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Top Forums Shell Programming and Scripting Need help comparing Base Pairs within PERL Post 302651297 by drossy on Tuesday 5th of June 2012 09:46:21 AM
Old 06-05-2012
Need help comparing Base Pairs within PERL

Hi I have a multi-step project I am working on and have been finding it difficult to come up with the correct approach.
The data I have been given resembles:

Code:
 
Index      Chr       Genotype   Mutation Type
1           Chr1           TT            Intronic
2           Chr1           AA            Exonic
3           Chr1           AG            Exonic
4           Chr1           CC            Frameshift
5           Chr1           CA            Intronic
...         ...              ....

My goal here is to compare a large file such as this one to a set of references that are a single letter (T,A,C,G). I need to split the genotype in the given file into two individual letters and then compare this to the reference. If either matches the reference, then the program should move on to the next reference. If, however, neither letter is consistant, then the program should give an output of the index number and mutation type that corresponds to that data.
I am still fairly new to this so all help would be greatly appreciated.
Thanks!
 

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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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