Trimming ends


 
Thread Tools Search this Thread
Top Forums UNIX for Dummies Questions & Answers Trimming ends
# 1  
Old 06-18-2015
Trimming ends

My files look like this

Quote:
>GHXCZCC01AJ8CJ
ACGTGCGTGGGAAATTGATGTGCTTGGTGTGTATCATTTCTGGGAAGCCCTACGCCCCGGGGC
>GHXCZCC01APUO5
ACGTGCGTGGGAAAT-ATGTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCAGCCCTACCCGGGGCGA
>GHXCZCC01AQSRP
ACGTGCGTGGGAAATTGATGTTA---AGCTGGATTTTCTGGGACGCCCCGGGGAGCCCTA
>GHXCZCC01AQSRP
TTGTTGCCAGCTAGCTGAGCCCTAGATTTTCTGGGGCCCCGGGG
>GHXCZCC01AQSRP
TTGATGTTGCCCAGCCCTATAGCTGGATTTTCTGGGACGCCCCGGGGTGC
I need to remove the sequence GGGAAA and anything before that

I also need to remove the sequence AGCCCTA and anything after that

So I will end up with something like this
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCTTGGTGTGTATCATTTCTGGGA
>GHXCZCC01APUO5
T-ATGTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGC
>GHXCZCC01AQSRP
TTGATGTTA---AGCTGGATTTTCTGGGACGCCCCGGGG
>GHXCZCC01AQSRP
TTGTTGCCAGCTAGCTG
>GHXCZCC01AQSRP
TTGATGTTGCCC
The left side is done but I cannot get the right side correctly. I would like to use one AWK script to accomplish the whole think instead of multiple steps
Thanks for any help!
# 2  
Old 06-18-2015
Hello Xterra,

Could you please try following and let us know if this helps.
Code:
 awk '{sub(/.*GGGAAA/,X,$0);sub(/AGCCCTA.*/,X,$0);print}'  Input_file

Thanks,
R. Singh
# 3  
Old 06-18-2015
You could simplify RavinderSingh13's fine approach a bit:
Code:
awk '{gsub(/^.*GGGAAA|AGCCCTA.*$/,"",$0)} 1'  file

This User Gave Thanks to RudiC For This Post:
# 4  
Old 06-18-2015
Awesome!
Thanks!
 
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

How to find a file which are not ends with ".zip" and which are ends with "*.log*" or "*.out*"?

I am new to bash/shell scripting. I want to find all the files in directory and subdirectories, which are not ends with “.zip” and which are contains in the file name “*.log*” or “*.out*”. I know below command to get the files which ends with “.log”; but I need which are not ends with this... (4 Replies)
Discussion started by: Mallikgm
4 Replies

2. Shell Programming and Scripting

Trimming in between the words

Hi i have a log file P12345_15728710:DEBUG:Begin P12345_15728710:DEBUG:Being P12345_15729310:DEBUG:GetAgen P12345_15726510:DEBUG:end i want to trim this file and i want like this 15728710 15728710 15729310 15726510 i tried sed ..but not working.. sed "s/.*P12345__ \(.*\)... (4 Replies)
Discussion started by: navsan420
4 Replies

3. Shell Programming and Scripting

Trimming a string

Hi I need to trim white spaces from strings in a file. Input file is like this: 1_rrc_CatalogGroups.csv = 607 1_rrc_Sales_TopCatalogGroups.csv = 4 1_rrc_Sales_CatalogEntries_CatalogGroup_Rel.csv = 7 Need to trim space before and after = symbol. This is my script: #!/usr/bin/ksh ... (2 Replies)
Discussion started by: sukhdip
2 Replies

4. Shell Programming and Scripting

trimming sequences

My file looks like this: But I would like to 'trim' all sequences to the same lenght 32 characters, keeping intact all the identifier (>GHXCZCC01AJ8CJ) Would it be possible to use awk to perform this task? (2 Replies)
Discussion started by: Xterra
2 Replies

5. Shell Programming and Scripting

Trimming output

I'm trying to parse an output log and I've managed to reduce the output to the lines I need. But I'm having trouble pulling out only the info I'm interested in. The output is 40+ lines and here is a sample Installing AppFresh 0.8.5.pkg from ./InstallerFiles/CustomPKG/26 (26) Installing... (2 Replies)
Discussion started by: kaltekar
2 Replies

6. Shell Programming and Scripting

trimming lines

hi have output as i have trim of lines before CREATE statement and lins after last ")" any idea how to achieve it ? (3 Replies)
Discussion started by: crackthehit007
3 Replies

7. UNIX for Advanced & Expert Users

Trimming the spaces

Hi, How can I remove the unwanted spaces in the line. 123456 789 ABC DEF. - I wanna remove the sapces in this line, I need the output 123456789ABCDEF. Pls help me...... (3 Replies)
Discussion started by: sharif
3 Replies

8. UNIX for Advanced & Expert Users

trimming zeros

Hi, I want to trim +with leading zero's with amount fields.I know using awk for trimming leading zeros with +,but I want get the entire row itself. cat file_name |awk -F " " '{printf "%14.4f%f\n",$4}' ex: 10 xyz bc +00000234.4500 20 yzx foxic +002456.000 Expexted 10 xyz bc... (3 Replies)
Discussion started by: mohan705
3 Replies

9. UNIX for Advanced & Expert Users

while never ends

Hi i have question, is this ok in ksh, like while ] do something read true done loop runs but never ends even i pass y/Y. can any body please resolve it (4 Replies)
Discussion started by: Raom
4 Replies

10. UNIX for Dummies Questions & Answers

trimming a file...

Hi everyone I have this script that appends a line to a file to log the running status of an application. I need to write another script to run as a scheduled job in cron to trim the first x number of lines of this file. Could someone give me an idea how to do this? Regards (1 Reply)
Discussion started by: alwayslearningunix
1 Replies
Login or Register to Ask a Question