#!/usr/bin/perl-w                                                                           
#  perl program to find motif in text file eith its positions.            
 
use strict;
use Bio::SeqIO;
 
open(my $outfile, ">", "Motif_Result.txt");
 
my $file = 'seq.txt';
 
 
print {$outfile}"\t\t\t\t\t Positions\n";
print {$outfile}"\tPattern Name\tSequence Name\tStart\tEnd\tLength of Sequence\n\n";
 
 
my $patternseq= 'pat.txt';
open(FIH, $patternseq);
 
my $in;
my %patsmap;      my @residue;   my @pats;      my $seqcount = 0;
while ($in=<FIH>)
{
         chomp($in);
         my @pats=split " ",$in;
         my $residue=shift@pats;
         foreach my $nnn (@pats)  # @pats = (AAAAA, TTTTT, GGGGG);
         {
         $patsmap{$nnn}=@residue;
         }
 
        print "Patterns\t"; print "@pats";             print "\n";
        my $length = @pats;
        print "Total Patterns are: $length"; print "\n";
 
 
my $seqobj;
my $in = Bio::SeqIO->new(-format => 'fasta',
                         -file   => $file);
 
my $motif_count = 0;
 
 
 
   while ( my $seq = $in->next_seq)
        {
        $seqcount++;                  # count the number of sequences
        my $head = $seq->display_id();
        my $str = $seq->seq;          # get the sequence as a string
        $str =~ s/\*//g;              # remove all '*' from sequence
 
my $i;
for ($i=0; $i<=$length; $i++) {
             while ( $str =~ m/(?=$pats<a href="?node=%24i">$i</a>)/ig)
                 {
                 my @l = split('', $str);
                 my $length=@l;
         print {$outfile}"\t"; print {$outfile}$pats<a href="?node=%24i">$i</a>; 
         printf {$outfile}"\t\t$head\t\t%d", pos($str)+1;
         printf {$outfile}"\t%d", pos($str)+5;
         print {$outfile}"\t";  print {$outfile}$length; print {$outfile}"\n";
                
                 }
        }
 
}
 
print {$outfile}"\n\tTotal Sequences in file name $file\t:$seqcount\n";
 
exit;
     }