Hi Graham,really thanks 4 ur wonderful help.

I have a file,containing amino acid seq.like

MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIIEMIPER
NEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPPTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVK
IRRRVDTNPGHADLSAKEAQDVIMEVVFPNEVGARILTSESQLTITKEKKEELQDCKIAPLMVAYMLERE

I need o count each individual character,so I used this script;

#!usr/bin/perl -w
open(FILE,"<FASTA1.fa") or die "cant open file:$!\n";
$sequence = '';
@data=<FILE>;
foreach $line (@data){
if ($line =~m/^\s*$/) {
           next;
} elsif($line =~m/^\s*#/) {
           next;
} elsif($line =~m/^>/) {
           next;      
} else {
           $sequence .= $line;
       }
            }

$sequence =~ s/\s//g;

@sq=split(//,$sequence);
$count_of_A = 0;
$count_of_C = 0;
$count_of_G = 0;
$count_of_T = 0;
$count_of_Q=0;
$count_of_S=0;
$count_of_R=0;
$count_of_W=0;
$count_of_Y=0;
$count_of_I=0;
$count_of_H=0;
$count_of_D=0;
$count_of_E=0;
$count_of_M=0;
$count_of_N=0;
$count_of_P=0;
$count_of_V=0;
$count_of_F=0;
$count_of_K=0;
$count_of_M=0;
$errors     = 0;

foreach $char(@sq) {

   if     ( $char eq 'A' ) {
       ++$count_of_A;
   } elsif ( $char eq 'C' ) {
       ++$count_of_C;
   } elsif ( $char eq 'G' ) {
       ++$count_of_G;
   } elsif ( $char eq 'T' ) {
       ++$count_of_T;
   }
     elsif ( $char eq 'S' ) {
       ++$count_of_S;
   }
     elsif ( $char eq 'D' ) {
       ++$count_of_D;
   }
     elsif ( $char eq 'P' ) {
       ++$count_of_P;
   }
     elsif ( $char eq 'V' ) {
       ++$count_of_V;
   }
     elsif ( $char eq 'L' ) {
       ++$count_of_L;
   }
     elsif ( $char eq 'I' ) {
       ++$count_of_I;
   }
     elsif ( $char eq 'M' ) {
       ++$count_of_M;
   }
     elsif ( $char eq 'F' ) {
       ++$count_of_F;
   }
     elsif ( $char eq 'Y' ) {
       ++$count_of_Y;
   }
     elsif ( $char eq 'W' ) {
       ++$count_of_W;
   }
     elsif ( $char eq 'H' ) {
       ++$count_of_H;
   }
     elsif ( $char eq 'K' ) {
       ++$count_of_K;
   }
     elsif ( $char eq 'R' ) {
       ++$count_of_R;
   }
     elsif ( $char eq 'Q' ) {
       ++$count_of_Q;
   }
     elsif ( $char eq 'N' ) {
       ++$count_of_N;
   }
     elsif ( $char eq 'E' ) {
       ++$count_of_E;
   }
      else {
       print "!!!!!!!! Error - I don\'t recognize this char: $char\n";
       ++$errors;
   }
                  }

print "A = $count_of_A\n";
print "C = $count_of_C\n";
print "G = $count_of_G\n";
print "T = $count_of_T\n";
print "Q = $count_of_Q\n";
print "S = $count_of_S\n";
print "R = $count_of_R\n";
print "W = $count_of_W\n";
print "Y = $count_of_Y\n";
print "I = $count_of_I\n";
print "H = $count_of_H\n";
print "D = $count_of_D\n";
print "E = $count_of_E\n";
print "L = $count_of_L\n";
print "N = $count_of_N\n";
print "P = $count_of_P\n";
print "V = $count_of_V\n";
print "F = $count_of_F\n";
print "K = $count_of_K\n";
print "M = $count_of_M\n";
print "errors = $errors\n";
     
close FILE;


This is working finely,but it is really large.Is there any way to do this same work with much smaller script??

I am not sure this will be any fastser than your existing code but you can try:

Code:

#!usr/bin/perl use strict; use warnings; use Data::Dumper; my @SEQ = qw(A C D E F G H I K L M N P Q R S T V W Y); my %counts = map{ $_ => 0} @SEQ; my %errors = (); open(FILE,"<FASTA1.fa") or die "cant open file:$!\n"; while ( <FILE> ) {   if (m/^\s*$/ ) {      next;   }   elsif ( m/^\s*#/ ) {      next;   }   elsif ( m/^>/ ) {      next;   }   else {      while (/(.)/g) {         my $c = $1;         if ( exists $counts{$c} ) {            $counts{$c}++;         }         else {            $errors{$c}++;         }      }   } } close FILE; print Dumper \%counts, \%errors;

I used Data:umper only for convenience, you print the results however you want.

you can use the wonder full "substr"
Here is a partial code, i have used to do the same thing u are doing.
if(/[ARNDCQEGHILKMFPSTWYVJU]+[\n\r]+/) #regex to capture peptide sequences
          {
           $pep_seq = $&;
            #print "$&";
              $len = length($&); #lenght of peptides
             #print "==>$len";
             
             #print "Len==>$len";
           
           for ($i=0;$i<$len;$i++) #Loop that uses lenght of the peptides as sentinal value.
           {
             $temp = substr $&,$i,1;#use of perl function substr to capture each and every AA in the current peptide sequence


ignore the commented part..thats just the way I test my scripts. But this should get u going. My regex might be different then what u need, so u can change it accordingly.

Opps just realized, u will need to compare the "temp" with the 20 AA. I  "had" to do it as  I am doing various processing on each AA.

This can slow down your perl scripts:

$pep_seq = $&;

For reasons I am not sure of, if you use $& (or even worse: $` or $') they can slow down perl scripts. Perl is forced to use them in all regexps if used in one and this can have an impact on performance.



on 11/24/07 at 22:48:58, KevinAD wrote:

This can slow down your perl scripts: $pep_seq = $&; For reasons I am not sure of, if you use $& (or even worse: $` or $') they can slow down perl scripts.

My understanding is that if you match against a string that is (say) 8 Mbytes in length, then every single match in your program will write 8 Mbytes of temporary variables if there is any mention of $& $' or $`.

See longer article ....

http://www.wellho.net/mouth/1444_Using-English-can-slow-you-right-down-.html

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