Task 212: .FAA File Format
Task 212: .FAA File Format
.FAA File Format Specifications
The .FAA file format is a text-based FASTA format specifically used for representing amino acid (protein) sequences in bioinformatics. It follows the general FASTA specification, where sequences are stored in plain text. The format originated from the FASTA program by William Pearson and has no formal version number or magic bytes for identification; it's recognized by its structure starting with a '>' character for definition lines. Unlike binary formats, it lacks embedded metadata like checksums or headers beyond the definition lines. Files can contain one or multiple sequences.
1. List of Properties Intrinsic to the File Format
Based on the FASTA specification for .FAA files, the intrinsic properties (structural elements inherent to the format's design and not dependent on external file system attributes like size or timestamps) are:
- Definition Line (Defline): Each sequence begins with a line starting with '>', followed by an identifier (unique code, typically until the first space) and an optional description (remaining text on the line).
- Sequence Data: One or more lines immediately following the defline, containing the amino acid sequence in single-letter codes (e.g., A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y; may include ambiguities like B, X, Z or gaps '-'). Lines are typically 60-80 characters long, but this is conventional, not enforced.
- Multi-Sequence Support: The file can contain multiple sequence entries, separated by new deflines.
- Text Encoding: ASCII or UTF-8 compatible, with no binary data.
- Line Endings: Platform-agnostic (Unix LF or Windows CRLF), but consistent within the file.
- No Fixed Header or Footer: No global file-level metadata; identification relies on the presence of '>' lines and valid amino acid characters.
These properties define the parseable content. Derived properties (e.g., sequence length, composition) can be calculated but are not intrinsic storage elements.
2. Two Direct Download Links for .FAA Files
Here are two direct FTP download links to example .FAA files (gzipped, as commonly distributed; unzip to get the plain .faa file) from NCBI RefSeq assemblies for E. coli strains:
- ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_protein.faa.gz (E. coli str. K-12 substr. MG1655 protein sequences).
- ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/249/815/GCF_000249815.1_ASM24981v2/GCF_000249815.1_ASM24981v2_protein.faa.gz (E. coli O157:H7 str. Sakai protein sequences).
3. Ghost Blog Embedded HTML/JavaScript for Drag-and-Drop .FAA File Dump
This is a self-contained HTML page with embedded JavaScript. It allows dragging and dropping a .FAA file, parses it, and dumps the properties (identifier, description, sequence for each entry) to the screen in a pre-formatted block. Save as an .html file and open in a browser.
Drag and Drop .FAA File
Drop .FAA file here
4. Python Class for .FAA File Handling
This Python class FaaFile can open, decode (parse), read, write, and print the properties to console.
import os
class FaaFile:
def __init__(self, filepath=None):
self.filepath = filepath
self.sequences = [] # List of dicts: {'identifier': str, 'description': str, 'sequence': str}
def read(self, filepath=None):
if filepath:
self.filepath = filepath
if not self.filepath or not os.path.exists(self.filepath):
raise FileNotFoundError("File not found.")
with open(self.filepath, 'r') as f:
content = f.read()
self.sequences = self._parse(content)
def _parse(self, content):
lines = content.splitlines()
sequences = []
current_seq = None
for line in lines:
if line.startswith('>'):
if current_seq:
sequences.append(current_seq)
defline = line[1:].strip()
parts = defline.split(maxsplit=1)
identifier = parts[0] if parts else ''
description = parts[1] if len(parts) > 1 else ''
current_seq = {'identifier': identifier, 'description': description, 'sequence': ''}
elif current_seq:
current_seq['sequence'] += line.strip()
if current_seq:
sequences.append(current_seq)
return sequences
def print_properties(self):
if not self.sequences:
print("No sequences loaded.")
return
for idx, seq in enumerate(self.sequences, 1):
print(f"Sequence {idx}:")
print(f" Identifier: {seq['identifier']}")
print(f" Description: {seq['description']}")
print(f" Sequence: {seq['sequence']}")
print()
def write(self, filepath=None, sequences=None):
if sequences:
self.sequences = sequences
if not self.sequences:
raise ValueError("No sequences to write.")
if filepath:
self.filepath = filepath
if not self.filepath:
raise ValueError("No filepath specified.")
with open(self.filepath, 'w') as f:
for seq in self.sequences:
defline = f">{seq['identifier']} {seq['description']}\n"
f.write(defline)
# Write sequence in chunks of 80 chars
sequence = seq['sequence']
for i in range(0, len(sequence), 80):
f.write(sequence[i:i+80] + '\n')
# Example usage:
# faa = FaaFile('example.faa')
# faa.read()
# faa.print_properties()
# faa.write('output.faa')
5. Java Class for .FAA File Handling
This Java class FaaFile can open, decode (parse), read, write, and print the properties to console. Compile and run with Java.
import java.io.*;
import java.util.ArrayList;
import java.util.List;
public class FaaFile {
private String filepath;
private List<Sequence> sequences = new ArrayList<>();
static class Sequence {
String identifier;
String description;
String sequence;
Sequence(String id, String desc, String seq) {
identifier = id;
description = desc;
sequence = seq;
}
}
public FaaFile(String filepath) {
this.filepath = filepath;
}
public void read() throws IOException {
sequences.clear();
try (BufferedReader reader = new BufferedReader(new FileReader(filepath))) {
String line;
Sequence currentSeq = null;
StringBuilder seqBuilder = new StringBuilder();
while ((line = reader.readLine()) != null) {
if (line.startsWith(">")) {
if (currentSeq != null) {
currentSeq.sequence = seqBuilder.toString();
sequences.add(currentSeq);
seqBuilder.setLength(0);
}
String defline = line.substring(1).trim();
String[] parts = defline.split("\\s+", 2);
String id = parts.length > 0 ? parts[0] : "";
String desc = parts.length > 1 ? parts[1] : "";
currentSeq = new Sequence(id, desc, "");
} else if (currentSeq != null) {
seqBuilder.append(line.trim());
}
}
if (currentSeq != null) {
currentSeq.sequence = seqBuilder.toString();
sequences.add(currentSeq);
}
}
}
public void printProperties() {
if (sequences.isEmpty()) {
System.out.println("No sequences loaded.");
return;
}
for (int i = 0; i < sequences.size(); i++) {
Sequence seq = sequences.get(i);
System.out.println("Sequence " + (i + 1) + ":");
System.out.println(" Identifier: " + seq.identifier);
System.out.println(" Description: " + seq.description);
System.out.println(" Sequence: " + seq.sequence);
System.out.println();
}
}
public void write(String outputPath) throws IOException {
try (BufferedWriter writer = new BufferedWriter(new FileWriter(outputPath))) {
for (Sequence seq : sequences) {
writer.write(">" + seq.identifier + " " + seq.description + "\n");
String sequence = seq.sequence;
for (int j = 0; j < sequence.length(); j += 80) {
writer.write(sequence.substring(j, Math.min(j + 80, sequence.length())) + "\n");
}
}
}
}
// Example usage:
// public static void main(String[] args) throws IOException {
// FaaFile faa = new FaaFile("example.faa");
// faa.read();
// faa.printProperties();
// faa.write("output.faa");
// }
}
6. JavaScript Class for .FAA File Handling
This JavaScript class FaaFile is for Node.js (requires fs module). It can open, decode (parse), read, write, and print the properties to console.
const fs = require('fs');
class FaaFile {
constructor(filepath = null) {
this.filepath = filepath;
this.sequences = []; // Array of {identifier, description, sequence}
}
read(filepath = null) {
if (filepath) this.filepath = filepath;
if (!this.filepath || !fs.existsSync(this.filepath)) {
throw new Error('File not found.');
}
const content = fs.readFileSync(this.filepath, 'utf8');
this.sequences = this._parse(content);
}
_parse(content) {
const lines = content.split(/\r?\n/);
const sequences = [];
let currentSeq = null;
lines.forEach(line => {
if (line.startsWith('>')) {
if (currentSeq) sequences.push(currentSeq);
const defline = line.slice(1).trim();
const parts = defline.split(/\s+/);
const identifier = parts.shift() || '';
const description = parts.join(' ') || '';
currentSeq = { identifier, description, sequence: '' };
} else if (currentSeq) {
currentSeq.sequence += line.trim();
}
});
if (currentSeq) sequences.push(currentSeq);
return sequences;
}
printProperties() {
if (!this.sequences.length) {
console.log('No sequences loaded.');
return;
}
this.sequences.forEach((seq, index) => {
console.log(`Sequence ${index + 1}:`);
console.log(` Identifier: ${seq.identifier}`);
console.log(` Description: ${seq.description}`);
console.log(` Sequence: ${seq.sequence}`);
console.log('');
});
}
write(filepath = null, sequences = null) {
if (sequences) this.sequences = sequences;
if (!this.sequences.length) {
throw new Error('No sequences to write.');
}
if (filepath) this.filepath = filepath;
if (!this.filepath) {
throw new Error('No filepath specified.');
}
let output = '';
this.sequences.forEach(seq => {
output += `>${seq.identifier} ${seq.description}\n`;
const sequence = seq.sequence;
for (let i = 0; i < sequence.length; i += 80) {
output += sequence.slice(i, i + 80) + '\n';
}
});
fs.writeFileSync(this.filepath, output);
}
}
// Example usage:
// const faa = new FaaFile('example.faa');
// faa.read();
// faa.printProperties();
// faa.write('output.faa');
7. C++ Class for .FAA File Handling
This C++ class FaaFile can open, decode (parse), read, write, and print the properties to console. Compile with g++ -o faa_handler faa_handler.cpp (assuming file name faa_handler.cpp).
#include <iostream>
#include <fstream>
#include <vector>
#include <string>
#include <sstream>
struct Sequence {
std::string identifier;
std::string description;
std::string sequence;
};
class FaaFile {
private:
std::string filepath;
std::vector<Sequence> sequences;
public:
FaaFile(const std::string& fp = "") : filepath(fp) {}
void read(const std::string& fp = "") {
if (!fp.empty()) filepath = fp;
std::ifstream file(filepath);
if (!file.is_open()) {
std::cerr << "File not found." << std::endl;
return;
}
sequences.clear();
std::string line;
Sequence currentSeq;
std::string seqBuffer;
bool inSequence = false;
while (std::getline(file, line)) {
if (line[0] == '>') {
if (inSequence) {
currentSeq.sequence = seqBuffer;
sequences.push_back(currentSeq);
seqBuffer.clear();
}
std::string defline = line.substr(1);
std::istringstream iss(defline);
iss >> currentSeq.identifier;
std::getline(iss, currentSeq.description);
currentSeq.description = currentSeq.description.substr(1); // Remove leading space
inSequence = true;
} else if (inSequence) {
seqBuffer += line;
}
}
if (inSequence) {
currentSeq.sequence = seqBuffer;
sequences.push_back(currentSeq);
}
file.close();
}
void printProperties() const {
if (sequences.empty()) {
std::cout << "No sequences loaded." << std::endl;
return;
}
for (size_t i = 0; i < sequences.size(); ++i) {
std::cout << "Sequence " << (i + 1) << ":" << std::endl;
std::cout << " Identifier: " << sequences[i].identifier << std::endl;
std::cout << " Description: " << sequences[i].description << std::endl;
std::cout << " Sequence: " << sequences[i].sequence << std::endl;
std::cout << std::endl;
}
}
void write(const std::string& outputPath) const {
std::ofstream file(outputPath);
if (!file.is_open()) {
std::cerr << "Could not open file for writing." << std::endl;
return;
}
for (const auto& seq : sequences) {
file << ">" << seq.identifier << " " << seq.description << "\n";
const std::string& sequence = seq.sequence;
for (size_t j = 0; j < sequence.length(); j += 80) {
file << sequence.substr(j, 80) << "\n";
}
}
file.close();
}
};
// Example usage:
// int main() {
// FaaFile faa("example.faa");
// faa.read();
// faa.printProperties();
// faa.write("output.faa");
// return 0;
// }