One-line solution

ruby -e 'first_line = true; while line = STDIN.gets; line.chomp!; if line =~ /^>/; puts unless first_line; print line[1..-1]; print ","; else; print line; end; first_line = false; end; puts' < s001.fasta

Simple script

Here is a Ruby script that does this:

#!/usr/bin/ruby

first_line = true

while line = STDIN.gets
  line.chomp!

  if line =~ /^>/
    puts unless first_line
    print line[1..-1]
    print ","  # <-- Change this to "\t" and it's a convert-fasta-to-tab
  else
    print line
  end

  first_line = false
end
puts

1. Just save it to a file.
2. Name the file convert-fasta-to-csv
3. to make it executable, run chmod +x ./convert-fasta-to-csv

Usage

./convert-fasta-to-csv < f001.fasta > f001.fasta.csv

To do it in batch run all .fasta files in current folder:

for i in *.fasta; do ./convert-fasta-to-csv < $i > $i.csv; done

System Requirements

You probably already have Ruby but it may not always be installed by default.

• To install it on Ubuntu or Debian run: sudo apt-get install ruby
• On RedHat or CentOS, run: sudo yum install ruby
• On Windows, install from http://rubyinstaller.org/
• On Mac, you already have it (it's a part of the operating system).

I always thought the Scriptome project was a really cool idea, but it doesn't seem to have been updated in a while.

However, there might be some nuggets you could glean from this about how to structure a little script:

http://sysbio.harvard.edu/csb/resources/computational/scriptome/Windows/Tools/Change.html

Use your text editor's regexp search-and-replace feature.

Vim

In Vim, press Esc (normal mode) and paste the following sequence of commands:

:0,$s/>\(.*\)\n/>\1,/
:0,$s/\(.*\)\n\([^>]\)/\1\2/
:0,$s/^>//

And press Enter.

One-line Solution

input_file=001.fasta; vim -c '0,$s/>\(.*\)\n/>\1,/' -c '0,$s/\(.*\)\n\([^>]\)/\1\2/' -c 'w! alex-tmp.fasta.csv' -c 'q!'  $input_file; mv alex-tmp.fasta.csv $input_file.csv

Have a look at BioSql and the howto on bioperl for Open Biological Data Access for which it is a subset of. It does take a bit of figuring out, but once you do the biogetseq.pl script is very useful and can load both local and remote data sources.

In the spirit of other one-line solutions, here's the (almost) inevitable perl version:

perl -e '$/=">"; while(<STDIN>) { next if length == 1; @x=split /\n/; printf "$x[0],$x[1]\n" } ' < your_sequence_file.fasta

I imagine it could be shorter still...

Late to the party but here is my implementation in C#:

using System;
using System.Collections.Generic;
using System.Text;
using System.IO;

namespace ConvertFASTA
{
    class fasta
    {
        static void Main(string[] args)
        {
            StreamWriter writer = new StreamWriter(args[1]);

            using (StreamReader reader = new StreamReader(args[0]))
            {
                string temp= "", line= "";
                bool firstLine = true;

                while ((line = reader.ReadLine()) != null)
                {
                    line = line.Replace("|", ",");
                    if (line.Substring(0, 1) != ">")
                    {
                        temp = line;
                    }
                    else
                    {
                        if (firstLine) temp = line + ",";
                        else temp = "\n" + line + ",";
                    }

                    firstLine = false;
                    writer.Write(temp,true);
                }
            }

            writer.Dispose();
            writer.Close();
        }
    }
}

Compile and use like this

fasta.exe input.fa output