I have this script below, but wish to define some essential genes and exclude any insertions within those genes from the output. Can anyone direct me on how to get this done. A more illustrative suggestion will be more appreciated as I am new to writing script with perl.
!/usr/bin/perl
use warnings; use Bio::SeqIO;
my $in=Bio::SeqIO->new(-file=>"k12.gbk", -format=>"genbank"); while (my $seq=$in->next_seq){ #Do things with each sequence here
my@random_set; my%seen;
for (1 .. 100){ my $number = int rand(100); redo if$ seen {$number} ++; push @random_set, $number; }
Random number generation code.
for my $position (@random_set) { print ">$position\n", $seq->subseq($position+1, $position+100), "\n";
my $subseq = $seq->subseq($position-1, $position-100);
$subseq is a string
my $rcseq = reverse $subseq; $rcseq =~tr/ACGT/TGCA/;
print " $rcseq, \n"; } }
