How to remove lines without a particular string in either column?

Login or Register to Ask a Question and Join Our Community

How to remove lines without a particular string in either column?

Tags

awk, linux, solved

Login to Discuss or Reply to this Discussion in Our Community

Operating Systems Linux How to remove lines without a particular string in either column?

10-19-2015

Registered User

18, 0

Join Date: Sep 2015

Last Activity: 19 November 2015, 1:13 AM EST

Posts: 18

Thanks Given: 16

Thanked 0 Times in 0 Posts

How to remove lines without a particular string in either column?

I have a file that looks like this:

Code:

DIP-27772N       DIP-18408N refseq:NP_523941
DIP-23436N|refseq:NP_536784       DIP-23130N|refseq:NP_652017
DIP-22958N|refseq:NP_651195       DIP-20072N|refseq:NP_724597
DIP-22928N|refseq:NP_569972       DIP-22042N|refseq:NP_536744|uniprotkb:P54622
DIP-20065N|refseq:NP_731331       DIP-17103N

I want to remove those lines that do not contain "refseq:NP" in either column (the 1st and last line in the given example)

required output

Code:

DIP-23436N|refseq:NP_536784       DIP-23130N|refseq:NP_652017
DIP-22958N|refseq:NP_651195       DIP-20072N|refseq:NP_724597
DIP-22928N|refseq:NP_569972       DIP-22042N|refseq:NP_536744|uniprotkb:P54622

How can I do it using grep? Any help would be highly appreciated.

Syeda Sumayya

View Public Profile for Syeda Sumayya

Find all posts by Syeda Sumayya

10-19-2015

Moderator

3,105, 1,603

Join Date: May 2013

Last Activity: 31 August 2020, 1:46 AM EDT

Location: Chennai

Posts: 3,105

Thanks Given: 1,269

Thanked 1,603 Times in 1,369 Posts

Hello Syeda,

Could you please try following and let me know if this helps.

Code:

awk '{count=gsub(/refseq:NP/,"refseq:NP",$0);if(count==NF){print}}'  Input_file

Output will be as follows.

Code:

DIP-23436N|refseq:NP_536784       DIP-23130N|refseq:NP_652017
DIP-22958N|refseq:NP_651195       DIP-20072N|refseq:NP_724597
DIP-22928N|refseq:NP_569972       DIP-22042N|refseq:NP_536744|uniprotkb:P54622

Thanks,
R. Singh

This User Gave Thanks to RavinderSingh13 For This Post:

RavinderSingh13

View Public Profile for RavinderSingh13

Find all posts by RavinderSingh13

10-19-2015

Registered User

15,129, 5,008

Join Date: Jul 2012

Last Activity: 4 May 2020, 4:31 PM EDT

Location: Aachen, Germany

Posts: 15,129

Thanks Given: 735

Thanked 5,008 Times in 4,483 Posts

Try also

Code:

awk '2==gsub(/refseq:NP/,"&")' file
DIP-23436N|refseq:NP_536784       DIP-23130N|refseq:NP_652017
DIP-22958N|refseq:NP_651195       DIP-20072N|refseq:NP_724597
DIP-22928N|refseq:NP_569972       DIP-22042N|refseq:NP_536744|uniprotkb:P54622

---------- Post updated at 12:45 ---------- Previous update was at 12:43 ----------

If there's more than two columns, use NF== as RavinderSingh13 does.

This User Gave Thanks to RudiC For This Post:

RudiC

View Public Profile for RudiC

Find all posts by RudiC

10-19-2015

Registered User

18, 0

Join Date: Sep 2015

Last Activity: 19 November 2015, 1:13 AM EST

Posts: 18

Thanks Given: 16

Thanked 0 Times in 0 Posts

Thanks a lot R. Singh

Syeda Sumayya

View Public Profile for Syeda Sumayya

Find all posts by Syeda Sumayya

10-19-2015

Registered User

5,091, 1,931

Join Date: May 2012

Last Activity: 15 July 2020, 4:46 AM EDT

Location: Simplicity

Posts: 5,091

Thanks Given: 565

Thanked 1,931 Times in 1,668 Posts

With grep:

Code:

grep -v 'refseq:NP.*refseq:NP' file

Not asked here, but I want to mention that sed can delete the nth occurrence, here the 2nd:

Code:

sed 's/|refseq:NP[_0-9]*//2' file

---------- Post updated at 09:22 AM ---------- Previous update was at 08:55 AM ----------

Thanks to RavinderSingh, I see you want to do the opposite, then it's

Code:

grep 'refseq:NP.*refseq:NP' file

BTW you can use a back reference as follows

Code:

grep '\(refseq:NP\).*\1' file

This User Gave Thanks to MadeInGermany For This Post:

MadeInGermany

View Public Profile for MadeInGermany

Find all posts by MadeInGermany

Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

Remove newline character from column spread over multiple lines in a file

Hi, I came across one issue recently where output from one of the columns of the table from where i am creating input file has newline characters hence, record in the file is spread over multiple lines. Fields in the file are separated by pipe (|) delimiter. As header will never have newline...

2. Shell Programming and Scripting

Remove duplicate consecutive lines with specific string

Hello, I'm trying to remove the duplicate consecutive lines with specific string "WARNING". File.txt abc; WARNING 2345 WARNING 2345 WARNING 2345 WARNING 2345 WARNING 2345 bcd; abc; 123 123 123 WARNING 1234 WARNING 2345 WARNING 2345 efgh;

3. Shell Programming and Scripting

Remove lines matching a substring in a specific column

Dear group, I have following input text file: Brit 2016 11 18 12 00 10 1.485,00 EUR Brit 2016 11 18 12 00 10 142,64 EUR Brit 2016 11 18 12 00 10 19,80 EUR Brit 2016 11 18 12 00 10 545,00 EUR Brit 2016 11 18 12 00 10 6.450,00 EUR...

4. Shell Programming and Scripting

Remove multiple lines from a particular string to particular string

Hi, I have a file containing the DDLs of tables in a schema. From that I need to remove all the lines from a starting string till a specific string. Here is an example. File1.txt ------------- CREATE TABLE "SCHEMA1"."LKP11_TBL_USERS" ( "ID" NUMBER(8,0) NOT NULL ENABLE, "USER_ID"...

5. UNIX for Dummies Questions & Answers

Remove lines in a positional file based on string value

Gurus, I am relatively new to Unix scripting and am struck with a problem in my script. I have positional input file which has a FLAG indicator in at position 11 in every record of the file. If the Flag has value =Y, then the record from the input needs to be written to a new file.However if...

6. UNIX for Dummies Questions & Answers

Remove lines contain certain string

i have file input aa,20120626 bb,45Cexpect to remove all lines when $2 doesn't end with 'C" output bb,45Ci tried this sed -i -nl -e '/\<C\>/ {p;} ' file1 but the result : sed illegal option -i

7. UNIX for Dummies Questions & Answers

[SOLVED] remove lines that have duplicate values in column two

Hi, I've got a file that I'd like to uniquely sort based on column 2 (values in column 2 begin with "comp"). I tried sort -t -nuk2,3 file.txtBut got: sort: multi-character tab `-nuk2,3' "man sort" did not help me out Any pointers? Input: Output:

8. Shell Programming and Scripting

Remove lines that match string at end of column

I have this: 301205 0000030000041.49000000.00 2011111815505 908 301205 0000020000029.10000000.00 2011111815505 962 301205 0000010000027.56000000.00 2011111815505 3083 312291 ...

9. Shell Programming and Scripting

Remove lines based on column value

Hi All, I just need a quick fix here. I need to delete all lines containing "." in the 6th column. Input: 1 1055498 . G T 5.46 . 1 1902377 . C T 7.80 . 1 1031540 . A G 34.01 PASS 1 ...

10. UNIX for Dummies Questions & Answers

How to remove a string from a specific column in a file

Hello, A basic query. How can I remove a string from a specific column. For example, remove "abcd" just from column 2 in example file: abcd abcd1 abcd abcd2 abcd abcd3 to get output: abcd 1 abcd 2 abcd 3 Thank you!:)

Login or Register to Ask a Question