Emboss Cons for getting consensus sequence for many files, not just one

Question

I installed and configured emboss and can run the simple command line arguments for getting the consensus of one previously aligned multifasta file:

% cons

Create a consensus sequence from a multiple alignment

Input (aligned) sequence set: dna.msf

output sequence [dna.fasta]: aligned.cons

This is perfect for dealing with one file at a time, but I have hundreds to process. I have started to write a perl script with a foreach loop to try and process this for every file, but I guess I need to be outside of the script to run these commands. Any clue on how I can run a command line friendly program for getting a single consensus sequence in fasta format from a previously aligned multifasta file, for many files in succession? I don't have to use emboss- I could use another program. Here is my code so far:

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

   my $dir = ("/Users/roblogan/Documents/Clustered_Barcodes_Aligned");

    my @ArrayofFiles = glob "$dir/*"; #put all files in the directory into an array

    #print join("\n", @ArrayofFiles), "\n";  #diagnostic print

    foreach my $file (@ArrayofFiles){
            print 'cons', "\n";
            print "/Users/roblogan/Documents/Clustered_Barcodes_Aligned/Clustered_Barcode_Number_*.*.Sequences.txt.out", "\n";
            print "*.*.Consensus.txt", "\n"; 
    } 

Answer 1

EMBOSS cons has two mandatory qualifier:

1. - sequence( to provide the input sequence)

2. - outseq (for output).

so you need to provide the above to field .

Now change your code little bit to run multiple program:

my $count=1;
foreach my $file (@ArrayofFiles){
            $output_path= "/Users/roblogan/Documents/Clustered_Barcodes_Aligned/";
            my $output_file = $output_path. "out$count";# please change here to get your desired output filename 
            my $command = "cons -sequence '$file' -outseq '$output_file' "; 
            system($command);
            $count ++;
} 

Hope the above code will work for you.