Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

Sequence in one single line

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Sequence in one single line
# 1  
Old 06-18-2010
Sequence in one single line
My file looks like this (60 characters per line):
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACGC
CCCGGGGC
>GHXCZCC01APUO5
TGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCCC
CGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACG
CCCCGGGG
But I need something like this (the entire sequence in one line):
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACGC CCCGGGGC
>GHXCZCC01APUO5
TGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCCC CGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACG CCCCGGGG
The sequences are of different lengths.
Any help will be very much appreciated!
# 2  
Old 06-18-2010
Try this:
Code:
awk '{printf("%s%s",$0,NR%3==2?" ":"\n")}' file

# 3  
Old 06-18-2010
Franklin
Thank you very much. However, there is a problem with the code. I just need to remove the newline at the end of each sequence lines and leave the ID intact. Using your code this is what I get:
Quote:
>GHL8OVD01A44BI
TTGATGTGCCAGCTGCCGTTGGTGTTGATCAGCTGGACGTTCTGATTGGCGCCTGGGTTA AGAGACCAGCAAGCCTGCTCACGGTGCGGCTGGCAGCCTCCCCGGTGGTGTGGGTTTTCG
CGTCAACGCCGGCAAATAGCAGCAGCACTACCAAGACCTTTGCCCAGTTCCCCACCATGG
AGAAATACGCTATGCCCCGCCAGGACTCCCCCAGTGGGCACCAGCGATCATGTCCAAGAT GGCTTGTGGGATCCGGAGCAGCTGCGCTACTACCAATGCCGTCGTAGGGGACCAGTTCAT
CATCATATCCTGTCGA
>GHL8OVD01AL2MI TTGATGTGCCAGCTGCCGTTGGTGTTGATCAGCTGGAC
>GHL8OVD01A9GNF
TTGATGTGCCAGCTGCCGTTGGTGTTGATCAGCTGGACGTT >GHL8OVD01AYRUS
TTGATGTGCCAGCTGCCGTTGGTGTTGATCAGCTGG
>GHL8OVD01AL5XY TTGATGTGCCAGCTGCCGTTGGTGTTGATCAGCTGGACGTTCTGATTGGCGCCTGGGTTA
AAGAGACCAGCAAGCCTGCTCACGGTGCGGCTGGCAGCCTCCCCGGTGGTGTGGGTTCTC
GCGTCAACGCCGGCAAAATAGCAGCAGCACTACCAAGACCTTTGCCCAGTTCCCCACCAT GGAGAAATACGCTATGCCCGCCAGGACTCCCCAGTGGGCACCAGCGATCATGTCCAAGAT
GGCTTGTGGGATCCGGAGCAGCTGCGCTACTACCAATGCCGTCGTAGGGGACCAGTTCAT
CATCATATCCTGTCGA >GHL8OVD01BGQC9
TTGATGTGCCAGCTGCCGTTGGTGTTGATCAGCTGGAC
>GHL8OVD01ALZ08 TTGATGTGCCAGCTGCCGTTGGTGTTGATCAGCTGGAC
>GHL8OVD01BP7ZA
TTGATGTGCCAGCTGCCGTTGGTGTTGATCAGCTGGAC >GHL8OVD01AL8W3
TTGATGTGCCAGCTGCCGTTGGTGTTGATCAGCTGGACGTT
>GHL8OVD01ALXG8 TTGATGTGCCAGCTGCCGTTGGTGTTGATCAGCTGGACTTTCTGATTGGCGCCTAGGTCA
AAGAGACCAGCAAACCTGCCCACGGTGCGGCCGGCAGCCTCCCCGGTGGTGTGGGTTTTC
GCGTCAACGCCGGCAAATAGCAGCAGCACTACCAAGACCTTTGCCCAGTTCCCCACCATG GAGAAATACGCTATGCCCGCCAGGACTCCCCAGTGGGCACCAGCGATCATGTCCAAGATG
GCTTGTGGGATCCGGAGCAGCTGCGCTACTACCAATGCCGTCGTAGGGGACCAGTTCATC
ATCATATCCTGTCGA >GHL8OVD01AL5V0
# 4  
Old 06-18-2010
You could try something like this:
Code:
awk '/^>/ { 
  print (buff ? buff RS : null) $0
  buff = null; next
  }
{ 
  buff = buff ? buff FS $0 : $0 
  }
END { print buff }' infile

# 5  
Old 06-18-2010
radoulov
Almost there! The problem is that there is a gap every 60 characters and it should be continuous instead. I have uploaded 3 files including the input, output and ideal file so you could see what is happening and what I would like to accomplish.
Thank you very much!
Ideal.txt (2.7 KB) 
Input.txt (3.0 KB) 
Output.txt (2.9 KB) 
# 6  
Old 06-18-2010
I believe, taking out the "FS" in the following line would do it:

Code:
  buff = buff ? buff FS $0 : $0

Change to:
Code:
  buff = buff ? buff $0 : $0

# 7  
Old 06-19-2010
What about this one ?
Code:
awk '{printf (/^>/)?((NR==1)?x:RS)$0 RS:$0}' file
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

Print Line as per the dependent sequence in shell script.

Hi i have a file like this as shown below: DA PROCESS_ID IDENTIFIER DA_FILE STATUS WAITING_FOR SCOPED_DEPENDENT 1836 21000 01052019 BH90P.TEMP.DA1836.FTP W NULL ... (6 Replies)
Discussion started by: krishnaswarnkar
6 Replies

2. Shell Programming and Scripting

Creating a sequence of numbers in a line for 1000 files

Hi, I try to explain my problem , I have a file like this: aasdsaffsc23 scdsfsddvf46567 mionome0001.pdb asdsdvcxvds dsfdvcvc2324w What I need to do is to create 1000 files in which myname line listing a sequence of numbers from 0001 to 1000. So I want to have : nomefile0001.txt that must... (10 Replies)
Discussion started by: danyz84
10 Replies

3. UNIX for Dummies Questions & Answers

To find and display the middle line in a file using single line command.

Hi all, How can i display the middle line of a file using a single line command? (6 Replies)
Discussion started by: Lakme Pemmaiah
6 Replies

4. Shell Programming and Scripting

find common entries and match the number with long sequence and cut that sequence in output

Hi all, I have a file like this ID 3BP5L_HUMAN Reviewed; 393 AA. AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3; DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot. DT 05-JUL-2004, sequence version 1. DT 05-SEP-2012, entry version 71. FT COILED 59 140 ... (1 Reply)
Discussion started by: manigrover
1 Replies

5. Shell Programming and Scripting

How to get line after occurence of sequence of patterns

In the past I needed a help with the problem how to search for pattern after the occurence of another pattern which is described in this thread: https://www.unix.com/shell-programmin...-pattern1.html Now I would need something quite similar, only the pattern which is to be searched must be... (3 Replies)
Discussion started by: sameucho
3 Replies

6. Shell Programming and Scripting

Multiple lines in a single column to be merged as a single line for a record

Hi, I have a requirement with, No~Dt~Notes 1~2011/08/1~"aaa bbb ccc ddd eee fff ggg hhh" Single column alone got splitted into multiple lines. I require the output as No~Dt~Notes 1~2011/08/1~"aaa<>bbb<>ccc<>ddd<>eee<>fff<>ggg<>hhh" mean to say those new lines to be... (1 Reply)
Discussion started by: Bhuvaneswari
1 Replies

7. Shell Programming and Scripting

filter out a sequence from multiple lines line

Hi, I have an unwanted string at random lines of my verilog (*.v) file. (* abccddee *) input A; (* xyz *) input B; (* 1234 *) output C; I want a clean file like this: input A; input B; output C; the unwanted string begins with "(*" and ends with "*)" at multiple lines. Any help... (2 Replies)
Discussion started by: return_user
2 Replies

8. Shell Programming and Scripting

printing sequence of line no. with comma separated

Kindly i want to concatenate every 12 lines ina file, using a comma separator between fields (each line)? can anyone help please? thanks a lot in advance. (5 Replies)
Discussion started by: m_wassal
5 Replies

9. UNIX for Dummies Questions & Answers

Executing a sequence of commands as a single background process

I'm writing a PHP script which will take a given media file and convert it into a flash (flv) file. In addition to this, once the flv file has been generated I create two thumbnails (of different sizes) from the newly generated flv file. In order to do this I'm calling ffmpeg from the command... (4 Replies)
Discussion started by: phatphug
4 Replies

10. Shell Programming and Scripting

Reorder the sequence of line groupings/QIF export

Hi All, I need to reorder the sequence of line groupings - specifically the output from a bank QIF (Quicken Interchange Format) export. Sample is like this: !Type:Bank D12/05/2008 T-10.00 N1 Details of Charge 1 ^ D07/05/2008 T-20.00 N2 Details of Charge 2 ^ D17/04/2008 T-30.00 (0 Replies)
Discussion started by: mark101
0 Replies
Login or Register to Ask a Question