Hi dear monkes, i have protein file in fasta format and i ve written folloing code for finding frequency of each amino acid (alphabet), but there is a problem. the result file is very big. i mean i expect a very smaller file. please take a look at my code.

#!/usr/bin/perl -w

use bio::seqIO;
my $outputfile;



#protein file bringing in.
$outputfile="countaa";
unless(open(IN,">>$outputfile"))
{print" cant open file \"$outputfile\ to write to !!\n\n";
exit;}

my $proteinio=Bio::SeqIO->new (-file=>"ec 1.1.1.fasta",-format=>'fasta
+');

while(my $seq=$proteinio ->next_seq() ){

foreach(my $protein=$seq->seq){ 
$count_A=0;$count_C=0;$count_D=0;$count_E=0;$count_F=0;$count_G=0;$cou
+nt_H=0;$count_I=0;
$count_K=0;$count_L=0;$count_M=0;$count_N=0;$count_P=0;$count_Q=0;$cou
+nt_R=0;$count_S=0;
$count_T=0;$count_V=0;$count_W=0;$count_Y=0;

my @protein=split('',$protein);
foreach (@protein){

if (/A/) {++$count_A;}
elsif (/C/) {++$count_C;}
elsif (/D/) {++$count_D;}
elsif (/E/) {++$count_E;}
elsif (/F/) {++$count_F;}
elsif (/G/) {++$count_G;}
elsif (/H/) {++$count_H;}
elsif (/I/) {++$count_I;}
elsif (/K/) {++$count_K;}
elsif (/L/) {++$count_L;}
elsif (/M/) {++$count_M;}
elsif (/N/) {++$count_N;}
elsif (/P/) {++$count_P;}
elsif (/Q/) {++$count_Q;}
elsif (/R/) {++$count_R;}
elsif (/S/) {++$count_S;}
elsif (/T/) {++$count_T;}
elsif (/V/) {++$count_V;}
elsif (/W/) {++$count_W;}
elsif (/Y/) {++$count_Y;}
print IN "$count_A $count_C $count_D $count_E $count_F $count_G $count
+_H $count_I $count_K 

$count_L $count_M $count_N $count_P $count_Q $count_R $count_S $count_
+T $count_V $count_W 

$count_Y\n";}

}}
 close IN;

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In reply to alphabet counting by Anonymous Monk

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