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Top Forums Shell Programming and Scripting grep multiple rows from file. Post 302352843 by yifangt on Sunday 13th of September 2009 10:37:53 PM
Old 09-13-2009
grep multiple rows from file.

Hi, I have file1 that contains many columns as show the first three below:
Code:
"At1g29930"     198     2105
"At5g46430"     5569     9576
"At1g64740"     1908     2505
"At5g46430"     6717     11317
"At1g64740"     453     655
"At1g12470"     33     18
"At1g80680"     149     262
"At1g23040"     6351     2620
"At1g31390"     -18     87
"At5g19860"     -30     68
"At1g80470"     -49     85
"IC-At1g29930-1 um"     2203     1713
"IC-At1g29930-5 um"     4873     3668
"At5g19860.1"     90     132
"At5g20520"     6     81
"At1g80680.1"     123     186

What I want is to extract the rows from file1 by the first column that contains my following list in file2:

Code:
At5g46430
At1g64740
At1g12470
At1g80680
At1g23040
At1g31390
At5g19860
At1g80470
At1g29930
At5g20520

Members in file2 are unique but in file1 they may have multiple copies or iso-forms, like At1g80680 and At1g80680.1. My challenge is to get the rows in file1 that matches exactly by

Code:
grep -wf file2 file1 > file3;

If there is multiple match, get one (or the first one?) and ignore the rest (eg At1g29930, not IC-At1g29930-1 um or IC-At1g29930-5 um), but it did not work. Any help is highly appreciated!

Last edited by vgersh99; 09-14-2009 at 09:51 AM.. Reason: code tags, PLEASE!
 

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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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