trimming sequences


 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting trimming sequences
# 1  
Old 06-22-2010
trimming sequences

My file looks like this:
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACGC
CCCGGGGC
>GHXCZCC01APUO5
TGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCCC
CGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACG
CCCCGGGG
But I would like to 'trim' all sequences to the same lenght 32 characters, keeping intact all the identifier (>GHXCZCC01AJ8CJ)
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCCAGCTGCCGTTGGTGTGTATCAG
CCCGGGGC
>GHXCZCC01APUO5
TGATGTGCCAGCTGCCGTTGGTGTGTATCAGC
CGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTGCCAGCTGCCGTTGGTGTGTATCA
CCCCGGGG
Would it be possible to use awk to perform this task?
# 2  
Old 06-22-2010
If the identifier won't get longer than 32 chars you could try this:
Code:
cut -c1-32 file

This User Gave Thanks to pseudocoder For This Post:
# 3  
Old 06-22-2010
Excelent!

The Id is never longer than 32.
Thank you very much!
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

Trimming ends

My files look like this 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 The left side is done but I cannot get the right side correctly. I would like to use... (3 Replies)
Discussion started by: Xterra
3 Replies

2. 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

3. Shell Programming and Scripting

Trimming sequences based on Reference

My file looks something like this Wnat I need is to look for the Reference sequence (">Reference1") and based on the length of that sequence trim all the entries in that file. So, the rersulting file will contain all sequences with the same length, like this Thus, all sequences will keep... (5 Replies)
Discussion started by: Xterra
5 Replies

4. Shell Programming and Scripting

Trimming sequences based on specific pattern

My files look like this And I need to cut the sequences at the last "A" found in the following 'pattern' -highlighted for easier identification, the pattern is the actual file is not highlighted. The expected result should look like this Thus, all the sequences would end with AGCCCTA... (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. Shell Programming and Scripting

Trimming a string

Hi, I am trying to find a script command that will let me trim leading and trailing space from a string. I have coded a SQL Select and sending the output to a file. Later I am parsing the file and reading each field. The problem is that each field uses the same size as the DB2 type it was defined... (2 Replies)
Discussion started by: fastgoon
2 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