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mirna-target-scan.pl
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#!/usr/bin/perl
=head1 usage
detect miRNA target site in Input sequence
usage:
perl mirna-target-scan.pl -m=mrna.fa -s=mirna.fa
=cut
use strict;
use warnings;
use Getopt::Long;
use Bio::SeqIO;
## global variable=======================================
my($mirna_file, $mrna_file);
my %mirna_record;
my %target_8mer;
my %target_7mera1;
my %target_7merm8;
my %target_6mer;
my %target_os6mer;
## main================================================
GetOptions("m=s" => \$mrna_file,
"s=s" => \$mirna_file) or die "Commandline error.";
parse_mirna($mirna_file);
parse_mrna($mrna_file);
## functions================================================
sub parse_mirna{
my($input_file) = @_;
my $mirna_fh = Bio::SeqIO->new(-file => $input_file, -format => "fasta");
while(my $mirna = $mirna_fh->next_seq){
#print $mirna->id, revcomp($mirna->seq), "\n";
my $tmseq = $mirna->seq;
$tmseq =~ tr/T/U/;
$mirna->seq($tmseq);
$mirna_record{$mirna->id} = $mirna->seq;
# canonical target site
$target_8mer{$mirna->id} = revcomp(substr($mirna->seq, 1, 7)) . "A";
$target_7mera1{$mirna->id} = revcomp(substr($mirna->seq, 1, 6)) . "A";
$target_7merm8{$mirna->id} = revcomp(substr($mirna->seq, 1, 7));
# marginal target site
$target_6mer{$mirna->id} = revcomp(substr($mirna->seq, 1, 6));
$target_os6mer{$mirna->id} = revcomp(substr($mirna->seq, 2, 6));
}
}
sub revcomp{
my($instr) = @_;
my $outstr = reverse $instr;
$outstr =~ tr/UACG/AUGC/;
return $outstr;
}
sub parse_mrna{
my($input_file) = @_;
my $mrna_fh = Bio::SeqIO->new(-file => $input_file, -format => "fasta");
while(my $mrna = $mrna_fh->next_seq){
scan_target($mrna);
}
}
sub scan_target{
my($mrna) = @_;
foreach my $mirna(sort keys %mirna_record){
my $tmseq = $mrna->seq;
$tmseq =~ tr/T/U/;
my($regex, $rep, $site_type);
# find 8mer site
$regex = $target_8mer{$mirna};
$site_type = "8mer";
$rep = 'N' x length($regex);
while($tmseq =~ /$regex/g){
#print join("\t", $mirna, $mrna->id, $-[0] + 1, $+[0], $site_type, $regex, $mirna_record{$mirna}, $mrna->seq), "\n";
print join("\t", $mirna, $mrna->id, $-[0] + 1, $+[0], $site_type), "\n";
}
$tmseq =~ s/$regex/$rep/g;
# find 7mera1 site
$regex = $target_7mera1{$mirna};
$site_type = "7mera1";
$rep = 'N' x length($regex);
while($tmseq =~ /$regex/g){
print join("\t", $mirna, $mrna->id, $-[0] + 1, $+[0], $site_type), "\n";
}
$tmseq =~ s/$regex/$rep/g;
# find 7merm8 site
$regex = $target_7merm8{$mirna};
$site_type = "7merm8";
$rep = 'N' x length($regex);
while($tmseq =~ /$regex/g){
print join("\t", $mirna, $mrna->id, $-[0] + 1, $+[0], $site_type), "\n";
}
$tmseq =~ s/$regex/$rep/g;
# find 6mer site
$regex = $target_6mer{$mirna};
$site_type = "6mer";
$rep = 'N' x length($regex);
while($tmseq =~ /$regex/g){
print join("\t", $mirna, $mrna->id, $-[0] + 1, $+[0], $site_type), "\n";
}
$tmseq =~ s/$regex/$rep/g;
# find offset 6mer site
$regex = $target_os6mer{$mirna};
$site_type = "os6mer";
$rep = 'N' x length($regex);
while($tmseq =~ /$regex/g){
print join("\t", $mirna, $mrna->id, $-[0] + 1, $+[0], $site_type), "\n";
}
$tmseq =~ s/$regex/$rep/g;
}
return 0;
}