Find the file format specifications for the .PHY file format.

The .PHY file format refers to the PHYLIP format, a text-based format used in phylogeny for representing multiple sequence alignments or distance matrices. It is commonly used in bioinformatics for evolutionary tree inference. The format is simple and plain text.

The file starts with a header line containing two integers separated by spaces: the number of taxa (species or sequences) and the number of characters (sequence length or matrix size).

Following the header, the data is listed. For sequence data (the most common type):

Taxon names are typically 10 characters long, padded with spaces if shorter.

Sequences are listed after the name on the same line.

The data can be sequential (all sequence for one taxon on one line, then the next) or interleaved (sequences split into blocks, with one block per chunk of characters, all taxa in each block).

For distance matrices, the header is the number of taxa (number of characters is implied as the matrix size), followed by taxon names and distances.

This response focuses on the sequential sequence format for simplicity, as it is common and the sample files use it.

1. Make a list of all the properties of this file format intrinsic to its file system.

Number of taxa (integer)

Number of characters (integer)

Taxon names (list of strings, usually up to 10 characters each)

Sequences (list of strings, one per taxon, length equal to number of characters)

1. Find two direct download links for files of format .PHY.

https://raw.githubusercontent.com/edgardomortiz/vcf2phylip/main/test_dataset/min_4_samples.vcf.min4.phy

https://raw.githubusercontent.com/edgardomortiz/vcf2phylip/main/test_dataset/min_4_samples.vcf.min4.varsites.phy

1. Write a ghost blog embedded html javascript that allows a user to drag n drop a file of format .PHY and it will dump to screen all these properties.

PHY File Parser

1. Write a python class that can open any file of format .PHY and decode read and write and print to console all the properties from the above list.

import sys

class PHYFile:
    def __init__(self, filepath=None):
        self.num_taxa = 0
        self.num_chars = 0
        self.taxon_names = []
        self.sequences = []
        if filepath:
            self.read(filepath)

    def read(self, filepath):
        with open(filepath, 'r') as f:
            lines = f.readlines()
        lines = [line.strip() for line in lines if line.strip()]
        header = lines[0].split()
        self.num_taxa = int(header[0])
        self.num_chars = int(header[1])
        for line in lines[1:]:
            name = line[:10].strip()
            seq = line[10:].replace(' ', '')
            self.taxon_names.append(name)
            self.sequences.append(seq)

    def write(self, filepath):
        with open(filepath, 'w') as f:
            f.write(f"{self.num_taxa} {self.num_chars}\n")
            for name, seq in zip(self.taxon_names, self.sequences):
                padded_name = name.ljust(10)
                f.write(f"{padded_name}{seq}\n")

    def print_properties(self):
        print(f"Number of taxa: {self.num_taxa}")
        print(f"Number of characters: {self.num_chars}")
        print("Taxon names:")
        for name in self.taxon_names:
            print(name)
        print("Sequences:")
        for seq in self.sequences:
            print(seq)

# Example usage
if __name__ == '__main__':
    if len(sys.argv) > 1:
        phy = PHYFile(sys.argv[1])
        phy.print_properties()
        phy.write('output.phy')  # Example write

1. Write a java class that can open any file of format .PHY and decode read and write and print to console all the properties from the above list.

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;

public class PHYFile {
    private int numTaxa;
    private int numChars;
    private List<String> taxonNames;
    private List<String> sequences;

    public PHYFile() {
        taxonNames = new ArrayList<>();
        sequences = new ArrayList<>();
    }

    public void read(String filepath) throws Exception {
        BufferedReader br = new BufferedReader(new FileReader(filepath));
        String line = br.readLine().trim();
        String[] header = line.split("\\s+");
        numTaxa = Integer.parseInt(header[0]);
        numChars = Integer.parseInt(header[1]);
        while ((line = br.readLine()) != null) {
            line = line.trim();
            if (!line.isEmpty()) {
                String name = line.substring(0, Math.min(10, line.length())).trim();
                String seq = line.substring(10).replaceAll("\\s+", "");
                taxonNames.add(name);
                sequences.add(seq);
            }
        }
        br.close();
    }

    public void write(String filepath) throws Exception {
        PrintWriter pw = new PrintWriter(filepath);
        pw.println(numTaxa + " " + numChars);
        for (int i = 0; i < taxonNames.size(); i++) {
            String paddedName = String.format("%-10s", taxonNames.get(i));
            pw.println(paddedName + sequences.get(i));
        }
        pw.close();
    }

    public void printProperties() {
        System.out.println("Number of taxa: " + numTaxa);
        System.out.println("Number of characters: " + numChars);
        System.out.println("Taxon names:");
        for (String name : taxonNames) {
            System.out.println(name);
        }
        System.out.println("Sequences:");
        for (String seq : sequences) {
            System.out.println(seq);
        }
    }

    public static void main(String[] args) throws Exception {
        if (args.length > 0) {
            PHYFile phy = new PHYFile();
            phy.read(args[0]);
            phy.printProperties();
            phy.write("output.phy"); // Example write
        }
    }
}

1. Write a javascript class that can open any file of format .PHY and decode read and write and print to console all the properties from the above list.

Note: JavaScript in browser can't directly open local files without user interaction, but for node.js, we can use fs. Assuming node.js for this class.

const fs = require('fs');

class PHYFile {
    constructor(filepath = null) {
        this.numTaxa = 0;
        this.numChars = 0;
        this.taxonNames = [];
        this.sequences = [];
        if (filepath) {
            this.read(filepath);
        }
    }

    read(filepath) {
        const text = fs.readFileSync(filepath, 'utf8');
        const lines = text.trim().split('\n').map(line => line.trim()).filter(line => line);
        const header = lines[0].split(/\s+/).map(Number);
        this.numTaxa = header[0];
        this.numChars = header[1];
        for (let i = 1; i < lines.length; i++) {
            const line = lines[i];
            const name = line.substring(0, 10).trim();
            const seq = line.substring(10).replace(/\s+/g, '');
            this.taxonNames.push(name);
            this.sequences.push(seq);
        }
    }

    write(filepath) {
        let content = `${this.numTaxa} ${this.numChars}\n`;
        for (let i = 0; i < this.taxonNames.length; i++) {
            const paddedName = this.taxonNames[i].padEnd(10);
            content += `${paddedName}${this.sequences[i]}\n`;
        }
        fs.writeFileSync(filepath, content);
    }

    printProperties() {
        console.log(`Number of taxa: ${this.numTaxa}`);
        console.log(`Number of characters: ${this.numChars}`);
        console.log('Taxon names:');
        this.taxonNames.forEach(name => console.log(name));
        console.log('Sequences:');
        this.sequences.forEach(seq => console.log(seq));
    }
}

// Example usage
if (process.argv.length > 2) {
  const phy = new PHYFile(process.argv[2]);
  phy.printProperties();
  phy.write('output.phy');
}

1. Write a c class that can open any file of format .PHY and decode read and write and print to console all the properties from the above list.

Assuming C++ for "c class" as C doesn't have classes, but C++ does.

#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include <iomanip>

using namespace std;

class PHYFile {
private:
    int numTaxa;
    int numChars;
    vector<string> taxonNames;
    vector<string> sequences;

public:
    PHYFile(string filepath = "") {
        numTaxa = 0;
        numChars = 0;
        if (!filepath.empty()) {
            read(filepath);
        }
    }

    void read(string filepath) {
        ifstream file(filepath);
        string line;
        getline(file, line);
        stringstream header(line);
        header >> numTaxa >> numChars;
        while (getline(file, line)) {
            if (!line.empty()) {
                string name = line.substr(0, 10);
                name.erase(remove(name.begin(), name.end(), ' '), name.end()); // trim spaces
                string seq = line.substr(10);
                seq.erase(remove(seq.begin(), seq.end(), ' '), seq.end());
                taxonNames.push_back(name);
                sequences.push_back(seq);
            }
        }
        file.close();
    }

    void write(string filepath) {
        ofstream file(filepath);
        file << numTaxa << " " << numChars << endl;
        for (size_t i = 0; i < taxonNames.size(); ++i) {
            file << left << setw(10) << taxonNames[i] << sequences[i] << endl;
        }
        file.close();
    }

    void printProperties() {
        cout << "Number of taxa: " << numTaxa << endl;
        cout << "Number of characters: " << numChars << endl;
        cout << "Taxon names:" << endl;
        for (const string& name : taxonNames) {
            cout << name << endl;
        }
        cout << "Sequences:" << endl;
        for (const string& seq : sequences) {
            cout << seq << endl;
        }
    }
};

int main(int argc, char* argv[]) {
    if (argc > 1) {
        PHYFile phy(argv[1]);
        phy.printProperties();
        phy.write("output.phy"); // Example write
    }
    return 0;
}