External program called with backticks still produces output

Question

so I call an external program in perl and want to capture it's output:

my @RNAalifoldOut = `RNAalifold some parameters`;

If called from command line the output consists of three lines, e.g:

4 sequences; length of alignment 48.
__GCCGA_UGUAGCUCAGUUGGG_AGAGCGCCAGACUGAAAAUCAGA 
...((((.....((((.........)))).(((((.......)))))

However my array @RNAalifoldOut contains only the two last lines and the first line appears directly on the screen when the line is being executed.

How can this be? I thought maybe the program writes the first line to STDERR, but isn't that discarded by the backticks operator? And what could I do to hide this output?

Regards Nick

Answer 1

You are likely seeing the standard error from RNAalifold. Backticks capture only the standard output.

Capture both standard output and standard error by changing your code to

my @RNAalifoldOut = `RNAalifold some parameters 2>&1`;

To discard the standard error, use

my @RNAalifoldOut = `RNAalifold some parameters 2>/dev/null`;

on Unix-like platforms. On Windows, use

my @RNAalifoldOut = `RNAalifold some parameters 2>nul`;