Sponsored Content
Top Forums Shell Programming and Scripting Grep two files: -F flag gives weird output Post 303007372 by Don Cragun on Wednesday 15th of November 2017 05:36:09 PM
Old 11-15-2017
You say MEF2C is in the gene list, but it is not present in the file you provided???

What operating system are you using? The standards don't specify the meaning of a grep -w option. Note also that by some definitions of "word" the line:
Code:
19 19257646 19257646 exonic MEF2B,MEF2BNB-MEF2B nonsynonymous SNV

does not contain the word MEF2BNB-MEF2B, but does the three words MEF2B (twice), MEF2BNB (once), and SNV (once). Are you sure that grep -w is using the same definition of "word" that you are expecting?

Is there by any chance an empty line in your gene file?

Are the files you're processing UNIX text files? (Or, might they be DOS text files?)
This User Gave Thanks to Don Cragun For This Post:
 

10 More Discussions You Might Find Interesting

1. AIX

Weird bootlist output

just setup a new system today - 9117 570, using HMC for console but not partitioned. I installed this system twice. the first time it started off as 5300-00, then updated to ML03. before the update, I believe I mirrored the rootvg, and then altered the bootlist, at that point, the display was... (4 Replies)
Discussion started by: davew1099
4 Replies

2. Shell Programming and Scripting

weird behavior of grep -P

I met a problem in using grep -P. There is a text file, temp.txt, whose content is: dddd abc I ran the command: grep -P "\s*abc" temp.txt The result I expected is: abc But, the actual result is: dddd abc Could anyone tell me what is wrong? Thanks. (2 Replies)
Discussion started by: pankai
2 Replies

3. Shell Programming and Scripting

weird echo output?

#!/bin/bash INPUT=$1 if then INPUT=0$1 TRACKNUMBER=$INPUT fi TRACKNUMBER=$INPUT echo "Track Number:" $TRACKNUMBER if then echo "File Does Not Exist!: split-track"${TRACKNUMBER}".wav" exit 0 fi CUEFILE="$2" (6 Replies)
Discussion started by: TinCanFury
6 Replies

4. Shell Programming and Scripting

format of output is weird

hi all, have a ksh script which connects to a database and runs a sql and dumps it to a '.csv' file. The problem is the result is in multiple rows with long spaces in between when it should be just a single line and this screws up the format in the '.csv' file. script is : #!/bin/ksh... (1 Reply)
Discussion started by: cesarNZ
1 Replies

5. UNIX for Dummies Questions & Answers

weird 'ls' output

Hi, Anyone knows why I can't display the contents of my directory and how to fix this? http://i50.tinypic.com/4smfth.jpg Thanks in advance for any advise. Deanne Double post. Continued here. (0 Replies)
Discussion started by: Deanne
0 Replies

6. Shell Programming and Scripting

In bash getting weird output from function ?

My script- result="" times() { echo "inside the times function" result=8 echo "Inside function $result" return $result } result=$(times) echo "the value is "$? echo "the value of result $result" when I run I get this, why the value still remain 0. $ ./func the value is 0 the value... (5 Replies)
Discussion started by: boy18nj
5 Replies

7. Shell Programming and Scripting

Traceroute script weird output

This script is giving weird output #!/bin/bash NETPATH=(`/bin/traceroute -n 4.2.2.2 | awk '{print $2}'`) for i in "${NETPATH}" do echo $i done The output: to 11.11.11.1 1.1.1.1 99.111.208.2 traceroute_test.sh traceroute_test.sh (7 Replies)
Discussion started by: thumbs
7 Replies

8. Shell Programming and Scripting

Weird tail output over ssh

Hello; Am trying to correct the formatting of tail output over ssh. Using the following code: echo "" > $FILE for BOX in $SERVERS do echo "Processing on $BOX" |tee -a $FILE echo "===============================" >> $FILE sudo ssh $BOX 'TERMINAL="vt100" /usr/bin/sh -s' <... (2 Replies)
Discussion started by: delphys
2 Replies

9. HP-UX

[Solved] Weird 'ls -l' output

Hello folks, I've found an HP-UX server with a rare 'ls -l' output. Please see the attached file. Anybody knows how can I change the output to not have this extra tabulations? Thanks in advance! (10 Replies)
Discussion started by: carpannav
10 Replies

10. UNIX for Advanced & Expert Users

Weird output from ps command

Hi Guys, I am regular Solaris user. I came across a weird problem that puzzled me. Hope you guys can help. I found that process's state(command & arguments) in two different variants of ps command is different. Can anyone explain how is this possible? bash-3.2$ ps -eLo pid,s,comm,args |... (2 Replies)
Discussion started by: brij123
2 Replies
ZGREP(1)						    BSD General Commands Manual 						  ZGREP(1)

NAME
zgrep, zegrep, zfgrep -- print lines matching a pattern in gzip-compressed files SYNOPSIS
zgrep [grep-flags] [--] pattern [files ...] zegrep [grep-flags] [--] pattern [file ...] zfgrep [grep-flags] [--] pattern [file ...] DESCRIPTION
zgrep runs grep(1) on files or stdin, if no files argument is given, after decompressing them with zcat(1). The grep-flags and pattern arguments are passed on to grep(1). If an -e flag is found in the grep-flags, zgrep will not look for a pattern argument. zegrep calls egrep(1), while zfgrep calls fgrep(1). EXIT STATUS
In case of missing arguments or missing pattern, 1 will be returned, otherwise 0. SEE ALSO
egrep(1), fgrep(1), grep(1), gzip(1), zcat(1) AUTHORS
Thomas Klausner <wiz@NetBSD.org> BSD
December 28, 2003 BSD
All times are GMT -4. The time now is 04:07 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy