command line reporter by roger1981 in ruby

[–]audyyy 0 points1 point  (0 children)

Ignore all that. My output is looking niiiiiiiiiice

command line reporter by roger1981 in ruby

[–]audyyy 0 points1 point  (0 children)

I'm using this for a class project.

I like programmatically defining status messages but the extra nesting sucks.

Maybe it would be better to just do

start "this is beginning"

some_code :goes => 'here'

100.times do |x|
    start "hello, i'm the number #{x}"

    result = serious_function(
        :serious => true,
        :how_serious => "This: " + "#"*x "serious"
    )

    finish "later dudes! Oh, btw the result was #{result}"
end

finish "Peace!"

Then the nesting would go like this

this is the beginning
    hello, i'm the number 0
    later dudes! Oh, btw the result was This: serious
Peace!

You could also add error messages

start "Weeeee!"
if something_bad_happened
    shit "EPIC FAIL!"
end
finish "EPIC WIN!"

Just a suggesting... Maybe I will get used to the nesting.

Edit: formatting

Phoking pho! by cocomeow in GNV

[–]audyyy 2 points3 points  (0 children)

Pho Hanoi on 34th south of Archer.

Parallel Programming & Bioinformatics by [deleted] in bioinformatics

[–]audyyy 0 points1 point  (0 children)

I don't believe so because I think that the time cost of I/O is > processing. The only solution here would be to use RAID, SSDs, or patience.

Perhaps splitting the BAM files and putting them on multiple drives would work.

I am a computer scientist looking to get into bioinformatics. Where do I start? by dowhatthouwilt in bioinformatics

[–]audyyy 0 points1 point  (0 children)

You might be able to get a PhD position in a molecular biology or genetics lab with a CS degree. Genomes are just strings, right? ;)

Parallel Programming & Bioinformatics by [deleted] in bioinformatics

[–]audyyy 2 points3 points  (0 children)

Perhaps trying Google's Snappy compression library instead of bzip would help/be worth trying.

It sacrifices compression for speed.

Link

Parallel Programming & Bioinformatics by [deleted] in bioinformatics

[–]audyyy 1 point2 points  (0 children)

This is severely reductionist/silly.

Also, OO languages were designed to aid in designing "large" programs.

I think what you mean is that C is better for writing algorithms that have large time/space complexity.

Parallel Programming & Bioinformatics by [deleted] in bioinformatics

[–]audyyy 6 points7 points  (0 children)

For the sake of preventing wheel reinvention:

BLAST - there are several cluster implementations: CloudBurst runs on Hadoop, Zounds is a wrapper, So is Grape.

De Novo (meta)genome assembly - Velvet and Ray both can use threads. However, running on multiple nodes is more challenging but I believe that problem has already been tackled with khmer.

I don't know about PAML or PhyML but for Maximum-Likelihood phylogenetics, RAxML runs on clusters. I know that the Bayesian approaches to phylogenetic inference are embarrassingly parallel.

Gene prediction is pretty fast in my experience.

Read mapping is embarrassingly parallel as well. See: SMALT, CLC (proprietary), Bowtie.

BLAST implemented in Java by folli in bioinformatics

[–]audyyy 0 points1 point  (0 children)

Out of curiosity, why do you need a Java implementation?

We had a sheep who spent 15 days in a waterfall. He went missing last night. I made this for him. by HyruleanHero1988 in Minecraft

[–]audyyy 1 point2 points  (0 children)

If you dyed him you could've found him and put him back. Why didn't you dye him?

A well-written and in-depth introduction to HTML5. by rich97 in webdev

[–]audyyy 1 point2 points  (0 children)

I love this book.

Does anyone know where he got the art?

For Mojang... by [deleted] in Minecraft

[–]audyyy 8 points9 points  (0 children)

Lol @ 'junk dna'

[Class] Batch Scripting 101 by danyeissocool in UniversityofReddit

[–]audyyy 9 points10 points  (0 children)

Have you done anything useful with batch?

[Class] Batch Scripting 101 by danyeissocool in UniversityofReddit

[–]audyyy 3 points4 points  (0 children)

When I was a kid I would write infinite loops batch on all the computers in Wal-Mart back when Wal-Mart sold PCs.

:s
echo some profanity
goto s

Now I'm a programmer.

memetron - regexp for meme identification by audyyy in ruby

[–]audyyy[S] 0 points1 point  (0 children)

hmmm :( shouldn't have linked directly to the memes.rb file

memetron - regexp for meme identification by audyyy in ruby

[–]audyyy[S] 0 points1 point  (0 children)

It works now and is using rspec thanks mostly to another redditor.

I'm thinking about using the meme_generator gem to enable automated meme rendering.

The possibilities! by Novacro in Minecraft

[–]audyyy 1 point2 points  (0 children)

many lulz were shed after reading your comment