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hey i have a code (given below) which counts A,T,G,C and GC,and GC percentage in between 0-200, 1-201, 2-202 regions. But i have to count a lenghty sequence upto 10,000 basepairs, so this would be very lenghty and less efficient. What modification can i do in this code so that it can automateically count upto 10,000 bases.

#!/usr/bin/perl use warnings;my$seq;my$file;my$line;my$len;my@seq; print "Select the region where you want to find CpG Island\n"; print "1. Region 1-200\n"; print "2. Region 2-202\n"; print "3. Region 3-203\n"; $choice =<STDIN>; chomp($choice); if($choice == 1){ &region1; } if($choice == 2){ &region2; } if($choice == 3){ &region3; } sub region1 { $file = 'd:\perl\1.txt'; open(INPUT, $file) or die ("File not found"); foreach($line = <INPUT>){ $a = substr($line,0,200) =~tr/A//; $t = substr($line,0,200) =~tr/T//; $g = substr($line,0,200) =~tr/G//; $c = substr($line,0,200) =~tr/C//; $cg = substr($line,0,200) =~tr/ CG //; $total = substr($line,0,200) =~tr/ATGC//; } $CpG = ($cg)/$total*100; print"Count of A = $a\n"; print"Count of T = $t\n"; print"Count of G = $g\n"; print"Count of C = $c\n"; print"CG = $cg\n"; print"total count of ATGC = $total\n"; print"CpG percentage = $CpG\n"; if ($CpG>=60){ print"CpG present";} else{ print"CpG absent";} } sub region2 { $file = 'd:\perl\1.txt'; open(INPUT, $file) or die ("File not found"); foreach($line = <INPUT>){ $a = substr($line,1,201) =~tr/A//; $t = substr($line,1,201) =~tr/T//; $g = substr($line,1,201) =~tr/G//; $c = substr($line,1,201) =~tr/C//; $total = substr($line,1,201) =~tr/ATGC//; } $CpG = ($g+$c)/$total*100; regarding perl,So i need your help for the same. print"Count of A = $a\n"; print"Count of T = $t\n"; print"Count of G = $g\n"; print"Count of C = $c\n"; print"total count of ATGC = $total\n"; print"CpG percentage = $CpG\n"; if ($CpG>=60){ print"CpG present";} else{ print"CpG absent";} } sub region3 { $file = 'd:\perl\1.txt'; open(INPUT, $file) or die ("File not found"); foreach($line = <INPUT>){ $a = substr($line,2,203) =~tr/A//; $t = substr($line,2,203) =~tr/T//; $g = substr($line,2,203) =~tr/G//; $c = substr($line,2,203) =~tr/C//; $total = substr($line,2,203) =~tr/ATGC//; } $CpG = ($g+$c)/$total*100; print"Count of A = $a\n"; print"Count of T = $t\n"; print"Count of G = $g\n"; print"Count of C = $c\n"; print"total count of ATGC = $total\n"; print"CpG percentage = $CpG\n"; if ($CpG>=60){ print"CpG present";} else{ print"CpG absent";} }

In reply to Re^14: how to access elements in perl by grewal7634
in thread how to access elements in perl by grewal7634

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