Fasta File Vs Fa File: Merging and Conversion

Introduction

FASTA files (.fasta, .fa, .fsa) are commonly used in bioinformatics to store nucleotide or protein sequences. The .fa extension is just a shorthand for .fasta, and both formats are identical in structure. Below, we will discuss how to merge multiple .fa files into a single .fasta file and how to handle sequence headers during the process.

Step-by-Step Instructions

1. Download .fa Files from UCSC

If you are downloading chromosome-specific .fa files from UCSC, you can use wget to fetch them. For example:

URL=http://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/
for chrom in {1..22} X Y M; do
    wget ${URL}/chr${chrom}.fa.gz
done

This will download all human chromosomes (1-22, X, Y, and mitochondrial).

2. Uncompress .fa.gz Files

The downloaded files are compressed. Use gunzip to decompress them:

gunzip *.fa.gz

3. Merge .fa Files into a Single .fasta File

To concatenate all .fa files into a single .fasta file, use the cat command:

cat *.fa > merged_genome.fasta

This will combine all sequences into one file, preserving the headers.

4. Handling Headers

If you want to merge files but ensure only one header is retained, you can use sed to remove headers from all files except the first:

sed -s '1{/^>/!d;}' *.fa > merged_genome.fasta

This command keeps the first header and removes all others.

5. Convert .fa to .fasta (if needed)

Since .fa and .fasta are the same format, no conversion is necessary. However, if you need to manipulate the file (e.g., extract specific sequences), you can use tools like Biopython in Python.

Example Scripts

Python (Biopython)

To extract a specific sequence from a multi-FASTA file:

from Bio import SeqIO

def extract_sequence(fasta_file, sequence_id):
    with open(fasta_file) as f:
        for record in SeqIO.parse(f, "fasta"):
            if record.id == sequence_id:
                print(f">{record.id}\n{record.seq}")

# Usage
extract_sequence("merged_genome.fasta", "chr1")

Install Biopython if not already installed:

pip install biopython

Perl

To merge .fa files and clean up headers:

use strict;
use warnings;

open(my $out, '>', 'merged_genome.fasta') or die "Could not open file: $!";
my $first_file = 1;

foreach my $file (glob("*.fa")) {
    open(my $in, '<', $file) or die "Could not open file: $!";
    while (<$in>) {
        if ($_ =~ /^>/) {
            if ($first_file) {
                $first_file = 0;
            } else {
                next;
            }
        }
        print $out $_;
    }
    close($in);
}
close($out);

R

To read and manipulate FASTA files in R:

library(seqinr)

# Read a FASTA file
sequences <- read.fasta("merged_genome.fasta")

# Extract a specific sequence
sequence_chr1 <- sequences$chr1
cat(">chr1\n", sequence_chr1, "\n")

Online Tools and Software

1. UCSC Genome Browser: Download .fa files directly.
2. BioPython: For scripting and sequence manipulation.
3. SeqKit: A cross-platform tool for FASTA/Q file manipulation.
   • Install: conda install -c bioconda seqkit
   • Merge files: seqkit concat *.fa -o merged_genome.fasta
4. Galaxy: A web-based platform for bioinformatics analysis, including FASTA manipulation.

Summary

• .fa and .fasta files are identical in format.
• Use cat to merge .fa files into a single .fasta file.
• Use sed, Biopython, or Perl to handle headers during merging.
• No conversion is needed between .fa and .fasta.

By following these steps, you can efficiently merge and manipulate FASTA files for your bioinformatics workflows.