Re: [MUMmer-help] standard input for repeat-match

[Adam P. <aph...@gm...>]

Hey Lee,
Not my program, but I checked the code and it requires a file name on the
command line. You may be able to trick it by doing:

> repeat-match /dev/stdin

Best,
-Adam


On Tue, Jan 8, 2013 at 9:46 PM, Lee Katz <ls...@gm...> wrote:

> is it possible to do standard input for repeat-match?  I have a script
> where I am running it many times in multiple threads, and I think it is
> slowing my script because of hard drive IO.  I am hoping that it will be
> faster to do something like
>
> #!/usr/bin/env perl
> $repeat=`echo 'AAAAATTAAAAA' | repeat-match -n 4 -t -E | tail -n +3 | sort
> -k1,1n -k2,2n`
>
> One more thing is that I tried this CLI trick, but it didn't work (not
> really sure what I expected to happen)
> $ perl -e '`repeat-match -n 4 -t -E <(echo "AAAAATTAAAAA")`'
>
> This does work though
> $ repeat-match -n 4 -E -t <(echo "AAAAATTCAAAAA") # no results though
>
> Thank you for your help!
>
> --
> Lee Katz, Ph.D.
>
>
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