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  • get DNA sequence through UCSC DAS server

    Hi All,

    I am trying out the perl code from UCSC help desk posted on biostar to retrieve DNA sequence from UCSC DAS server. After run this script, I didn't get any sequence at all. Could someone have a quick look and point out what might be wrong?

    Many thanks!

    Stuart
    ****************************

    zzong@bugaboo:~/programming> cat retrieve_dna_from_ucsc.pl
    use strict;
    use Bio::das; #actually Das

    #### USAGE
    unless(@ARGV == 2) {
    die("USAGE: $0 | Input BED file | Output FASTA file\n\n");
    }

    #### Access files
    open(INPUT, "<$ARGV[0]") or die("Could not open input!\n");
    open(OUTPUT, ">$ARGV[1]") or die("Could not open output!\n");

    #### DAS db
    my $das = Bio::das->new(-source => 'http://genome.cse.ucsc.edu/cgi-bin/das/', -dsn=>'hg19');

    #### Line counter
    my $count = 0;

    #### Work thru each line of BED file
    while(defined(my $line = <INPUT>)) {
    #### Make sure line begins with chr
    unless($line =~ /^chr/) { next }

    #### Count lines
    $count++;
    print "1$count $line\n";

    #### Split line
    my ($chr, $start, $end, $label) = '';
    my @line_bits = ();

    @line_bits = split(/\t/, $line);

    $chr = $line_bits[0];
    $start = $line_bits[1];
    $end = $line_bits[2];
    $label = $line_bits[3];
    chomp($label);

    #### Define segment of genome
    my $segment = $das->segment("$chr\:$start\,$end");

    #### Get DNA
    my $dna = $segment->dna;

    #### Print sequence to output
    print OUTPUT "\>$chr:$start-$end\_$label\n$dna\n";
    }

    #### Close files
    close(INPUT);
    close(OUTPUT);

    exit;

    *******************
    Last edited by [email protected]; 05-24-2013, 04:04 PM.

  • #2
    get DNA sequence through UCSC DAS server

    Did you get any error messages when you ran the script?

    Comment


    • #3
      I figured this out. Minor code changes. The only thing needs to keep in mind is that the input file needs to be tab delimited and every line starts with "chr***.

      Regards!

      Stuart

      **********************

      use strict;
      use Bio:as;

      #### USAGE
      unless(@ARGV == 2) {
      die("USAGE: $0 Input BED file Output FASTA file\n\n");
      }

      #### Access files
      open(INPUT, "<$ARGV[0]") or die("Could not open input!\n");
      open(OUTPUT, ">$ARGV[1]") or die("Could not open output!\n");

      #### DAS db

      #my $das = Bio:as->new(-source => 'http://genome.cse.ucsc.edu/cgi-bin/das/', -dsn=>'hg19');
      my $das = Bio:as->new(-source => 'http://genome.ucsc.edu/cgi-bin/das/', -dsn=>'hg19');
      #### Line counter
      my $count = 0;

      #### Work thru each line of BED file
      while(defined(my $line = <INPUT>)) {
      #### Make sure line begins with chr
      unless($line =~ /^chr/) { next }

      #### Count lines
      $count++;

      #print "1$count $line\n";
      print "$count $line\n";
      #### Split line
      my ($chr, $start, $end, $label) = '';
      my @line_bits = ();

      @line_bits = split(/\t/, $line);

      $chr = $line_bits[0];
      $start = $line_bits[1];
      $end = $line_bits[2];
      $label = $line_bits[3];
      chomp($label);

      # print "$chr is","$start is","$end is", "$label is";
      #### Define segment of genome
      my $segment = $das->segment("$chr\:$start\,$end");
      #print $segment;
      #### Get DNA
      my $dna = $segment->dna;
      #print $dna;
      #### Print sequence to output
      print OUTPUT "\>$chr:$start-$end\_$label\n$dna\n";
      #print OUTPUT "\>$chr:$start-$end\_$label\n";
      }

      #### Close files
      close(INPUT);
      close(OUTPUT);

      exit;

      Comment

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