Sponsored Content
Top Forums Shell Programming and Scripting Count specific characters at specific column positions Post 302739575 by thienxho on Tuesday 4th of December 2012 12:06:27 PM
Old 12-04-2012
Count specific characters at specific column positions

Hi all, I need help.

I have an input text file (input.txt) like this:

Code:
21	GTGCAACACCGTCTTGAGAGG	50
21	GACCGAGACAGAATGAAAATC	73
21	CGGGTCTGTAGTAGCAAACGC	108
21	CGAAAAATGAACCCCTTTATC	220
21	CGTGATCCTGTTGAAGGGTCG	259

Now I need to count A/T/G/C numbers at each character location in column 2, in this case is always 21 characters, but can be variable.

Output (output.txt) will need to be:

Code:
A	0	1	1	1	3	3	1	2	0	3	1	1	2	1	1	2	3	2	3	0	0
T	0	0	1	0	1	1	1	1	2	0	1	2	0	1	0	1	1	1	1	2	0
G	2	3	2	2	1	0	1	1	1	1	3	0	1	1	1	2	1	2	0	2	2
C	3	0	1	2	0	1	2	1	2	1	0	1	2	1	2	0	0	0	1	1	3

I can do this in Excel, but my file is way bigger than Excel can handle.

Thanks!

Last edited by Scott; 12-04-2012 at 01:07 PM.. Reason: Please use code tags
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

count characters in specific records

I have a text file which represents a http flow like this: HTTP/1.1 200 OK Date: Fri, 23 Jan 2009 17:16:24 GMT Server: Apache Last-Modified: Fri, 23 Jan 2009 17:08:03 GMT Accept-Ranges: bytes Cache-Control: max-age=540 Expires: Fri, 23 Jan 2009 17:21:31 GMT Vary: Accept-Encoding ... (1 Reply)
Discussion started by: littleboyblu
1 Replies

2. Shell Programming and Scripting

Insert a text from a specific row into a specific column using SED or AWK

Hi, I am having trouble converting a text file. I have been working for this whole day now, still i couldn't make it. Here is how the text file looks: _______________________________________________________ DEVICE STATUS INFORMATION FOR LOCATION 1: OPER STATES: Disabled E:Enabled ... (5 Replies)
Discussion started by: Issemael
5 Replies

3. Shell Programming and Scripting

Assigning a specific format to a specific column in a text file using awk and printf

Hi, I have the following text file: 8 T1mapping_flip02 ok 128 108 30 1 665000-000008-000001.dcm 9 T1mapping_flip05 ok 128 108 30 1 665000-000009-000001.dcm 10 T1mapping_flip10 ok 128 108 30 1 665000-000010-000001.dcm 11 T1mapping_flip15 ok 128 108 30... (2 Replies)
Discussion started by: goodbenito
2 Replies

4. UNIX for Dummies Questions & Answers

Unix command to count the number of files with specific characters in name

Hey all, I'm looking for a command that will search a directory (and all subdirectories) and give me a file count for the number of files that contain specific characters within its filename. e.g. I want to find the number of files that contain "-a.jpg" in their name. All the searching I've... (6 Replies)
Discussion started by: murphysm
6 Replies

5. Shell Programming and Scripting

How to count occurrences in a specific column

Hi, I need help to count the number of occurrences in $3 of file1.txt. I only know how to count by checking one by one and the code is like this: awk '$3 ~ /aku hanya poyo/ {++c} END {print c}' FS="\t" file1.txt But this is not wise to do as i have hundreds of different occurrences in that... (10 Replies)
Discussion started by: redse171
10 Replies

6. Shell Programming and Scripting

Can't figure out how to find specific characters in specific columns

I am trying to find a specific set of characters in a long file. I only want to find the characters in column 265 for 4 bytes. Is there a search for that? I tried cut but couldn't get it to work. Ex. I want to find '9999' in column 265 for 4 bytes. If it is in there, I want it to print... (12 Replies)
Discussion started by: Drenhead
12 Replies

7. Shell Programming and Scripting

Count specific column values

Hi all: quick question! I have the following data that resembles some thing like this: i am tired tired am i what is up hello people cool I want to count (or at least isolate) all of the unique elements in the 2nd column. I have tried this: cut -f 2 | uniq 'input' which does... (3 Replies)
Discussion started by: owwow14
3 Replies

8. Shell Programming and Scripting

Count frequency of unique values in specific column

Hi, I have tab-deliminated data similar to the following: dot is-big 2 dot is-round 3 dot is-gray 4 cat is-big 3 hot in-summer 5 I want to count the frequency of each individual "unique" value in the 1st column. Thus, the desired output would be as follows: dot 3 cat 1 hot 1 is... (5 Replies)
Discussion started by: owwow14
5 Replies

9. Shell Programming and Scripting

Overwrite specific column in xml file with the specific column from adjacent line

I have an xml file dumped from rrd file, that I want to "patch" so the xml file doesn't contain any blank hole in the resulting graph of the rrd file. Here is the file. <!-- 2015-10-12 14:00:00 WIB / 1444633200 --> <row><v> 4.0419731265e+07 </v><v> 4.5045912770e+06... (2 Replies)
Discussion started by: rk4k
2 Replies

10. Shell Programming and Scripting

Search and replace specific positions of specific lines

Hi, I have a file with hundreds of lines. I want to search for particular lines starting with 4000, search and replace the 137-139 position characters; which will be '000', with '036'. Can all of this be done without opening a temp file and then moving that temp file to the original file name. ... (7 Replies)
Discussion started by: dsid
7 Replies
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)
All times are GMT -4. The time now is 05:40 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy