merging fasta sequences into a single fasta sequence in large file

Question

[K]

Hi,

have a large file containing more than 10 contigs of different length.

Input:

seq_1 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAACGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC

seq_2 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAATGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC

seq_3 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGACCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT

seq_4 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT

seq_5 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT

seq_6 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAACGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC

seq_7 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAATGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC

seq_8 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGACCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT

seq_9 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT

seq_10 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT

I would like to merge some of the fasta sequences based on IDs

Output:

seq_1_seq_2 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAACGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTCAAGGGTTTAGAAAAAAACCAAACAAACAATCGAAATGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC

seq_3 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGACCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT

seq_4 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT

seq_5 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT

seq_6_seq_7 AAGGGTTTAGAAAAAAACCAAACAAACAATCGAAACGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTCAAGGGTTTAGAAAAAAACCAAACAAACAATCGAAATGAAATAGAAAAAGAAAAAGGGAAGGGGTTAAGTTC

seq_8_seq_9_seq_10 TTCATATAAAAATTGATATAGAATCTTTGAAAAAGACCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTTTTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTTTTCATATAAAAATTGATATAGAATCTTTGAAAAAGCCCTTTCTTCCTAAGAAAGAAAAGGCTTACTGTCTT

Thank you

[swbarnes2]

What have you tried? Are you hoping someone will just give you a complete script?

Answer 1

[Michael]

Here is a perl script I am using to join sequences from multiple fasta files by their sequence id.

Usage:

combineFasta.pl -out outputfile.fasta -in file1.fasta file2.fasta .... <more files>

Perl code:

#!/usr/bin/env perl

use strict;
use warnings;
use Getopt::Long;
use Bio::SeqIO;
use File::Basename qw(basename);


my @inputs = ();
my $out;
GetOptions ("out=s" => \$out, "in=s{1,}" => \@inputs);

my %h = ();

FILE: foreach my $f (@inputs) {
  print $f,"\n";
  my $in = Bio::SeqIO->new(-file => $f);
  while (my $seq = $in->next_seq) {
    my $gid = $seq->display_id;
    if (! ref $h{$gid}) {
       $h{$gid} = $seq;
    } else {
      $h{$gid}->seq ($h{$gid}->seq . $seq->seq);
    }
  }
}
print "finished reading input \n";

my $out = Bio::SeqIO->new(-format => 'fasta', -file => ">$out");
while (my ($k, $v) = each %h ) {
   $out->write_seq($v);
}