Open asgray opened 4 months ago
You have very few candidates to begin with, and the clean up process may determine all of them not valid.
Shujun
Hi @oushujun,
Should the line $trf=0 if /^-trf$/i and $ARGV[$k+1]!~/^-/;
be changed to $trf=$ARGV[$k+1] if /^-trf$/i and $ARGV[$k+1]!~/^-/;
in cleanup.pl?
I noticed that when specifying perl ./bin/cleanup.pl -trf 1, the trf program is not executed.
Hi @oushujun,
Should the line
$trf=0 if /^-trf$/i and $ARGV[$k+1]!~/^-/;
be changed to$trf=$ARGV[$k+1] if /^-trf$/i and $ARGV[$k+1]!~/^-/;
in cleanup.pl?I noticed that when specifying perl ./bin/cleanup.pl -trf 1, the trf program is not executed.
Good catch! You are correct. I have updated the code, and it will be pushed to GitHub in the next update. I don't think it's the solution of the initial post though.
Shujun
Hi, I'm in the process of updating to 2.9.9 from 2.9.0 and I'm seeing some odd outputs:
I believe the command that calls
cleanup.pl
is:perl ./bin/cleanup.pl -trf 1 -trf_path /usr/local/bin/trf -misschar N -nc 10 -nr 0.8 -minlen 100 -minscore 1000 -f dmel-smaller.fa.mod.ltrTE.fa > dmel-smaller.fa.mod.ltrTE.stg1
What is the expected behavior here?