#!/usr/bin/perl
use warnings;
use strict;
use Bio::SeqIO;
use Bio::Seq;
my $file = $ARGV[0]; # input fasta file (genome file)
my $out = $ARGV[1]; # output fasta file
my $chr="test"; #insertion chromosome
my $pos=10; # position of the insertion
my $seqI = "AAAA"; #sequence of the insertion
my $seq_in = Bio::SeqIO->new( -format => 'fasta',-file => $file);
my $seq_out = Bio::SeqIO->new( -format => 'fasta',-file => ">".$out);
while( my $seq = $seq_in->next_seq() ) {
if($seq->primary_id eq $chr){
my $length = length($seq->seq);
my $upstream=substr($seq->seq, 0, $pos);
my $downstream=substr($seq->seq, $pos,$length);
my $seq_obj = Bio::Seq->new(-seq => $upstream.$seqI.$downstream,-display_id => $seq->primary_id,-alphabet => "dna" );
$seq_out->write_seq($seq_obj);
}
else{
$seq_out->write_seq($seq);
}
}
