#!/usr/bin/perl

$file = "/home/birla/sandeep/Material/dataset/prokayotes/7_Chloroflexi/NC_012032.fna";

open (FH,$file) or die ($!);

my $genome;
while($line = <FH>){
	if($line =~ /^>/){ next ; }
	chomp($line);	
	$genome .= $line;
}

#print"$genome";


#$genome_size = length($genome),"\n\n";
#print"Genome size = $genome_size\n";
	
#$gene = "GAACGTCCCTCCGGGACTCGGTTCTCACATCCAGTGGGACAGAAGGATTGACGGAAGGATAGCTCAGGCGATGATGAGCATTCAGGCCATTAAAGGCGTTGAGATAGGACTTGGTTTTGAAGCCGCGAGGAGGTTCGGCTCTCAGGTTCACGACGAGATAGGCTGGAGTGAAGGGAAGGGCTACTTCAGGCATTCTAACAACCTCGGAGGAACGGAAGGAGGGATCACAAACGGCATGCCGATAGTTGTGAGAGTCGCGATGAAACCCATACCGACTTTAAAGAACCCTTTAAGGAGTGTTGATATAGAAACAAAGGAAGAGATGAAAGCAGGAAAGGAGAGGACGGATATAGTAGCAGTTCCCGCGGCATCTGTCGTGGGAGAAGCTATGCTCGCCATAGTTCTCGCGGATGCACTCCTTGAAAAACTCGGCGGAGACTTTATGGAAGAAGTAAAAAAGAGGTTTGAGGATTACGTGAACCACGTTAAGAGTTTCTAAG"; 
#$gene = "GTGTAATAGAGAATTCTCTCGGTAGTCGTAGTTTTACCCGCGTCAATGTGAGCAACTATACCTATGTTTCTCAATTTCTCTATAGGCACCTCTCTCGCCA";




$pos = (index($genome,$gene)+1);
#print "POS: ",$pos+200, "\n"; 
print "POS: ",$pos, "\n"; 
#
print"\n\n\n";



#for rev_gene 
#$gene_C = "CCATTAGAAGTCAGGCTTGAGAAGGAAATGGAAGGAGTCTCGGAAATGGGGCATAAGTTCTGGCACGGGGGACTTCCTTACATAACTCCTCGCCAAGCGAAATAGTTTCCTTCTGAATTTATGCTTGAGTTGAAGAAACTTGAAGAGGCTATTTGCGAAATAGAGGAGGGGATGGAAATCCTCTTCAAGGAGCGAGAGATAGCGCGTCCCAGGTCGATAGTGATTTTTGAAAAGGTATTGATGATTAAATTGGAATGAGATTTTTTCTCGACCTTCTTTGCGGGCTCTTCCACCCTTTAGCATTTCTCTTATCGGGGAAGTCGGAACATTTTCATTTGCTATTTCTTTTGTTCTTGCGACTCCTCCTTTTTGGAGTGCCCTTTCCAATGATACCCTAAAAAGGGAAAAAACCGAGAAGACATATACGAAAGCAACATTTCCTTTGGCGAATTTTTCGGATATTATGTATAACGACCTGCAAGGTAAAGACCTTTCCTATT";
#$gene_C = "TTTTCCGCAAATATGTTCTACTTCTTCTTTATTGAAAGATTTCCGGAGTTAGGAGAATTACTTCAGAGGAGTTTAATTTAA";

#$gene_C="TACGAGTGTCTCGGATGCGGAAAGCTGATATTTCACGACAATTACGAGTTCTGGAACTTGAGTGATTGCTGTGATGACAACTCCAAACTAGTGGAGGAAGGAGTTTTATGCGAAGTTTGTTACGCTAAAAGTCCTGAAAACCTAAAAGACTGGATTTTCTTCAAGCCTTCCTGGTATCAAAAGGTGGATTTTGAGAAGTA";
$gene_C="atgaaaccgacgccagcaggcgaagccattcaaatcagcaacgggcgcttgcaagtaccc
gatcatccaattattccattcgtagaaggtgacggtaccggacgtgacatctggcgggca
agtgtacgtgtcttcgacgcggcggttgcactggcttacggcggaaagcgtaagatcgag
tggcttgaggtgttggcaggcgaaaaagccttccacgagacgggtaactggctccccgac
gagacaattgagacgtttcagaagtacctggtcgggatcaaaggcccattgacaaccccg
gtcggcggtggcattcgctcgttgaacgttgccttgcgcaagcatctcgatctctacgtc
tgtcagcggccggttcgccattttgccggtgttccttcgccggtcaagcacccggagaag
gttgatatggttatcttccgtgagaacacggaggatgtttacaccggcatcgagtatcgc
ggcggtagcgaagaagcggcgaagatcatcgcatttttgcagcgtgaattcccgaaggat
ttcgacaagattcgcttcggcacgcctgaaaagactgatgaattccgccaactgatcggc
gaagaaccggaaggaaagattgaggttggcatcggtatcaagccaatcagccgcattggt
accgagcgcatcatggcagcggctattcagtacgccattacctacaagcgcaagagcatc
accctgatgcacaagggtaacatccagaaattcaccgagggcgctttccgcgattgggcc
tatgaatatgctgagcgggcctttggtgattatgtctatacgtgggcacaatgggagcgc
acgaaggctgcgcggggtgaagcagcggcgaatgccgagcagaaagaggcgctggccgcc
ggtaagattctggtcaaggacgcaattgccgacattatcttccagcaggttctgacccgc
cccgatgagtttgatgtgattgttgcgccgaacctcaacggcgactacctctctgacgcc
ctcgcggcccaggtcggtggcatcgggatcgcccctggcggtaacatcaattacgtcacc
ggtcacgctatcttcgaggctacccacggtacggcaccaaaatatgccgatcttgacaag
gtcaaccccggctcagtcattctgtcgggtgagatgatgctgcgctatatgggctggacg
gaagccgccgatctgattattgccggcctcgagcgcaccattgccgacaagacggtgaca
tacgactttgcccgtctgatggagggcgcgcgcgaggtgaagacctcggagtttgccagc
ctgatcattgccaacatggagaagatcgttgccggcgatgtgccgcatcccaccccgacc
ttcggcccggagattctgcgccgtgccgatggccgtgtttacccgcacggcagtgttggt
gcggtgatgacacgggcggtggtggcggtaccggcggaagcctcgctccgcgagacatcg
atctatatgcgtggacgtggcatccattcggtgattgtcaaacccgacgccagcggcgaa
tggggcattatgactatgcgtgacgtgttgaagaaggtcgtgcgcgagggccgggccatc
gatggtttgaccgtcggtgatctgacgagccggccattgctgagtgttagcccggatacg
ccgattaccgaatgcgcagcgttgatggtcgagcgcaatattcgccggctggcggtattt
gagaatggcgagccggttgggattatctctgagactgacatcttcagccacgtggcggag
tag";

$gene_C =~ s/\n//g;
$gene_C = uc $gene_C;
$gene_C =~ tr/ATGC/TACG/;
$rev_gene = reverse $gene_C;

print"Reverse TR : $rev_gene\n";

$pos = index($genome,$rev_gene);
#$pos = index($genome,$gene_C);

print "POS: ",$pos , "\n"; 

#print"$rev_gene\n";
#print substr($genome,9656,50);