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  • Need my reference sequence to be in a specific format

    I need my reference genome (S. cerevisiae strain S288c) to be in a specific format for some analysis but can't find anything matching what I need online.

    i.e. the data I have is in this format:
    >I [org=Saccharomyces cerevisiae] [strain=S288C] [chromosome=I]
    CCACACCACACCCACACACCCAC...etc

    But I need it to be in a table like:

    chr pos seq
    1 1 C
    1 2 C
    1 3 A
    1 4 C
    etc.

    I'm hoping that one of the following will be true, please let me know if you can help... Thanks!
    1. The data already exists somewhere online
    2. There's a program that can make this file for me out of my reference sequence (possibly PySAMstats?)
    3. Some hints to write my own R script to make the file?
    Last edited by mcrawford; 09-22-2015, 07:53 AM.

  • #2
    There will always be cooler ways of doing this. What follows happens to be one way. I am assuming chromosome 1 is followed by 2 etc in the genome file.
    Use at your own risk

    Save the code below in a file (e.g. table.pl).

    Code:
    use strict;
    use warnings;
    
    my $datafile = $ARGV[0];
    my $outfile = $ARGV[1];
    
    open (IN, $datafile) or die "can't open the datafile: $datafile\n";
    open (OUT, ">$outfile") or die "can't open the outputfile: $outfile\n";
    
    my $count = 1;
    my $chrom = 0;
    
    while(my $line = <IN>){
            if ($line =~ /^>/){
                    $chrom++;
                    $count = 1;
                    }
            else {
                    chomp $line;
                    my @nuc = split(//, $line);
                    while (@nuc){
                            my $a = pop(@nuc);
                            print OUT $chrom." ".$count." ".$a."\n";
                            $count++;
                            }
                    }
    
    }
    close IN;
    close OUT;
    Run like this

    Code:
    $ perl table.pl genome.fa table.txt

    Comment


    • #3
      Originally posted by GenoMax View Post
      There will always be cooler ways of doing this. What follows happens to be one way. I am assuming chromosome 1 is followed by 2 etc in the genome file.
      Use at your own risk
      Thanks so much GenoMax, this worked perfectly and produced exactly what I wanted! You're the best

      Comment

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