Say that again please. I couldn't understand your paragraph. Please write
it again differently--more completely and accurately.
I want to understand what the problem is before I look at the program.
The program has some non-understandable (to me) or Google-unsearchable
descriptions but may be useful clues to the advanced perl and UNIX users.
Hope that will help.
=head1 OPTIONS
none other than "-h" (the output of which you're reading),
but you will either want trf and nseg in your PATH, or you will want
to set the environment variables TRF_COMMAND and NSEG_COMMAND to provide
the executable.
=head1 DESCRIPTION
This tool takes a repeat library, which is a Fasta-formatted sequence file,
and
filters out any sequence that is deemed to be more than 50% low-complexity
by either
TRF or NSEG or both. Note that one algorithm needs to make the
determination; we don't
check the total number of unique bases masked out by TRF and NSEG
individually.
=head1 ENVIRONMENT VARIABLES
In order for this program to find TRF and NSEG, you need to either place
said programs
in your PATH, or you need to add the environment variables TRF_COMMAND and
NSEG_COMMAND.
The value of those variables should be the path at which the respective
program can be
found.
=cut