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

[Lee K. <ls...@gm...>]

Hey, it works!  Good trick!  Thanks!


On Mon, Jan 21, 2013 at 3:42 PM, Adam Phillippy <aph...@gm...>wrote:

> 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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>


-- 
Lee Katz, Ph.D.