Question: Emboss Cons for getting consensus sequence for many files, not just one
gravatar for roblogan6
2.5 years ago by
roblogan630 wrote:

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:

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"; 
ADD COMMENTlink written 2.5 years ago by roblogan630
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1470 users visited in the last hour