Dear all,

I am working with biological sequence data and I have a need to split sequences up at regions of one or more Ns (the other characters in the sequence are A,C,G, and T). The format is called fasta, with a name of the sequence starting with a > and the sequence on the next row. Here is an example:

>name1
AAAATATGACAAAGGGGTTNNNNNNNNNNNNNNGATGTCTGGTCAATAGGAT

This sequence would correctly be split into AAAATATGACAAAGGGGTT and GATGTCTGGTCAATAGGAT, and this I can manage (example code below).

The problem appears when I also have Ns at the beginning or end of the sequence. I do not want to split at these positions, only when I have Ns internally. This sequence for example would cause me problems:

>name1
NNNAAAATATGACAAAGGGGTTNNNNNNNNNNNNNNGATGTCTGGTCAATAGGAT

Could someone please help me get the regex right for the split function?

In my code I read a fasta-file (with multiple entries) in to a hash and then loop over the hash to produce the separate entries. See my code below

 
#!/usr/bin/perl

use warnings;
use strict;

my $infile=$ARGV[0];
my $header;
my %sequence=();

open FASTA, $infile or die "Couldn't open fasta-file";
open (OUTFILE,">fasta_report.txt");

# Populate a hash with the fasta-data
# fasta example:
#>fasta1
#NNNAGTCTGCAAANAATTTGCGGCTCACAAT
#>fasta2
#CGCAGCCATTAACATCTCAACAAGCCAAAAATTCCTTCTCAGAAATTCGGNNN

while (<FASTA>) {
  chomp;
  if (/^>(.*)$/){
    $header=$1;
  }
  elsif (/^(\S+)$/){
    $sequence{$header} .= $1 if $header;
  }
}
close FASTA;

#Go through the hash and split at Ns
foreach my $key (keys %sequence){ 
  my @contigs = split (/N+/, $sequence{$key});
  foreach my $element (@contigs){
    print OUTFILE "$element\n";
  }
}  
close OUTFILE;

[download]

I very much appreciate any help you can give me. Thanks!

In reply to Splitting only on internal pattern, not at start or end of string by BiologySwede

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