How To Split A Long Dna Sequence Into Certain Length Parts By Perl/Python ?

Question

[quge856]

Hi there,

Here is a long DNA sequence (in fasta), would you like to show me how to split it into certain length fragments (100nt) with 20nt overlapping? Like following:

Input:

>E.coli  
ACTG*****************************

Output:

>E.coli(1-100)  
ACTG***********************  
>E.coli(80-180)  
*******************************  
>E.coli(160-260)  
*******************************

Thank you in advance!

[Neilfws]

Would you like to tell us whether you tried to do this yourself, or if you don't know where to start with the problem?

[quge856]

A script, like JC's answer. Thank u also.

Answer 1

[Martin A Hansen]

This can be done with Biopieces www.biopieces.org) like this:

read_fasta -i data_in.fna | split_seq -w 100 -s 20 | write_fasta -o data_out.fna -x

[quge856]

Thank u martinahansen, after reading the Biopieces introduction, i realized it's a very very powerful tool!

Answer 2

[JC]

Perl option:

#!/usr/bin/perl

use strict;
use warnings;

my $len = 100;
my $over = 20;
my ($seq_id, $seq);

while (<>) {
    chomp;
    if (m/^>/) { $seq_id = $_; } else { $seq .= $_; }
}

for (my $i = 1; $i <= length $seq; $i += ($len - $over)) {
    my $s = substr ($seq, $i - 1, $len);
    print "$seq_id ($i-", $i + (length $s) - 1, ")\n$s\n";
}

[quge856]

Thank you JC, this is the script which exactly want, and it works very well. Thanks again.

Answer 3

[SES]

This can easily be done with genometools as:

gt shredder -minlength 100 -maxlength 100 -overlap 20 ecoli.fasta > ecoli_shredded.fasta

Note that there are also -coverage and -sample options for shredder that will allow you to control how your fragments are generated. Another good option is dwgsim, which is capable of doing sampling with various kinds of mutations, but this may be more than what you need. The Biopieces (mentioned by martinahansen) or genometools solutions are probably more appropriate based on your question.

[quge856]

Thanks for your input. it looks also a useful tool besides Biopieces.

Answer 4

[brentp]

You can use pyfasta to do this

pyfasta split -k 100 -o 20 input.fasta -n 1

[quge856]

Thank u! now I learn more skills from you guys. lol