Hi, Thank you. It works perfectly.

One last thing I would like my script to do is tho look at those "number of proteins" and tell me which entry in the original input file has the smallest number of proteins. So, it should look like following in the output:

A=11 D=5 E=12 F=1 G=5 I=6 K=3 L=7 M=2 N=4 P=2 Q=9 R=10 T=4 V=10

Number of proteins = 15

Entry ">sp|Q2M7X4|YICS_ECOLI Uncharacterized protein YicS OS=Escherichia coli (strain K12) OX=83333 GN=yicS PE=4 SV=1" has the least number of proteins

#!/usr/bin/perl
use strict;
use warnings;

my $report_name = 'aa_report.txt';
open my $out_file, '>', $report_name 
     or die "Cannot open '$report_name' because: $!";

print 'PLEASE ENTER THE FILENAME OF THE PROTEIN SEQUENCE: ';
chomp( my $prot_filename = <STDIN> );

open my $PROTFILE, '<', $prot_filename 
  or die "Cannot open '$prot_filename' because: $!";

$/ = ''; # Set paragraph mode

my @count=();
my $name;
while ( my $para = <$PROTFILE> ) {
    # Remove fasta header line
    if ( $para =~ s/^>(.*)//m ){
      $name = $1;
    };
    # Remove comment line(s)
    $para =~ s/^\s*#.*//mg;

    my %prot;
    $para =~ s/([A-Z])/ ++$prot{ $1 } /eg;
    
    my $num = scalar keys %prot;
    push @count,[$num,$name];
    printf "Counted %d for %s ..\n",$num,substr($name,0,50);
    
    print $out_file "$name\n";
    print $out_file join( ' ', map "$_=$prot{$_}", sort keys %prot ), 
+"\n";
    printf $out_file "Number of proteins = %d\n\n",$num ;
}

# sort names by count in ascending order to get lowest
my @sorted = sort { $a->[0] <=> $b->[0] } @count;
my $lowest = $sorted[0]->[0];

# maybe more than 1 lowest
printf $out_file "Least number of proteins is %d in these entries\n",$
+lowest;
my @lowest = grep { $_->[0] == $lowest } @sorted;
print $out_file "$_->[1]\n" for @lowest;

# show all results
print $out_file "\nAll results in ascending count\n";
for (@sorted){
  printf $out_file "%d  %s\n",@$_;
};
close $out_file;
print "Results in $report_name\n"
[download]

poj

Thank you so much. This is exactly what I was looking for. I really appreciate your help.

In the above written script, how can I make the script to spit out the length of the sequence that is being read? So, after the line  printf $out_file "Number of proteins = %d\n\n",$num ; in the above code, I tried -  printf $out_file "string length = length($num) ; but nothing happens. What am I doing wrong?

Hello Poj, In continuation to my previous question, I now want to count how many times a variable is absent. Ex: if in any given file, multiple entries don't have a W, I want the script to give me the output with the number of entries that don't have a W and similarly for other alphabets. So for instance, if 20 entries out of 100 in a file don't have a W, I want the output to be like W=20. How can that be done?