Sponsored Content
Top Forums Shell Programming and Scripting Average within reps reformat according to second file Post 302941797 by sheetalk on Tuesday 21st of April 2015 08:51:54 AM
Old 04-21-2015
Let me explain once more with a simpler example.

I have a datafile where the columns are in no particular order and missing values indicated as "NULL".

Code:
Sample 	Loc 	Rep	T1	T2	C1	C2	C3
S1	L1	1	5	6	6	NULL	TY
S1	L1	2	NULL	8	YU	TY	NULL
S1	L2	1	7	NULL	GG	MP	RU
S2	L1	1	4	6	TY	NULL	NULL

This also could have been

Code:
T1	T2	C1	C2	C3	Sample 	Loc 	Rep
5	6	6	NULL	TY	S1	L1	1
NULL	8	YU	TY	NULL	S1	L1	2
7	NULL	GG	MP	RU	S1	L2	1
4	6	TY	NULL	NULL	S2	L1	1

Now I want to find the average of certain columns (listed in a query file) by headernames Sample and Loc. If there is a columnname in the query file like T3 which doesnt exist in the datafile, then just ignore that name.

Query file
Code:
T1
T2
T3


Output from this step

Code:
Sample 	Loc 	T1	T2
S1	L1	5	7
S1	L2	7	NULL
S2	L1	4	6

This can be reformatted by transposing to

Code:
	S1	S2
T1_L1	 5	4
T1_L2 	7	NULL
T2_L1 	7	6
T2_L2 	NULL	NULL

Now, there is a 3rd matrix file with the samples as columns

Code:
	S2	S1	S3
G1	11	22	77
G2	33	44	88
G3	55	66	99

I want to reformat this matrix to have as many columns as the output in the previous step and in the same order. Only the common samples are to be outputted for both files and in the same order.

Code:
	S1	S2
G1	22	11
G2	44	33
G3	66	55

Please let me know if I can explain further.
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

reformat the file

Hi all, I ran into this problem, hope you can help I have a text file like this: Spriden ID First Name Last Name Term Code Detail Code Amount Trans Date Description ... (3 Replies)
Discussion started by: CamTu
3 Replies

2. Shell Programming and Scripting

Reformat Crontab file

I need help writing a script that will reformat a crontab file. The first thing the script is doing is a crontab -l > crontab.txt. I need the crontab.txt file to read "8.00 PM every weekday (Mon-Fri) only in Oct." instead of the orig format "0 20 * 10 1-5" (1 Reply)
Discussion started by: alnita
1 Replies

3. Shell Programming and Scripting

Please help me reformat this file

I am working with a file of the form; 4256 7726 1 6525 716 1 7626 0838 1 8726 7623 2 8625 1563 2 1662 2628 3 1551 3552 3 1542 7984 ... (3 Replies)
Discussion started by: digipak
3 Replies

4. Shell Programming and Scripting

Reformat the data of a file.

I have a file which have data like A.txt a 1Jan I am in a1. 1Jan I was born. 2Jan I am here. 3Jan I am in a3. b 1Jan I am in b1. c 2Jan I am in c2. d 2Jan I am in d2. 5jan I am in d5. date in the file might be vary evertime. (9 Replies)
Discussion started by: samkhu
9 Replies

5. Shell Programming and Scripting

Reformat a file

I have a csv file with 11 columns. The first columns contains the User Id. One User id can have multiple sub Id. The value of Sub Id is in column 10. 100026,captjason@hawaii.rr.com ,jason ,wolford ,1/16/1969, ,US, ,96761 ,15 ,seg_id 100026,captjason@hawaii.rr.com ,jason ,wolford ,1/16/1969,... (3 Replies)
Discussion started by: r_t_1601
3 Replies

6. Shell Programming and Scripting

Reformat file using nawk

Hi all, I have a file with records that look something like this, "Transaction ID",Date,Email,"Card Type",Amount,"NETBANX Ref","Root Ref","Transaction Type","Merchant Ref",Status,"Interface ID","Interface Name","User ID" nnnnnnnnn,"21 Nov 2011 00:10:47",someone@hotmail.co.uk,"Visa... (2 Replies)
Discussion started by: dazedandconfuse
2 Replies

7. Shell Programming and Scripting

Major File Reformat

Hello, I have many lengthy files that need to be reformatted. I was hoping a sed or awk script could fix this. Here is an example of the original format: P0037 # Degree: 32.999981 # COMMAND: 03 (#01A) Scale 1.296875, 52 (Wooden Crate w/ #2 Label, Bahko) v -3328.000000 12.101541 437.000000... (2 Replies)
Discussion started by: Blue Solo
2 Replies

8. Shell Programming and Scripting

awk reformat file

Hello: When I tried a perl-oneliner to re-format fasta file. infile.fasta >YAL069W-1.334 Putative promoter CCACACCACACCCACACACC ACACCACACCCACACACACA ACAGCCCTAATCTAACCC >YAL068C-7235.2170 Putative ABC sequence TACGAGAATAATTT ACGTAAATGAAGTT TATATATAAA >gi|31044174|gb|AY143560.1|... (15 Replies)
Discussion started by: yifangt
15 Replies

9. Shell Programming and Scripting

[Solved] File reformat

I am using the code below to reformat the input (hp.txt). The output (newhp.txt) is not in the desired format and I can not seem to figure it out. I have attached both. Thank you. perl -aF/\\t/ -lne 'print join(" ",@F) for ("0 A","0 G","0 C","0 T","A 0","G 0","C 0","T 0")' hp.txt > newhp.txt ... (4 Replies)
Discussion started by: cmccabe
4 Replies

10. Shell Programming and Scripting

awk to reformat output if input file is empty, but not if file has data in it

The below awk improved bu @MadeInGermany, works great as long as the input file has data in it in the below format: input chrX 25031028 25031925 chrX:25031028-25031925 ARX 631 18 chrX 25031028 25031925 chrX:25031028-25031925 ARX 632 14... (3 Replies)
Discussion started by: cmccabe
3 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 06:29 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy