in reply to Re^13: how to access elements in perl
in thread how to access elements in perl

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";}

}

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Re^15: how to access elements in perl
by wjw (Priest) on May 19, 2014 at 08:08 UTC
    Could you provide perhaps a single line or maybe even 2 or 3 of the input file?

    I modified your code a bit for brevity(untested). I am not all that familiar with microbiology(been 35 years since high school biology). I suspect there are CPAN modules that will handle problems like this. Do a search for like this one at bio:: and see if there might be something you can use if that is an option for you.

    Hope that is in some way helpful... 

    #!/usr/bin/perl
use strict;
use warnings;
print "Select the region where you want to find CpG Island\n";
my ($a,$t,$c,$g,$cg,$total);
print  "1. Region 1-200\n";
print  "2. Region 2-202\n";
print  "3. Region 3-203\n";
my $choice =<STDIN>;
chomp($choice);
my $file = 'd:\perl\1.txt';

if ( $choice == 1 ) {
   region(0);
} elsif ( $choice == 2 ) {
   region(1);
} elsif ( $choice == 3) {
   region(2);
}

sub region {
    my $start = shift;
    open(INPUT, $file) or die ("File not found");
    foreach(my $line = <INPUT>) {
        my $a = substr($line,$start,200) =~ tr/A//;
        my $t = substr($line,$start,200) =~ tr/T//;
        my $g = substr($line,$start,200) =~ tr/G//;
        my $c = substr($line,$start,200) =~ tr/C//;
        my $cg = substr($line,$start,200) =~ tr/ CG //;
        my $total = substr($line,$start,200) =~ tr/ATGC//;
    }
}

my $CpG = ($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";
}

    [download]
    Update: moved printing back outside the sub. What I get for messing with code at this hour of the morning...
    ...the majority is always wrong, and always the last to know about it...
    Insanity: Doing the same thing over and over again and expecting different results...
    wjw
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