Lowercase sequence and create one sequence per mutation

prepForSQRWL2.pl

#!/usr/bin/perl


use Getopt::Long;
our $opt_f = ();

sub usage {
        printf "Usage: $0 [flags] file...\n";
        printf "flags:\n";

        printf "    -i Infile   reads the input from fileIN \n";
        printf "    -mut Mutation\n";
        exit 1;
}

GetOptions( "i=s", "mut=s" );
usage() if !( $opt_i && $opt_mut);

$wt = substr($opt_mut,0,1);
$mt = substr($opt_mut,length($opt_mut)-1,1);
$pos = substr($opt_mut,1,length($opt_mut)-2);
#print "wt:$wt, mt:$mt, pos:$pos";

open( IN,  "<$opt_i" ) or die "Inputfile not found";

$sequence = "";
while(<IN>){
        chomp;
        @line = split('',$_);
                push(@sequence,@line);
}
$pos2 = $pos - 167;
for($i = 0; $i<scalar(@sequence); $i++){
                if ($i == $pos2){
                        if ($wt eq $sequence[$i]){
                        print $mt;
                        } else {print "\n problem with matching snp $wt$pos$mt (pos in edited sequence $pos2) to sequence \n";}
                } else {
                        print lc($sequence[$i]);
                }
}