I wrote a perl script as a wrapper for a couple of calls to binaries. One of which is a call to the EMBOSS merger as such:

    $mergeCMD = "merger -asequence temp1.fa -bsequence temp2.fa -outfile temp.me -outseq temp.fa;
    system($mergeCMD);

It insists on printing  "Merge two overlapping sequences" for every call which annoys me to no end and clutters up my terminal. There are no evident cmd line options to turn this off, so i was thinking it could be possible to redirect this output away from stdout? Better yet would of course be if someone knew an option to make merger quiet.

You can add `-auto` to your command to turn off prompts. That is an EMBOSS standard.

The above is the right solution, but for reference, there are correct ways to capture the output of commands with Perl. [Capture::Tiny](https://metacpan.org/pod/Capture::Tiny) is lightweight does a nice job and [IPC::System::Simple](https://metacpan.org/pod/IPC::System::Simple) is a drop-in replacement for system that works better than the built-in (and avoids the shell). On that note, it is better to give a list to [system](http://perldoc.perl.org/functions/system.html) to avoid the shell and it is good to test if the command succeeded. 

You can test a command by looking at the return value, but that is unfortunately not as simple as it might seem (e.g., you have to localize errors and test if an error is coming from Perl or the external command). Those are the reasons I mention these modules. They do the right thing without a lot of boilerplate or cryptic code. If you want to localize and catch the exceptions you can use [Try::Tiny](https://metacpan.org/pod/Try::Tiny). All that is just for your consideration to make life a little easier. The command will work fine as written but it is good to keep these things in mind if you are building a pipeline. It is worth mentioning that there are wrappers for EMBOSS in BioPerl, so you can do something like the following (untested).


    use strict;
    use warnings;
    use Bio::Factory::EMBOSS;

    my $usage = "perl $0 a.seq b.seq";
    my $aseq  = shift or die $usage;
    my $bseq  = shift or die $usage;

    my $factory = Bio::Factory::EMBOSS->new;
    my $merger  = $factory->program('merger'); 

    $merger->run({-asequence => $bseq,
                  -bsequence => $aseq,
                  -outseq    => 'out.seq',
                  -outfile   => 'out.merged'});