Pattern counter in fasta file - regex

Question

I am trying to get the count of matching patterns in the fasta file. I am starting from a fasta file containing 57k sequences. I want to pull out the count of my matching pattern sequence and show the starting position of the pattern
Input file:
chr1 ATTAG**CAGAT**GTGACGTCGATGT**CAGAT**TG
chr2 TGAGCTG**CAGAT**CGTAGATGATTCTGCAGGAACCT
chr3 TCTTT**CAGAT**GCCTCTG**CAGAT**TC
Searching pattern "CAGAT"
Output Required:
chr Count P1 P2
chr1 -- 2 -- 6 -- 25
chr2 -- 1 -- 8
chr3 -- 2 -- 6 -- 19
Thanks in advance

Answer 1

I am assuming your file to be seperated with tab as delimiter.
open(my $in,"<:utf8","in.txt") or die "Cannot open FILE in.txt : $!\n";
while(<$in>) {
chomp($_);
my $cur = $_;
#$print "iam $cur\n";
my #tt = split(/\t/,$cur); #assuming you file tobe tab seperated
my $s1 = $tt[1];
my $s2 = "CAGAT";
my #val;
print "$cur\t";
while ($s1 =~ /($s2)/g) {
push(#val, $-[0]); #$-[0] is the offset of the start of the last successful match.
}
my $count = #val;
#val = join(",",#val);
print " No of Matches:$count Starting positions:#val\n";
}
in.txt
chr1 ATTAG**CAGAT**GTGACGTCGATGT**CAGAT**TG
chr2 TGAGCTG**CAGAT**CGTAGATGATTCTGCAGGAACCT
chr3 TCTTT**CAGAT**GCCTCTG**CAGAT**TC