Visit Our UNIX and Linux User Community


Column problems with vi


 
Thread Tools Search this Thread
Top Forums UNIX for Dummies Questions & Answers Column problems with vi
# 1  
Old 08-03-2009
Column problems with vi

Basically I have a very large amount of genetic data in the format

marker_ID Species marker_ID marker_ID Parent1 Parent2 Sex Genotype

As you can see the data I have has marker_ID listed 3 times, I need to get rid of colum one and column three (both titled marker_ID). There are thousands of rows and columns and doing this by hand would probably take me all day.
I need to change the format in order to run this data in Plink, a whole genome association tool.
I have looked at similar posts and I dont think they are relevant as they do not need to delete 2 different columns.

The genotype column is actually over 24,000 columns as that is the genetic information - didnt explain that very well hence first reply

Thanks

Last edited by aistiby; 08-03-2009 at 02:44 PM..
# 2  
Old 08-03-2009
Code:
awk '{ print $2, $4, $5, $6, $7 }' inputfile >  newfile

 

Previous Thread | Next Thread
Test Your Knowledge in Computers #700
Difficulty: Medium
In the theory of Vernadsky, the noosphere is the fifth in a succession of phases of related to the development of the Earth.
True or False?

10 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

If pattern in column 3 matches pattern in column 2 (any row), print value in column 1

Hi all, I have searched and searched, but I have not found a solution that quite fits what I am trying to do. I have a long list of data in three columns. Below is a sample: 1,10,8 2,12,10 3,13,12 4,14,14 5,15,16 6,16,18 Please use code tags What I need to do is as follows: If a... (4 Replies)
Discussion started by: bleedingturnip
4 Replies

2. Shell Programming and Scripting

Bring values in the second column into single line (comma sep) for uniq value in the first column

I want to bring values in the second column into single line for uniq value in the first column. My input jvm01, Web 2.0 Feature Pack Library jvm01, IBM WebSphere JAX-RS jvm01, Custom01 Shared Library jvm02, Web 2.0 Feature Pack Library jvm02, IBM WebSphere JAX-RS jvm03, Web 2.0 Feature... (10 Replies)
Discussion started by: kchinnam
10 Replies

3. Shell Programming and Scripting

Problems with awk (fatal error) and paste (two variables into one column-by-column)

Hello, I have a script extracting columns of useful numbers from a data file, and manipulating the numbers with awk commands. I have problems with my script... 1. There are two lines assigning numbers to $BaseForAveraging. If I use the commented line (the first one) and let the second one... (9 Replies)
Discussion started by: vgbraymond
9 Replies

4. Shell Programming and Scripting

awk Print New Column For Every Two Lines and Match On Multiple Column Values to print another column

Hi, My input files is like this axis1 0 1 10 axis2 0 1 5 axis1 1 2 -4 axis2 2 3 -3 axis1 3 4 5 axis2 3 4 -1 axis1 4 5 -6 axis2 4 5 1 Now, these are my following tasks 1. Print a first column for every two rows that has the same value followed by a string. 2. Match on the... (3 Replies)
Discussion started by: jacobs.smith
3 Replies

5. Shell Programming and Scripting

Converting Single Column into Multiple rows, but with strings to specific tab column

Dear fellows, I need your help. I'm trying to write a script to convert a single column into multiple rows. But it need to recognize the beginning of the string and set it to its specific Column number. Each Line (loop) begins with digit (RANGE). At this moment it's kind of working, but it... (6 Replies)
Discussion started by: AK47
6 Replies

6. Shell Programming and Scripting

Difference of the same column when two other column matches and one column differs less than 1 hour

This is my input file : # cat list 20130430121600, cucm, location,76,2 20130430121600,cucm1,location1,76,4 20130430122000,cucm,location,80,8 20130430122000,cucm1,location1,90,8 20130430140000,cucm1,location1,87,11 20130430140000, cucm,location,67,9 This is the required output ... (1 Reply)
Discussion started by: Lakshmikumari
1 Replies

7. UNIX for Dummies Questions & Answers

Rename a header column by adding another column entry to the header column name

Hi All, I have a file example.csv which looks like this GrpID,TargetID,Signal,Avg_Num CSCH74_1_1,2007,61,256 CSCH74_1_1,212007,647,679 CSCH74_1_1,12007,3,32 CSCH74_1_1,207,299,777 I want the output as GrpID,TragetID,Signal-CSCH74_1_1,Avg_Num CSCH74_1_1,2007,61,256... (1 Reply)
Discussion started by: Vavad
1 Replies

8. Shell Programming and Scripting

Rename a header column by adding another column entry to the header column name URGENT!!

Hi All, I have a file example.csv which looks like this GrpID,TargetID,Signal,Avg_Num CSCH74_1_1,2007,61,256 CSCH74_1_1,212007,647,679 CSCH74_1_1,12007,3,32 CSCH74_1_1,207,299,777 I want the output as GrpID,TragetID,Signal-CSCH74_1_1,Avg_Num CSCH74_1_1,2007,61,256... (4 Replies)
Discussion started by: Vavad
4 Replies

9. Shell Programming and Scripting

Match column 3 in file1 to column 1 in file 2 and replace with column 2 from file2

Match column 3 in file1 to column 1 in file 2 and replace with column 2 from file2 file 1 sample SNDK 80004C101 AT XLNX 983919101 BB NETL 64118B100 BS AMD 007903107 CC KLAC 482480100 DC TER 880770102 KATS ATHR 04743P108 KATS... (7 Replies)
Discussion started by: rydz00
7 Replies

10. Shell Programming and Scripting

Changing one column of delimited file column to fixed width column

Hi, Iam new to unix. I have one input file . Input file : ID1~Name1~Place1 ID2~Name2~Place2 ID3~Name3~Place3 I need output such that only first column should change to fixed width column of 15 characters of length. Output File: ID1<<12 spaces>>Name1~Place1 ID2<<12... (5 Replies)
Discussion started by: manneni prakash
5 Replies

Featured Tech Videos