Sponsored Content
Top Forums UNIX for Dummies Questions & Answers Problem to grep contents from a file Post 302970381 by Skrynesaver on Wednesday 6th of April 2016 06:44:07 AM
Old 04-06-2016
Perhaps explicitly state that you want to grep against STDIN...

Code:
 gzip -dc ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz | grep -f HIGH_conf_chrom2.txt - > 1000G_chrom2.txt

 

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

how to strip out the contents of file using grep

Hi, I am receving a file from remote site which has EDI information for 830, 862 and 997 and I want to extect the data for 997 using grep's or any other methods. The data look like this: ISA~000 0000-0001-1000~997 AK1000~m 000~IEA~M ISA~000 0000-0001-1000~849 000~IEA~M ISA~000... (11 Replies)
Discussion started by: isingh786
11 Replies

2. Shell Programming and Scripting

Copy subsequent contents of a file from first occurance of grep

There is a file which logs all errors and alerts of the database called alert log. I have a requirement as follows: 1. Check the current date and search for the first occurance of the current date in the alert log. 2. As soon as the first occurance is found, copy the subsequent contents... (5 Replies)
Discussion started by: sunpraveen
5 Replies

3. Shell Programming and Scripting

Execution problem with sort the file based on contents

My input file: >ali ASSDDGHFHFHJFJHJDSDGSDGSDGSDGSDGSDGSDGDSGDSGSDGDSGSDGSDGDSGSDGGDSG >zzz ASdASDASDSADSADDSADJKHJDSADKLJADKLSAJDLJLKJLDASDDSADd >abu ASDASDFSAFASFSADFASDASDSADSADSADSADSADSADASDASdSADSADSADA >aaa... (2 Replies)
Discussion started by: patrick87
2 Replies

4. Shell Programming and Scripting

find file and print only contents with a hit by grep

Hi, can someone help me. I have some files and search a content in this files. If i have a hit I will print a output: filename:content But are more hits in one file: The output is always filename:content E.G. Seach about "three" file1 {one, two, three, four, three} file2... (5 Replies)
Discussion started by: Timmää
5 Replies

5. Shell Programming and Scripting

How to grep the contents inside a tar file

Hi All I have searched the possibility of this options everywhere but am unable to find it in any forum. I have a tar file inside which there are n number of files and i dont know them. I need to grep a word inside the tar file and need to know in which file the word resides. > cat a... (2 Replies)
Discussion started by: Whiteboard
2 Replies

6. Shell Programming and Scripting

Grep a pattern given in one file at other file and display its corresponding contents as output.

***************************************** Right now i have this current system. I have two files say xxx.txt and yyy.txt. xxx.txt is with list of patterns within double quotes. Eg. "this is the line1" "this is the line2" The yyy.txt with lot of lines. eg: "This is a test message which... (7 Replies)
Discussion started by: abinash
7 Replies

7. Shell Programming and Scripting

script to grep a pattern from file compare contents with another file and replace

Hi All, Need help on this I have 2 files one file file1 which has several entries as : define service{ hostgroup_name !host1,!host5,!host6,.* service_description check_nrpe } define service{ hostgroup_name !host2,!host4,!host6,.* service_description check_opt } another... (2 Replies)
Discussion started by: namitai
2 Replies

8. Shell Programming and Scripting

Grep -v contents of a list file from another file.

Hello, I am trying to get output from FILE2 that excludes servers from list FILE1. I've tried a for loop with no success. Any ideas how to go about this? FILE1 contains: server1 server2 server3 server4 server5 FILE2 contains: server1:ERROR:user1: error message... (2 Replies)
Discussion started by: LinuxRacr
2 Replies

9. Shell Programming and Scripting

Problem with the awk in searching the contents in a file

Hello all, I am a newbie in awk. I am struggling in this problem for a long.Actually I have two files, filea and fileb. File a is actually a search key through it I have to find the corresponding japanese tag from file b. filea contains the data like this: sm982882 sm1893548 sm2420025... (3 Replies)
Discussion started by: csim_mohan
3 Replies

10. Shell Programming and Scripting

need to grep contents of a file within specific time span. regex i am using is not working

Hi , I am trying to extract contents of a file between specified time stamp. but it does not seem to work. i am trying to extract output of /var/adm/messages between 15:00:00 to 15:23:59 . i have tried two regex the first one seems to kind of work. it displays some output. the second one is... (13 Replies)
Discussion started by: chidori
13 Replies
XZGREP(1)							     XZ Utils								 XZGREP(1)

NAME
xzgrep - search compressed files for a regular expression SYNOPSIS
xzgrep [grep_options] [-e] pattern file... xzegrep ... xzfgrep ... lzgrep ... lzegrep ... lzfgrep ... DESCRIPTION
xzgrep invokes grep(1) on files which may be either uncompressed or compressed with xz(1), lzma(1), gzip(1), or bzip2(1). All options specified are passed directly to grep(1). If no file is specified, then the standard input is decompressed if necessary and fed to grep(1). When reading from standard input, gzip(1) and bzip2(1) compressed files are not supported. If xzgrep is invoked as xzegrep or xzfgrep then egrep(1) or fgrep(1) is used instead of grep(1). The same applies to names lzgrep, lze- grep, and lzfgrep, which are provided for backward compatibility with LZMA Utils. ENVIRONMENT
GREP If the GREP environment variable is set, xzgrep uses it instead of grep(1), egrep(1), or fgrep(1). SEE ALSO
grep(1), xz(1), gzip(1), bzip2(1), zgrep(1) Tukaani 2009-07-05 XZGREP(1)
All times are GMT -4. The time now is 07:34 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy