On 28 Jul 2014, at 20:49, Sullivan, Catherine <[email protected]>
wrote:
> Sorry new to programming. Just wrote my first perl script, and using
> samtools piped into grep to get an calls at a specific location. However,
> each time it run the script and it runs samtools, I get this in STDOUT:
>
> [mpileup] 1 samples in 1 input files
> <mpileup> Set max per-sample depth to 8000
Samtools has always printed these messages to stderr, so to be precise I guess
the problem is that these messages are appearing on your terminal. Perhaps
your samtools/grep command looks something like
system("samtools arg arg arg | grep pattern");
so you could suppress these two lines with
system("samtools arg arg arg 2> /dev/null | grep pattern");
However that would also suppress any error messages output by samtools if
anything went wrong. So it would be better to redirect to a temporary file
("2> foo.tmp") and then have your Perl script check that for any lines other
than the two annoying ones and print them and exit if there are any.
(There are also more advanced techniques, but not ones that are recommended for
your first Perl script!)
> Anyway to re-direct this or prevent this, so I just get the output from the
> grep it is piped into? Doing this for multiple locations and want to create
> a file of the results, but have these two lines between each result.
One of these days we should probably add some sort of --quiet option to mpileup
to silence these messages for situations like this one.
John
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