Sponsored Content
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!
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

How to handle multiple rows in a file

I have a FILE a.txt which has the following data 113901.94,113901.94,56950.97,56950.97,NOT MATCHING,NOT MATCHING 10693.04,10693.04,5346.52,5346.52,NOT MATCHING,NOT MATCHING 1901.94,1901.94,550.97,550.97,NOT MATCHING,NOT MATCHING 103.04,103.04,53.52,53.52,NOT MATCHING,NOT MATCHING #### This... (2 Replies)
Discussion started by: ksmbabu
2 Replies

2. UNIX for Dummies Questions & Answers

Converting rows into multiple-rows

Hi every one; I have a file with 22 rows and 13 columns which includes floating numbers. I want to parse the file so that every five columns in the row would be a new record (row). For example, the first line in the old file should be converted into three lines with first two lines contain 5... (6 Replies)
Discussion started by: PHL
6 Replies

3. UNIX for Dummies Questions & Answers

grep command to find multiple strings in multiple lines in a file.

I want to search files (basically .cc files) in /xx folder and subfolders. Those files (*.cc files) must contain #include "header.h" AND x() function. I am writing it another way to make it clear, I wanna list of *.cc files that have 'header.h' & 'x()'. They must have two strings, header.h... (2 Replies)
Discussion started by: ritikaSharma
2 Replies

4. Shell Programming and Scripting

Split single rows to multiple rows ..

Hi pls help me out to short out this problem rm PAB113_011.out rm: PAB113_011.out: override protection 644 (yes/no)? n If i give y it remove the file. But i added the rm command as a part of ksh file and i tried to remove the file. Its not removing and the the file prompting as... (7 Replies)
Discussion started by: sri_aue
7 Replies

5. Shell Programming and Scripting

connecting to table to extract multiple rows into file from unix script

I need to extract the data from oracle table and written the below code. But it is not working.There is some problem with the query and output is shown is No rows selected" . If I run the same query from sql developer there is my required output. And if I run the shell script with simple sql... (7 Replies)
Discussion started by: giridhar276
7 Replies

6. UNIX for Dummies Questions & Answers

Write the total number of rows in multiple files into another file

Hello Friends, I know you all are busy and inteligent too... I am stuck with one small issue if you can help me then it will be really great. My problem is I am having some files i.e. Input.txt1 Input.txt2 Input.txt3 Now my task is I need to check the total number of rows in... (4 Replies)
Discussion started by: malaya kumar
4 Replies

7. Shell Programming and Scripting

awk to grep rows by multiple fields

Hello, I met a challenge to extract part of the table. I'd like to grep the first three matches based on field1 and field2. Input: D A 92.85 1315 83 11 D A 95.90 757 28 3 D A 94.38 480 20 7 D A 91.21 307 21 6 D A 94.26 244 ... (6 Replies)
Discussion started by: yifangt
6 Replies

8. Shell Programming and Scripting

How to get multiple rows from a file?

Gents, I have a big file, where I would like to get some rows.. Then file1 contains. Obs_Report_Result : Shot_Report : ... (4 Replies)
Discussion started by: jiam912
4 Replies

9. Shell Programming and Scripting

Grep and replace multiple strings in a file with multiple filenames in a file

Hi, I have a file containing list of strings like i: Pink Yellow Green and I have file having list of file names in a directory j : a b c d Where j contains of a ,b,c,d are as follows a: Pink (3 Replies)
Discussion started by: madabhg
3 Replies

10. Shell Programming and Scripting

Grep from multiple patterns multiple file multiple output

Hi, I want to grep multiple patterns from multiple files and save to multiple outputs. As of now its outputting all to the same file when I use this command. Input : 108 files to check for 390 patterns to check for. output I need to 108 files with the searched patterns. Xargs -I {} grep... (3 Replies)
Discussion started by: Diya123
3 Replies
comm(1) 							   User Commands							   comm(1)

NAME
comm - select or reject lines common to two files SYNOPSIS
comm [-123] file1 file2 DESCRIPTION
The comm utility reads file1 and file2, which must be ordered in the current collating sequence, and produces three text columns as output: lines only in file1; lines only in file2; and lines in both files. If the input files were ordered according to the collating sequence of the current locale, the lines written will be in the collating sequence of the original lines. If not, the results are unspecified. OPTIONS
The following options are supported: -1 Suppresses the output column of lines unique to file1. -2 Suppresses the output column of lines unique to file2. -3 Suppresses the output column of lines duplicated in file1 and file2. OPERANDS
The following operands are supported: file1 A path name of the first file to be compared. If file1 is -, the standard input is used. file2 A path name of the second file to be compared. If file2 is -, the standard input is used. USAGE
See largefile(5) for the description of the behavior of comm when encountering files greater than or equal to 2 Gbyte ( 2^31 bytes). EXAMPLES
Example 1 Printing a list of utilities specified by files If file1, file2, and file3 each contain a sorted list of utilities, the command example% comm -23 file1 file2 | comm -23 - file3 prints a list of utilities in file1 not specified by either of the other files. The entry: example% comm -12 file1 file2 | comm -12 - file3 prints a list of utilities specified by all three files. And the entry: example% comm -12 file2 file3 | comm -23 -file1 prints a list of utilities specified by both file2 and file3, but not specified in file1. ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of comm: LANG, LC_ALL, LC_COLLATE, LC_CTYPE, LC_MESSAGES, and NLSPATH. EXIT STATUS
The following exit values are returned: 0 All input files were successfully output as specified. >0 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWesu | +-----------------------------+-----------------------------+ |CSI |enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ SEE ALSO
cmp(1), diff(1), sort(1), uniq(1), attributes(5), environ(5), largefile(5), standards(5) SunOS 5.11 3 Mar 2004 comm(1)
All times are GMT -4. The time now is 04:48 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy