File Format Specifications for .FA

The .FA file extension refers to the FASTA format, a text-based standard widely used in bioinformatics for representing nucleotide (DNA/RNA) or amino acid (protein) sequences. It was originally developed by David J. Lipman and William R. Pearson in 1985 as part of the FASTA software package. The format is simple and human-readable, with no binary components or fixed headers. Key specifications:

• The file is plain text (ASCII or UTF-8).
• It can contain one or more sequences.
• Each sequence begins with a definition line (defline) starting with a greater-than symbol (">"), followed by a unique sequence identifier (SeqID, typically alphanumeric without spaces), and an optional description separated by spaces.
• The defline is immediately followed by one or more lines of sequence data, consisting of single-letter codes (e.g., A, C, G, T for DNA; A-Z for proteins). Sequence lines can be of arbitrary length but are conventionally 60-80 characters.
• Sequences are separated by the next defline or end-of-file.
• No file-level magic number, version, or metadata; validation is based on structure.
• Case-insensitive extension (.fa, .FA, .fasta, .fna for nucleotides, .faa for proteins).
• Whitespace and empty lines are ignored, but sequences should not contain numbers or special characters beyond the alphabet.
• Alphabet is context-dependent: DNA/RNA (A, C, G, T/U, N for ambiguous), Protein (20 standard amino acids + X for unknown).
• No checksums or compression in the base format (though files may be gzipped externally).

Sources for specs include NCBI documentation and Wikipedia.

1. List of all properties of this file format intrinsic to its file system:

• Text-based structure: The file is plain text with no binary encoding, relying on line-based parsing.
• Multi-sequence support: Can contain zero or more sequence entries.
• Definition line (defline): Starts with ">", followed by sequence identifier and optional description.
• Sequence identifier (SeqID): Mandatory alphanumeric string immediately after ">", no spaces.
• Description: Optional text following the SeqID on the defline, providing context (e.g., organism, gene name).
• Sequence data: One or more lines of single-letter codes representing the biological sequence.
• Line length flexibility: Sequence lines have no fixed length, but typically wrapped for readability.
• Alphabet validation: Characters must match DNA/RNA (A, C, G, T, U, N, -, etc.) or protein (A-Z, *, -) sets; invalid chars indicate errors.
• No file header/footer: No global metadata; properties are per-sequence.
• Whitespace tolerance: Leading/trailing spaces, empty lines ignored during parsing.
• Case sensitivity: Sequences are usually uppercase, but lowercase is allowed and often normalized.
• End-of-sequence: Implicitly ends at the next ">" or EOF.

These are the core structural properties; file system-level attributes (e.g., size, permissions) are not format-specific.

Two direct download links for files of format .FA:

• https://ilmn-dragen-giab-samples.s3.amazonaws.com/FASTA/hg38.fa (Human genome reference in FASTA format)
• http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa (GRCh38 human reference genome with decoys)

Ghost blog embedded HTML JavaScript for drag-and-drop .FA file dumper:

Drag and Drop .FA File to Dump Properties

1. Python class for .FA file handling:

import os

class FASTAHandler:
    def __init__(self, filepath):
        self.filepath = filepath
        self.sequences = []
        self.properties = {}

    def read_and_decode(self):
        with open(self.filepath, 'r') as f:
            content = f.read()
        lines = content.splitlines()
        current_seq = None
        for line in lines:
            line = line.strip()
            if line.startswith('>'):
                if current_seq:
                    self.sequences.append(current_seq)
                parts = line[1:].strip().split()
                current_seq = {
                    'seqID': parts[0],
                    'description': ' '.join(parts[1:]),
                    'sequence': '',
                    'length': 0,
                    'alphabet': 'unknown'
                }
            elif current_seq and line:
                current_seq['sequence'] += line
                current_seq['length'] += len(line)
        if current_seq:
            self.sequences.append(current_seq)

        # Infer alphabets
        for seq in self.sequences:
            seq_upper = seq['sequence'].upper()
            if all(c in 'ACGTN-' for c in seq_upper):
                seq['alphabet'] = 'DNA/RNA'
            elif all(c in 'ACDEFGHIKLMNPQRSTVWY*-' for c in seq_upper):
                seq['alphabet'] = 'Protein'

        # Set file properties
        self.properties = {
            'text_based': True,
            'multi_sequence': len(self.sequences) > 1,
            'num_sequences': len(self.sequences),
            'whitespace_tolerance': True,
            'case_sensitivity': 'flexible',
            'line_length_flexibility': True,
            'no_header_footer': True,
            'sequences': self.sequences
        }

    def print_properties(self):
        if not self.properties:
            print("No properties loaded. Call read_and_decode() first.")
            return
        print("File Properties:")
        print(f"- Text-based structure: {self.properties['text_based']}")
        print(f"- Multi-sequence support: {self.properties['multi_sequence']}")
        print(f"- Number of sequences: {self.properties['num_sequences']}")
        print(f"- Whitespace tolerance: {self.properties['whitespace_tolerance']}")
        print(f"- Case sensitivity: {self.properties['case_sensitivity']}")
        print(f"- Line length flexibility: {self.properties['line_length_flexibility']}")
        print(f"- No file header/footer: {self.properties['no_header_footer']}")
        for idx, seq in enumerate(self.properties['sequences'], 1):
            print(f"\nSequence {idx}:")
            print(f"  - Definition line: >{seq['seqID']} {seq['description']}")
            print(f"  - Sequence identifier: {seq['seqID']}")
            print(f"  - Description: {seq['description'] or 'None'}")
            print(f"  - Sequence data (first 50 chars): {seq['sequence'][:50]}...")
            print(f"  - Sequence length: {seq['length']}")
            print(f"  - Alphabet: {seq['alphabet']}")

    def write(self, output_path):
        if not self.sequences:
            print("No sequences to write.")
            return
        with open(output_path, 'w') as f:
            for seq in self.sequences:
                f.write(f">{seq['seqID']} {seq['description']}\n")
                # Wrap sequence to 80 chars per line
                for i in range(0, len(seq['sequence']), 80):
                    f.write(seq['sequence'][i:i+80] + '\n')

# Example usage:
# handler = FASTAHandler('example.fa')
# handler.read_and_decode()
# handler.print_properties()
# handler.write('output.fa')

1. Java class for .FA file handling:

import java.io.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

public class FASTAHandler {
    private String filepath;
    private List<Map<String, Object>> sequences;
    private Map<String, Object> properties;

    public FASTAHandler(String filepath) {
        this.filepath = filepath;
        this.sequences = new ArrayList<>();
        this.properties = new HashMap<>();
    }

    public void readAndDecode() throws IOException {
        StringBuilder content = new StringBuilder();
        try (BufferedReader reader = new BufferedReader(new FileReader(filepath))) {
            String line;
            while ((line = reader.readLine()) != null) {
                content.append(line).append("\n");
            }
        }
        String[] lines = content.toString().split("\n");
        Map<String, Object> currentSeq = null;
        for (String line : lines) {
            line = line.trim();
            if (line.startsWith(">")) {
                if (currentSeq != null) {
                    sequences.add(currentSeq);
                }
                String[] parts = line.substring(1).trim().split("\\s+");
                currentSeq = new HashMap<>();
                currentSeq.put("seqID", parts[0]);
                StringBuilder desc = new StringBuilder();
                for (int i = 1; i < parts.length; i++) {
                    desc.append(parts[i]).append(" ");
                }
                currentSeq.put("description", desc.toString().trim());
                currentSeq.put("sequence", "");
                currentSeq.put("length", 0);
                currentSeq.put("alphabet", "unknown");
            } else if (currentSeq != null && !line.isEmpty()) {
                String seq = (String) currentSeq.get("sequence") + line;
                currentSeq.put("sequence", seq);
                currentSeq.put("length", (int) currentSeq.get("length") + line.length());
            }
        }
        if (currentSeq != null) {
            sequences.add(currentSeq);
        }

        // Infer alphabets
        for (Map<String, Object> seq : sequences) {
            String seqStr = ((String) seq.get("sequence")).toUpperCase();
            if (seqStr.matches("^[ACGTN-]+$")) {
                seq.put("alphabet", "DNA/RNA");
            } else if (seqStr.matches("^[ACDEFGHIKLMNPQRSTVWY*-]+$")) {
                seq.put("alphabet", "Protein");
            }
        }

        // Set properties
        properties.put("text_based", true);
        properties.put("multi_sequence", sequences.size() > 1);
        properties.put("num_sequences", sequences.size());
        properties.put("whitespace_tolerance", true);
        properties.put("case_sensitivity", "flexible");
        properties.put("line_length_flexibility", true);
        properties.put("no_header_footer", true);
        properties.put("sequences", sequences);
    }

    public void printProperties() {
        if (properties.isEmpty()) {
            System.out.println("No properties loaded. Call readAndDecode() first.");
            return;
        }
        System.out.println("File Properties:");
        System.out.println("- Text-based structure: " + properties.get("text_based"));
        System.out.println("- Multi-sequence support: " + properties.get("multi_sequence"));
        System.out.println("- Number of sequences: " + properties.get("num_sequences"));
        System.out.println("- Whitespace tolerance: " + properties.get("whitespace_tolerance"));
        System.out.println("- Case sensitivity: " + properties.get("case_sensitivity"));
        System.out.println("- Line length flexibility: " + properties.get("line_length_flexibility"));
        System.out.println("- No file header/footer: " + properties.get("no_header_footer"));
        @SuppressWarnings("unchecked")
        List<Map<String, Object>> seqs = (List<Map<String, Object>>) properties.get("sequences");
        for (int i = 0; i < seqs.size(); i++) {
            Map<String, Object> seq = seqs.get(i);
            System.out.println("\nSequence " + (i + 1) + ":");
            System.out.println("  - Definition line: >" + seq.get("seqID") + " " + seq.get("description"));
            System.out.println("  - Sequence identifier: " + seq.get("seqID"));
            System.out.println("  - Description: " + (seq.get("description").toString().isEmpty() ? "None" : seq.get("description")));
            String seqData = (String) seq.get("sequence");
            System.out.println("  - Sequence data (first 50 chars): " + (seqData.length() > 50 ? seqData.substring(0, 50) + "..." : seqData));
            System.out.println("  - Sequence length: " + seq.get("length"));
            System.out.println("  - Alphabet: " + seq.get("alphabet"));
        }
    }

    public void write(String outputPath) throws IOException {
        if (sequences.isEmpty()) {
            System.out.println("No sequences to write.");
            return;
        }
        try (BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath))) {
            for (Map<String, Object> seq : sequences) {
                writer.write(">" + seq.get("seqID") + " " + seq.get("description") + "\n");
                String seqStr = (String) seq.get("sequence");
                for (int j = 0; j < seqStr.length(); j += 80) {
                    writer.write(seqStr.substring(j, Math.min(j + 80, seqStr.length())) + "\n");
                }
            }
        }
    }

    // Example usage:
    // public static void main(String[] args) throws IOException {
    //     FASTAHandler handler = new FASTAHandler("example.fa");
    //     handler.readAndDecode();
    //     handler.printProperties();
    //     handler.write("output.fa");
    // }
}

1. JavaScript class for .FA file handling:

class FASTAHandler {
    constructor(filepath) {
        this.filepath = filepath;
        this.sequences = [];
        this.properties = {};
    }

    async readAndDecode() {
        // Note: In Node.js, use fs module; this assumes Node environment
        const fs = require('fs');
        const content = fs.readFileSync(this.filepath, 'utf8');
        const lines = content.split('\n');
        let currentSeq = null;
        lines.forEach(line => {
            line = line.trim();
            if (line.startsWith('>')) {
                if (currentSeq) this.sequences.push(currentSeq);
                const parts = line.slice(1).trim().split(/\s+/);
                currentSeq = {
                    seqID: parts[0],
                    description: parts.slice(1).join(' '),
                    sequence: '',
                    length: 0,
                    alphabet: 'unknown'
                };
            } else if (currentSeq && line) {
                currentSeq.sequence += line;
                currentSeq.length += line.length;
            }
        });
        if (currentSeq) this.sequences.push(currentSeq);

        // Infer alphabets
        this.sequences.forEach(seq => {
            const seqUpper = seq.sequence.toUpperCase();
            if (/^[ACGTN-]+$/.test(seqUpper)) seq.alphabet = 'DNA/RNA';
            else if (/^[ACDEFGHIKLMNPQRSTVWY*-]+$/.test(seqUpper)) seq.alphabet = 'Protein';
        });

        // Set properties
        this.properties = {
            text_based: true,
            multi_sequence: this.sequences.length > 1,
            num_sequences: this.sequences.length,
            whitespace_tolerance: true,
            case_sensitivity: 'flexible',
            line_length_flexibility: true,
            no_header_footer: true,
            sequences: this.sequences
        };
    }

    printProperties() {
        if (Object.keys(this.properties).length === 0) {
            console.log('No properties loaded. Call readAndDecode() first.');
            return;
        }
        console.log('File Properties:');
        console.log(`- Text-based structure: ${this.properties.text_based}`);
        console.log(`- Multi-sequence support: ${this.properties.multi_sequence}`);
        console.log(`- Number of sequences: ${this.properties.num_sequences}`);
        console.log(`- Whitespace tolerance: ${this.properties.whitespace_tolerance}`);
        console.log(`- Case sensitivity: ${this.properties.case_sensitivity}`);
        console.log(`- Line length flexibility: ${this.properties.line_length_flexibility}`);
        console.log(`- No file header/footer: ${this.properties.no_header_footer}`);
        this.properties.sequences.forEach((seq, index) => {
            console.log(`\nSequence ${index + 1}:`);
            console.log(`  - Definition line: >${seq.seqID} ${seq.description}`);
            console.log(`  - Sequence identifier: ${seq.seqID}`);
            console.log(`  - Description: ${seq.description || 'None'}`);
            console.log(`  - Sequence data (first 50 chars): ${seq.sequence.substring(0, 50)}...`);
            console.log(`  - Sequence length: ${seq.length}`);
            console.log(`  - Alphabet: ${seq.alphabet}`);
        });
    }

    write(outputPath) {
        if (this.sequences.length === 0) {
            console.log('No sequences to write.');
            return;
        }
        const fs = require('fs');
        let output = '';
        this.sequences.forEach(seq => {
            output += `>${seq.seqID} ${seq.description}\n`;
            for (let i = 0; i < seq.sequence.length; i += 80) {
                output += seq.sequence.substring(i, i + 80) + '\n';
            }
        });
        fs.writeFileSync(outputPath, output);
    }
}

// Example usage in Node.js:
// const handler = new FASTAHandler('example.fa');
// await handler.readAndDecode();
// handler.printProperties();
// handler.write('output.fa');

1. C class (using C++ for class support) for .FA file handling:

#include <iostream>
#include <fstream>
#include <vector>
#include <string>
#include <regex>
#include <map>

class FASTAHandler {
private:
    std::string filepath;
    std::vector<std::map<std::string, std::string>> sequences;
    std::map<std::string, std::string> properties;

public:
    FASTAHandler(const std::string& fp) : filepath(fp) {}

    void readAndDecode() {
        std::ifstream file(filepath);
        if (!file.is_open()) {
            std::cerr << "Error opening file: " << filepath << std::endl;
            return;
        }
        std::string line, currentSeqID, currentDesc, currentSequence;
        while (std::getline(file, line)) {
            line.erase(0, line.find_first_not_of(" \t")); // Trim leading whitespace
            line.erase(line.find_last_not_of(" \t") + 1); // Trim trailing
            if (line.empty()) continue;
            if (line[0] == '>') {
                if (!currentSeqID.empty()) {
                    addSequence(currentSeqID, currentDesc, currentSequence);
                }
                size_t spacePos = line.find(' ', 1);
                if (spacePos != std::string::npos) {
                    currentSeqID = line.substr(1, spacePos - 1);
                    currentDesc = line.substr(spacePos + 1);
                } else {
                    currentSeqID = line.substr(1);
                    currentDesc = "";
                }
                currentSequence = "";
            } else {
                currentSequence += line;
            }
        }
        if (!currentSeqID.empty()) {
            addSequence(currentSeqID, currentDesc, currentSequence);
        }
        file.close();

        // Set properties
        properties["text_based"] = "true";
        properties["multi_sequence"] = (sequences.size() > 1 ? "true" : "false");
        properties["num_sequences"] = std::to_string(sequences.size());
        properties["whitespace_tolerance"] = "true";
        properties["case_sensitivity"] = "flexible";
        properties["line_length_flexibility"] = "true";
        properties["no_header_footer"] = "true";
    }

private:
    void addSequence(const std::string& id, const std::string& desc, const std::string& seq) {
        std::map<std::string, std::string> seqMap;
        seqMap["seqID"] = id;
        seqMap["description"] = desc;
        seqMap["sequence"] = seq;
        seqMap["length"] = std::to_string(seq.length());
        std::string seqUpper = seq;
        std::transform(seqUpper.begin(), seqUpper.end(), seqUpper.begin(), ::toupper);
        if (std::regex_match(seqUpper, std::regex("^[ACGTN-]+$"))) {
            seqMap["alphabet"] = "DNA/RNA";
        } else if (std::regex_match(seqUpper, std::regex("^[ACDEFGHIKLMNPQRSTVWY*-]+$"))) {
            seqMap["alphabet"] = "Protein";
        } else {
            seqMap["alphabet"] = "unknown";
        }
        sequences.push_back(seqMap);
    }

public:
    void printProperties() const {
        if (properties.empty()) {
            std::cout << "No properties loaded. Call readAndDecode() first." << std::endl;
            return;
        }
        std::cout << "File Properties:" << std::endl;
        std::cout << "- Text-based structure: " << properties.at("text_based") << std::endl;
        std::cout << "- Multi-sequence support: " << properties.at("multi_sequence") << std::endl;
        std::cout << "- Number of sequences: " << properties.at("num_sequences") << std::endl;
        std::cout << "- Whitespace tolerance: " << properties.at("whitespace_tolerance") << std::endl;
        std::cout << "- Case sensitivity: " << properties.at("case_sensitivity") << std::endl;
        std::cout << "- Line length flexibility: " << properties.at("line_length_flexibility") << std::endl;
        std::cout << "- No file header/footer: " << properties.at("no_header_footer") << std::endl;
        for (size_t i = 0; i < sequences.size(); ++i) {
            const auto& seq = sequences[i];
            std::cout << "\nSequence " << (i + 1) << ":" << std::endl;
            std::cout << "  - Definition line: >" << seq.at("seqID") << " " << seq.at("description") << std::endl;
            std::cout << "  - Sequence identifier: " << seq.at("seqID") << std::endl;
            std::cout << "  - Description: " << (seq.at("description").empty() ? "None" : seq.at("description")) << std::endl;
            std::string seqData = seq.at("sequence");
            std::cout << "  - Sequence data (first 50 chars): " << (seqData.length() > 50 ? seqData.substr(0, 50) + "..." : seqData) << std::endl;
            std::cout << "  - Sequence length: " << seq.at("length") << std::endl;
            std::cout << "  - Alphabet: " << seq.at("alphabet") << std::endl;
        }
    }

    void write(const std::string& outputPath) const {
        if (sequences.empty()) {
            std::cout << "No sequences to write." << std::endl;
            return;
        }
        std::ofstream outFile(outputPath);
        if (!outFile.is_open()) {
            std::cerr << "Error opening output file: " << outputPath << std::endl;
            return;
        }
        for (const auto& seq : sequences) {
            outFile << ">" << seq.at("seqID") << " " << seq.at("description") << "\n";
            std::string seqStr = seq.at("sequence");
            for (size_t j = 0; j < seqStr.length(); j += 80) {
                outFile << seqStr.substr(j, 80) << "\n";
            }
        }
        outFile.close();
    }
};

// Example usage:
// int main() {
//     FASTAHandler handler("example.fa");
//     handler.readAndDecode();
//     handler.printProperties();
//     handler.write("output.fa");
//     return 0;
// }