samtools extract the non-specified region

Question

[sapuizait]

Hi all

I am trying to extract specific regions from sequences in fasta files

Example file:

>oneseq GAATATGCTTTTCGCTATTTTGGTGGCAGAACAAAAGCAATTATGTATGACCAGGATAAAGTTTTTGTTGTAAGTGAGAATTTCGGCAATGTAATCTTTGTTCCGGAGT
>twoseq TCTGGAGGGACTGCCGGCGCAAGCCGTGAGGAAGGATGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGTCGGCACAGCGGGAAGCCATATGGTGACATAGAGCGGAACCCGAAAGCCGGTCTCAGTTCGGATCGGAGTCTGCAA
>threeseq CATCCGGTAGTTTCTTTCCCATATCCTGCACCGCCGGAACCTTCTTCTCATAGGTCTGTAACTGTGTATTGTTTTCTGCCATACAAACACCGCCCTTTCTATGATATTTCAGATATTTCAAGCAATATTTCAAAAAATTAAATCTAATCTTAACTTTATTCCAACCCTT

I often use samtools to do it using sth like this:

samtools faidx test.fas oneseq:2-10 twoseq:3-10

However, this time, instead of this, I would like to extract the non-specified regions In the above example, I would like to get as output this:

>oneseq
G-TTCGCTATTTTGGTGGCAGAACAAAAGCAATTATGTATGACCAGGATAAAGTTTTTGTTGTAAGTGAGAATTTCGGCAATGTAATCTTTGTTCCGGAGT
>twoseq
TC-CTGCCGGCGCAAGCCGTGAGGAAGGATGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGTCGGCACAGCGGGAAGCCATATGGTGACATAGAGCGGAACCCGAAAGCCGGTCTCAGTTCGGATCGGAGTCTGCAA

OR even better :)

>oneseq-upstream 
G
>oneseq-downstream TTCGCTATTTTGGTGGCAGAACAAAAGCAATTATGTATGACCAGGATAAAGTTTTTGTTGTAAGTGAGAATTTCGGCAATGTAATCTTTGTTCCGGAGT
>twoseq-upstream 
TC
>twoseq-downstream CTGCCGGCGCAAGCCGTGAGGAAGGATGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGTCGGCACAGCGGGAAGCCATATGGTGACATAGAGCGGAACCCGAAAGCCGGTCTCAGTTCGGATCGGAGTCTGCAA

I am aware it is possible if I first first get the sequence length and then subtract from it the selected region - But, I was just wondering if there is an easier way to do this?

Thanks

Answer 1

[JC]

one simple solution is a simple Perl script:

#!/usr/bin/perl

use strict;
use warnings;

$ARGV[1] or die "use perl split_seqs.pl FASTA COORD1 COORD2 ... > OUTPUT\n";

my $fasta  = shift @ARGV;
my @coords = @ARGV;

my %reg = ();
foreach my $coord (@coords) {
    my ($seq_id, $seq_coord) = split (/:/, $coord);
    $reg{$seq_id} = $seq_coord;
}

$/="\n>"; # read fasta in sequence blocks
open (my $fh, "<", $fasta) or die "cannot read $fasta\n";
while (<$fh>) {
    s/>//g;
    my ($seq_id, @seq) = split (/\n/, $_);
    next unless (defined $reg{$seq_id});

    my $seq = join "", @seq;
    my ($ini, $end) = split (/-/, $reg{$seq_id});

    # upstream
    my $u_seq = substr($seq, 0, $ini - 1);
    print ">$seq_id-upstream\n$u_seq\n";
    # downstream
    my $d_seq = substr($seq, $end, (length $seq) - $end);
    print ">$seq_id-downstream\n$d_seq\n";
}
close $fh;

then you can run as:

$ perl split_seq.pl seqs.fa  oneseq:2-10 twoseq:3-10
>oneseq-upstream
G
>oneseq-downstream
TTCGCTATTTTGGTGGCAGAACAAAAGCAATTATGTATGACCAGGATAAAGTTTTTGTTGTAAGTGAGAATTTCGGCAATGTAATCTTTGTTCCGGAGT
>twoseq-upstream
TC
>twoseq-downstream
CTGCCGGCGCAAGCCGTGAGGAAGGATGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGTCGGCACAGCGGGAAGCCATATGGTGACATAGAGCGGAACCCGAAAGCCGGTCTCAGTTCGGATCGGAGTCTGCAA