Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

Grep command

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Grep command
# 1  
Old 09-18-2013
Question Grep command
Hello,

I have a file which looks like this
Code:
C       Pos           Ref     BestGen BestQual  A+-     B+-     SP      CV
6       108858301       T       TT      ?2      +-      +-      TT      TT
6       108858304       C       CC      ?2      +       +       CC      CC
6       108858309       C       CC      ?3      +       +       CC      CC
6       108858312       C       CC      ?1      +       +       CC      CC
6       108858313       T       TT              +       +       TT      TT
6       108858315       T       TT      ?2      +       +       TT      TT
6       108858316       C       CC      ?2      +-      +-      CC      CC
6       108858317       T       TT      ?6      +       +       TT      TT
6       108858318       T       TT      ?2      +-      +-      TT      TT
6       108858321       T       TT      ?4      +-      +-      TT      TT
6       108858322       C       CC      ?8      +       +       CC      CC
6       108858325       T       TT              +-      +-      TT      TT
6       108858326       T       TT              +       +       TT      TT
6       108858328       A       AA      ?5      +       +       AA      AA
6       108858330       T       TT      ?6      +-      +-      TT      TT

I need to remove from the file all the lines which contain "?2" to "?8"

I tried using
Code:
grep -v '?2' '?3' '?4' '?5''?6' '?7' '?8'  filename > output

but I get an error
Code:
grep: ?3: No such file or directory
grep: ?4: No such file or directory
grep: ?5?6: No such file or directory
grep: ?7: No such file or directory
grep: ?8: No such file or directory

Any help is appreciated. Thank you
# 2  
Old 09-18-2013
try this:
Code:
grep -v '\?[0-9]' filename

If this is not what you wanted, post the output as well.
# 3  
Old 09-18-2013
The output should be something like this

Code:
C       Pos           Ref     BestGen BestQual  A+-     B+-     SP      CV
6       108858312       C       CC      ?1      +       +       CC      CC
6       108858313       T       TT              +       +       TT      TT
6       108858325       T       TT              +-      +-      TT      TT
6       108858326       T       TT              +       +       TT      TT

So basically I need all the information which have a blank value AND "?1" in that particular column..
# 4  
Old 09-18-2013
Like this:
Code:
awk ' $5 !~ /?[2-9]/{print $0}' filename

This User Gave Thanks to greet_sed For This Post:
nans
# 5  
Old 09-18-2013
With grep and extended REs:
Code:
grep -Ev '\?(2|3|4|5|6|7|8)'  file
C       Pos           Ref     BestGen BestQual  A+-     B+-     SP      CV
6       108858312       C       CC      ?1      +       +       CC      CC
6       108858313       T       TT              +       +       TT      TT
6       108858325       T       TT              +-      +-      TT      TT
6       108858326       T       TT              +       +       TT      TT

And, small corrections/improvement to greet_sed's proposal:
Code:
awk ' $5 !~ /\?[2-8]/' file

# 6  
Old 09-18-2013
Hi,
Here regular expression for grep command that check 5th field:
Code:
grep -Ev '^([^ ]+ +){4}\?[2-8]' file

Regards.
# 7  
Old 09-19-2013
@greet_sed
You do not need the print command, its default.
Code:
awk '$5!~/?[2-9]/' filename

Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

Help on grep command

for example i have a directory home/solaris/unix/samplefiles/ with defaults files in it.. those default files have 1 word in common "UNIX". how can i list the files without "UNIX" words in it using grep command thanks, im using unix solaris, korn shell.. (1 Reply)
Discussion started by: daveaztig14
1 Replies

2. Shell Programming and Scripting

Grep command giving different result for different users for same command

Hello, I am running below command as root user #nodetool cfstats tests | grep "Memtable switch count" Memtable switch count: 12 Where as when I try to run same command as another user it gives different result. #su -l zabbix -s /bin/bash -c "nodetool cfstats tests | grep "Memtable switch... (10 Replies)
Discussion started by: Pushpraj
10 Replies

3. Shell Programming and Scripting

Grep command

grep -i -f panel_genes.txt hg19_refGene.txt > match.txt seems to be pulling names the do not exist in the input file (panel_genes.txt) - the output is attached as well (match.txt) For example, RNF185 or ZNF146 are not genes in the input. I am trying to match the input file genes only and am... (9 Replies)
Discussion started by: cmccabe
9 Replies

4. Shell Programming and Scripting

help on grep command...

Hi I have lots of file in on folder and i want to egrep from only few files. List of files...... Polt_KJ_430_OutputRBS_istUt_CR2.log Polt_KN_4122_OutputRBS_ncChk_CR.log Polt_LN_2230_OutputRNC_Hth_CLKLKL.log Solt_KJ_430_OutputRBS_istUt_CR2.log Solt_KN_4122_OutputRBS_ncChk_CR3.log... (2 Replies)
Discussion started by: asavaliya
2 Replies

5. Shell Programming and Scripting

Grep Command

Hi, I have around 500 Text files and Each file will be having either String1 or String2. I want to list the file only which has String1 and Sting2 in a single command.. (5 Replies)
Discussion started by: balasubramani04
5 Replies

6. Shell Programming and Scripting

Help with using grep command with copy command

Hi, im taking an entry Unix class, and as part of my lab assignment I have to copy all files in the /home/david/lab3 directory that have the file extension .save to your lab3/temp directory. I'm having trouble getting the grep to do anything worth while I've been trying to do: cp... (6 Replies)
Discussion started by: Critical jeff
6 Replies

7. Shell Programming and Scripting

can anyone help with shell script command about searching word with grep command?

i want to search in the current directory all the files that contain one word for example "hello" i want to achieve it with the grep command but not with the grep * (2 Replies)
Discussion started by: aintour
2 Replies

8. UNIX for Advanced & Expert Users

how to exclude the GREP command from GREP

I am doing "ps -f" to see my process. but I get lines that one of it represents the ps command itself. I want to grep it out using -v flag, but than I get another process that belongs to the GREP itself : I would like to exclude # ps -f UID PID PPID C STIME TTY TIME CMD... (2 Replies)
Discussion started by: yamsin789
2 Replies

9. UNIX for Dummies Questions & Answers

grep command

hi all i have directory /usr under this directory i have subdirectories tmp1,tmp2,tmp3 like this /usr/tmp1 /usr/tmp2 /usr/tmp3 and so on i want to search string in files (i don't know the name of the files)and i want to serch it in all the directories under the /usr how shell i do... (3 Replies)
Discussion started by: naamas03
3 Replies

10. Shell Programming and Scripting

grep command

What is the meaning of this grep -v $object grant_BU.sql>temp (1 Reply)
Discussion started by: debasis.mishra
1 Replies
Login or Register to Ask a Question