Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

      Latest Articles

      Collapse

      • seqadmin
        Essential Discoveries and Tools in Epitranscriptomics
        by seqadmin




        The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
        04-22-2024, 07:01 AM
      • seqadmin
        Current Approaches to Protein Sequencing
        by seqadmin


        Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
        04-04-2024, 04:25 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Today, 08:47 AM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-11-2024, 12:08 PM
      0 responses
      60 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 10:19 PM
      0 responses
      59 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 09:21 AM
      0 responses
      54 views
      0 likes
      Last Post seqadmin  
      Working...
      X