calculating molecular weight in perl

Question

I have a perl script but it calculate molecular weight only when sequence is given. However I want to calculate molecular weight of protein sequences which is in fasta file.

print "Enter the amino acid sequence:
";  
$a = < STDIN > ; 
chomp($a);
my @a = ();
my $a = '';
$x = length($a); 
print "Length of sequence is : $x";
@a = split('', $a); 
$b = 0; 
my %data = ( 
    A=>71.09,  R=>16.19,  D=>114.11,  N=>115.09, 
    C=>103.15,  E=>129.12,  Q=>128.14,  G=>57.05, 
    H=>137.14,  I=>113.16,  L=>113.16,  K=>128.17, 
    M=>131.19,  F=>147.18,  P=>97.12,  S=>87.08, 
    T=>101.11,  W=>186.12,  Y=>163.18,  V=>99.14 
); 
foreach $i(@a) { 
    $b += $data{$i}; 
} 
$c = $b - (18 * ($x - 1)); 
print "
The molecular weight of the sequence is $c";             

Answer 1

first of all u must tell us what format has .fasta files. As i know they looks like

>seq_ID_1 descriptions etc 
ASDGDSAHSAHASDFRHGSDHSDGEWTSHSDHDSHFSDGSGASGADGHHAH
ASDSADGDASHDASHSAREWAWGDASHASGASGASGSDGASDGDSAHSHAS
SFASGDASGDSSDFDSFSDFSD

>seq_ID_2 descriptions etc
ASDGDSAHSAHASDFRHGSDHSDGEWTSHSDHDSHFSDGSGASGADGHHAH
ASDSADGDASHDASHSAREWAWGDASHASGASGASG

if we will make suggestion that your code works fine, and counts molecular weight all we need is to read fasta files, parse them and count weight by yours code. It's more easy that sounds like.

#!/usr/bin/perl

use strict;
use warnings;
use Encode;


for my $file (@ARGV) {
    open my $fh, '<:encoding(UTF-8)', $file;
    my $input = join q{}, <$fh>; 
    close $fh;
    while ( $input =~ /^(>.*?)$([^>]*)/smxg ) {
        my $name = $1;
        my $seq = $2;
        $seq =~ s/
//smxg;
        my $mass = calc_mass($seq);
        print "$name has mass $mass
";
    }
}

sub calc_mass {
    my $a = shift;
    my @a = ();
    my $x = length $a;
    @a = split q{}, $a;
    my $b = 0;
    my %data = (
        A=>71.09,  R=>16.19,  D=>114.11,  N=>115.09,
        C=>103.15,  E=>129.12,  Q=>128.14,  G=>57.05,
        H=>137.14,  I=>113.16,  L=>113.16,  K=>128.17,
        M=>131.19,  F=>147.18,  P=>97.12,  S=>87.08,
        T=>101.11,  W=>186.12,  Y=>163.18,  V=>99.14
    );
    for my $i( @a ) {
        $b += $data{$i};
    }
    my $c = $b - (18 * ($x - 1));
    return $c;
}