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Top Forums Shell Programming and Scripting Perl Hashes, reading and hashing 2 files Post 302292895 by silkiechicken on Sunday 1st of March 2009 11:54:25 PM
Old 03-02-2009
That's fine and understandable. I read the user agreement that we can't ask you all do our "hw" for us. I have no problem with trying to read up and figure it out, just need some direction on where to look when the Perl help isn't really help. All it was giving me was that I had an unassigned variable?

It's kind of "school work" in that it will ultimately be used for my thesis research. I'm working on my PhD in Molecular and Cellular Biology and our lab has a mouse microarray data set, for which our post doc is currently manually searching though the sets by hand! Background is in bioengineering, so I didn't feel that it was a very efficient method to go data mining. I've put the data though SAMExcel to find the genes from the array which had a 1.4 fold change and have an associated list of affyID's, but need to connect them with the data found in the affyannotation files. I wish Affy would just use the accession numbers so we could look them up on NCBI or MGI directly, but that's the way it is. I'll stop rambling now though. LOL

I'll keep playing with it! Thanks for the help and suggestions!
 

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bup-margin(1)						      General Commands Manual						     bup-margin(1)

NAME
bup-margin - figure out your deduplication safety margin SYNOPSIS
bup margin [options...] DESCRIPTION
bup margin iterates through all objects in your bup repository, calculating the largest number of prefix bits shared between any two entries. This number, n, identifies the longest subset of SHA-1 you could use and still encounter a collision between your object ids. For example, one system that was tested had a collection of 11 million objects (70 GB), and bup margin returned 45. That means a 46-bit hash would be sufficient to avoid all collisions among that set of objects; each object in that repository could be uniquely identified by its first 46 bits. The number of bits needed seems to increase by about 1 or 2 for every doubling of the number of objects. Since SHA-1 hashes have 160 bits, that leaves 115 bits of margin. Of course, because SHA-1 hashes are essentially random, it's theoretically possible to use many more bits with far fewer objects. If you're paranoid about the possibility of SHA-1 collisions, you can monitor your repository by running bup margin occasionally to see if you're getting dangerously close to 160 bits. OPTIONS
--predict Guess the offset into each index file where a particular object will appear, and report the maximum deviation of the correct answer from the guess. This is potentially useful for tuning an interpolation search algorithm. --ignore-midx don't use .midx files, use only .idx files. This is only really useful when used with --predict. EXAMPLE
$ bup margin Reading indexes: 100.00% (1612581/1612581), done. 40 40 matching prefix bits 1.94 bits per doubling 120 bits (61.86 doublings) remaining 4.19338e+18 times larger is possible Everyone on earth could have 625878182 data sets like yours, all in one repository, and we would expect 1 object collision. $ bup margin --predict PackIdxList: using 1 index. Reading indexes: 100.00% (1612581/1612581), done. 915 of 1612581 (0.057%) SEE ALSO
bup-midx(1), bup-save(1) BUP
Part of the bup(1) suite. AUTHORS
Avery Pennarun <apenwarr@gmail.com>. Bup unknown- bup-margin(1)
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