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  • Solexa data to fasta

    For the EULER-SR program a read.fasta file is needed with all the short reads of the solexa run in fasta format.

    Does anyone have a small script or program to do so?

    Thanks,
    JD

  • #2
    This small perl script will take a Solexa seq file and convert to FASTA.

    Code:
    #!/usr/bin/perl -w
    use strict;
    while (<ARGV>) {
      my @x = split m/:/;
      next unless @x == 7;
      print ">", join(':', @x[0..4]), "\n", $x[5],"\n";
    }

    Comment


    • #3
      Hi Torst,
      I just try the script, it can't work d?

      Comment


      • #4
        That script is intended to be used with stdout/stdin, e.g. assuming you saved this script as a file called script_name.pl, and using $ to represent the command prompt:

        $ perl script_name.pl < example.fastq > example.fasta

        If you mark the script as executable (not applicable to Windows), then just:

        $ ./script_name.pl < example.fastq > example.fasta

        If you want a Python version, try something based on this cookbook recipe:


        e.g. With Biopython 1.52 or later:

        Code:
        import sys
        from Bio import SeqIO
        SeqIO.convert(sys.stdin, "fastq-solexa", sys.stdout, "fasta")

        Comment


        • #5
          Thanks a lot, maudp.
          I will try it again later.
          See how is the output result.
          Thanks for your help again

          Comment

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