no subs

nosubs.pl

#!/usr/bin/env perl
######################################################################################
## enzyme_digestion.pl
#######################################################################################
use warnings;
use strict;
use diagnostics;

#Defining user options
use vars qw($opt_t $opt_l $opt_a $opt_v $opt_c $opt_h);
use Getopt::Std;

#Setting missed cleavages to a default value of 0
my $n_missed_cleavages = (defined $opt_c) ? $opt_c : 0;

#Declaring arrays and variables
my (@proteins, @sequences, @peptides, @mc_peptides);
my ($protein,$sequence, $peptide, $unusual_counter,$unknown_counter, $protein_size,$peptide_size, $mc_peptide_size,$n,$r,$s,$i,$j);

############################################################################
###########               Main subroutine
###########
############################################################################
@proteins=("DAAARAATTLTTTAKMTTTTTTCKMMFRPPPPPGGGGGGGGGGGG","ALTAMCMNVWEITYHKGSDVNRRASFAQPKPPQPPRPPLLARIKPASDASD");
main();
sub main {
        # If there is no user input, error message and usage are displayed and program closes
   #     if (!getopts ('tlavc:h')) {
    #            error_out("No arguments recognized");
        }
#        if ($opt_h) {
 #               help();
  #              exit;
        }
        # Reading FASTA file and eliminating header and blank spaces
        foreach $protein (@proteins) {
                if ($protein !~ /^>/) {
                        # Counting unusual and unknown aminoacids
                        if ($protein=~ m/(BOUJZ)/g){$unusual_counter++;}
                        if ($protein=~ m/X/g) {$unknown_counter++;}
                        $protein =~ s/\s//g;
                        @sequences = chomp ($protein);
                }
        }
####    print "Hasta aqui funciona\n";
        for $sequence (@sequences) {
           if ($opt_t) {
              my @peptides = split (/(?<=[RK])(?!P)/, $sequence);
           }
           elsif ($opt_l) {
              my @peptides = split (/(?<=[K])(?!P)/, $sequence);
           }
           elsif ($opt_a) {
              my @peptides = split (/(?<=[R])(?!P)/, $sequence);
           }
           elsif ($opt_v) {
              my @peptides = split (/(?<=[E])(?!P)/, $sequence);
           }
          else {
                  print "nope";
                   # If no enzymes are selected, error message and usage are printed on the screen
            #       error_out("No enzyme selected");
                }
        }
       print "Hasta aqui si llega\n"; 
}