#!/usr/bin/perl use strict; use warnings; open(FH1,"read.txt"); open(FH2,"qual.txt"); my @arr1=; my @arr2=; my $joi1=join(' ',@arr1); my $joi2=join(' ',@arr2); my @new=split('>',$joi1); my @numbers=split('>',$joi2); my @new; my @seqid; foreach(@new){ my($seq_id,$seq)=split(/\n/,$_); push(@alp,split(' ',$seq)); push(@seqid,$seq_id); } my @numbers; my @numid; foreach(@numbers){ my ($num_id,$numb)=split(/\n/,$_); push(@num,split(' ',$numb)); push(@numid,$num_id) } my @keep= grep {$_ < 1 || $num[$_]>=10 || $alp[$_-1] ne $alp[$_-0]} 0..$#num; print (join(' ',@alp[@keep]),"\n"); print (join(' ',@num[@keep]),"\n");