNum)
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{
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std::string line = remove_useless(lines[lineNum]);
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line = add_blen(line);
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line = add_support(line);
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lines[lineNum] = remove_slash(line);
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return lines;
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}
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void write_lines(const std::vector<std::string>& lines,
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const std::string& filename)
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{
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std::ofstream outfile(filename);
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if (!outfile.is_open()) {
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std::cout << "Failed to open the output file." << std::endl;
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}
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for (const std::string& line : lines) {
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outfile << line << std::endl;
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}
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outfile.close();
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}
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void interactive_commands(std::vector<std::string> lines)
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{
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std::string command, filename1, filename2;
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std::cout
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<< "~|~|\\ |~|~~)|~o(~|~|~._ _ _\n | | \\| | /_|~| _| | | }_}_"
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<< std::endl;
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std::cout << "TNT2FigTree\nMIT, Guoyi Zhang, 2024\nplease type help "
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"to see more commands"
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<< std::endl;
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while (true) {
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std::cout << "tnt2figtree> ";
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getline(std::cin, command);
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if (command == "help") {
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std::cout << "help\t\t\tshow interactive commands "
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"help\nimport <filename>\timport a TNT "
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"output nexus format tree by TNT export "
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"command\nexport <filename>\texport a "
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"nexus format tree file\nquit\t\t\tquit "
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"the program\nexit\t\t\texit the program"
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<< std::endl;
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}
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else if (command.find("import ") == 0) {
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std::stringstream ss(command.substr(7));
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ss >> filename1;
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if (filename1.empty()) {
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std::cout << "tnt2figtree> please specify a "
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"filename."
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<< std::endl;
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}
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else {
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lines = get_lines(filename1);
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}
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}
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else if (command.find("export ") == 0) {
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std::stringstream ss(command.substr(7));
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ss >> filename2;
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if (filename2.empty()) {
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std::cout << "tnt2figtree> please specify a "
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"filename."
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<< std::endl;
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}
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else {
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for (size_t i = 0; i < lines.size(); i++) {
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if (lines[i][0] == '(') {
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lines = process_line(lines, i);
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}
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}
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write_lines(lines, filename2);
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}
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||||
}
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else if (command == "quit" || command == "exit") {
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break;
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}
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else {
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std::cout << "tnt2figtree> unrecognized command. Type "
|
||||
"'help' for "
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||||
"a list of commands."
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<< std::endl;
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||||
}
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||||
}
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||||
}
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||||
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int main(int argc, char* argv[])
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{
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std::vector<std::string> lines;
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if (argc == 1) {
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interactive_commands(lines);
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return 0;
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||||
}
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else if (argc == 3) {
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lines = get_lines(argv[1]);
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for (size_t i = 0; i < lines.size(); i++) {
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||||
if (lines[i][0] == '(') {
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||||
lines = process_line(lines, i);
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||||
}
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}
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write_lines(lines, argv[2]);
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||||
}
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else {
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||||
std::cout << "Usage: " << argv[0]
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<< " <input_tnt_treefile> <output_nexus_treefile>"
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||||
<< std::endl;
|
||||
}
|
||||
return 0;
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||||
}
|
||||
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||||
|
|
@ -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)
|
||||
|
|
@ -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>
|
||||
```
|
||||
Loading…
Reference in a new issue