Login or Register to Ask a Question and Join Our Community


UNIX for Dummies Questions & Answers

Finding specific series of strings or characters

 
Thread Tools Search this Thread
Top Forums UNIX for Dummies Questions & Answers Finding specific series of strings or characters
# 1  
Old 10-07-2011
Finding specific series of strings or characters
After spending sometime playing around with my script I just cannot get it to do what I want. So I decided to ask. My file looks something like this:
Quote:
>Sequence1
AGACAGATGACAGTAGACAGAT-GACGATAGCAGT
>Sequence2
AGACAGATGACAGTAGACAGATAGACGATAGCAGT
>Sequence3
AGACAGATGACAGTAGACAGATCGACGATAGCAGT
>Sequence4
AGACAGATGA-AGTAGACAGATTGACGATAGCAGT
>Sequence5
AGAC*GATGA
I am using the following code to extract sequences that contain dashes
Code:
awk '/^>/{id=$0;next}{if (match($1,"-")) print id "\n" $0}' infile

Now, I actually need to do the opposite. I need to print the sequences that do not contain dashes. Moreover, I also would like to exclude the sequences that contain *. So the expected outfile is the following one:
Quote:
>Sequence2
AGACAGATGACAGTAGACAGATAGACGATAGCAGT
>Sequence3
AGACAGATGACAGTAGACAGATCGACGATAGCAGT
Any help will be greatly appreciated!
# 2  
Old 10-07-2011
Code:
egrep -v (-|Sequence) -B1

# 3  
Old 10-07-2011
Quote:
Originally Posted by Xterra
I need to print the sequences that do not contain dashes. Moreover, I also would like to exclude the sequences that contain *.
To remove '-' (dash) and '*' (asterisk):
Code:
grep -v '[-*]' File

# 4  
Old 10-07-2011
Since the >sequence5 is part of the file, why not use > as the record separator? awk will read each thing in one whack instead of having to spread your logic across many different lines.

Code:
$ cat sequence.awk

BEGIN { RS=">"; FS="\n"; OFS="\n"; ORS=">" }

/-/ { if(!P++) printf("%s", ORS); print }

$ awk -f sequence.awk < data
>Sequence1
AGACAGATGACAGTAGACAGAT-GACGATAGCAGT
>Sequence4
AGACAGATGA-AGTAGACAGATTGACGATAGCAGT

/-/ matches records containing -. ! /-/ would match records not containing -. ! /[-*]/ would match records not containing * or -. And so forth.

The if(!P++) printf("%s", ORS); is to print the very first >, which would otherwise be missing.
Last edited by Corona688; 10-07-2011 at 01:35 PM..
# 5  
Old 10-07-2011
Corona
I see quite cool! However, I have a couple of problems undertanding your script. First, I do not get anything if I use "/-*/. Second, let suppose I only want to print the sequences that do not contain an "*". Then, I use your code:
Code:
awk 'BEGIN { RS=">"; FS="\n"; OFS="\n"; ORS=">" } !/*/ { if(!P++) printf("%s", RS); print }' infile

This is what I get:
Quote:
>>Sequence1
AGACAGATGACAGTAGACAGAT-GACGATAGCAGT
>Sequence2
AGACAGATGACAGTAGACAGATAGACGATAGCAGT
>Sequence3
AGACAGATGACAGTAGACAGATCGACGATAGCAGT
>Sequence4
AGACAGATGA-AGTAGACAGATTGACGATAGCAGT
>
The script is adding ">" at the very beggining of the file which is wrong and the last ">" is retained.
Any suggestions?
# 6  
Old 10-07-2011
Code:
nawk '/Seq/{x=$0;next}$0!~/[-*]/{print x RS $0}' infile

Code:
$ cat f1
>Sequence1
AGACAGATGACAGTAGACAGAT-GACGATAGCAGT
>Sequence2
AGACAGATGACAGTAGACAGATAGACGATAGCAGT
>Sequence3
AGACAGATGACAGTAGACAGATCGACGATAGCAGT
>Sequence4
AGACAGATGA-AGTAGACAGATTGACGATAGCAGT
>Sequence5
AGAC*GATGA


Code:
$ nawk '/Seq/{x=$0;next}$0!~/[-*]/{print x RS $0}' f1
>Sequence2
AGACAGATGACAGTAGACAGATAGACGATAGCAGT
>Sequence3
AGACAGATGACAGTAGACAGATCGACGATAGCAGT

few code explainations

nawk ' call awk
/Seq/if "Seq" pattern is found in the scanned line
{x=$0;save the line in variable x
next}skip further awk instructions and process next line from beginning of awk instructions
$0!~/[-*]/If no occurence of - or * is found in the scanned line
{print x RS $0}print the last Sequence scanned , a Record Separator ("\n" by default) , and the current scanned line
' <yourfile>name of the file that is passed to awk (argument)
Last edited by ctsgnb; 10-07-2011 at 02:08 PM..
This User Gave Thanks to ctsgnb For This Post:
Xterra
# 7  
Old 10-07-2011
ctsgnb
That's what I was looking for!
Thank you very much!
Just one pretty quick question, what do I need "~" in the script?
 
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

Printing lines with specific strings at specific columns

Hi I have a file which is tab-delimited. Now, I'd like to print the lines which have "chr6" string in both first and second columns. Could anybody help? (3 Replies)
Discussion started by: a_bahreini
3 Replies

2. Shell Programming and Scripting

Finding Strings between 2 characters in a file

Hi All, Assuming i have got a file test.dat which has contains as follows: Unix = abc def fgt jug 111 2222 3333 Linux = gggg pppp qqq C# = ccc ffff llll I would like to traverse through the file, get the 1st occurance of "=" and then need to get the sting... (22 Replies)
Discussion started by: rtagarra
22 Replies

3. Shell Programming and Scripting

Count specific characters at specific column positions

Hi all, I need help. I have an input text file (input.txt) like this: 21 GTGCAACACCGTCTTGAGAGG 50 21 GACCGAGACAGAATGAAAATC 73 21 CGGGTCTGTAGTAGCAAACGC 108 21 CGAAAAATGAACCCCTTTATC 220 21 CGTGATCCTGTTGAAGGGTCG 259 Now I need to count A/T/G/C numbers at each character location in column... (2 Replies)
Discussion started by: thienxho
2 Replies

4. Shell Programming and Scripting

Can't figure out how to find specific characters in specific columns

I am trying to find a specific set of characters in a long file. I only want to find the characters in column 265 for 4 bytes. Is there a search for that? I tried cut but couldn't get it to work. Ex. I want to find '9999' in column 265 for 4 bytes. If it is in there, I want it to print... (12 Replies)
Discussion started by: Drenhead
12 Replies

5. Shell Programming and Scripting

finding the strings beween 2 characters "/" & "/" in .txt file

Hi all. I have a .txt file that I need to sort it My file is like: 1- 88 chain0 MASTER (FF-TE) FFFF 1962510 /TCK T FD2TQHVTT1 /jtagc/jtag_instreg/updateinstr_reg_1 dff1 (TI,SO) 2- ... (10 Replies)
Discussion started by: Behrouzx77
10 Replies

6. Shell Programming and Scripting

sed replacing specific characters and control characters by escaping

sed -e "s// /g" old.txt > new.txt While I do know some control characters need to be escaped, can normal characters also be escaped and still work the same way? Basically I do not know all control characters that have a special meaning, for example, ?, ., % have a meaning and have to be escaped... (11 Replies)
Discussion started by: ijustneeda
11 Replies

7. Shell Programming and Scripting

Finding Minimum in a Series

I have two LARGE files of data more than 20,000 line each, file-1 and file-2, and I wish to do the following if possible: file-1 1 2 5 7 9 2 4 6 3 8 9 4 6 8 9 3 2 1 3 1 2 . . . file-2 1 2 3 2 5 7 5 7 3 7 9 4 . (5 Replies)
Discussion started by: ali2011
5 Replies

8. Shell Programming and Scripting

Finding repitition of series

Dear friends, hello to everyone. I am new to this forum. I have a set of data where I need to find the repitition of series as below data format: 0001230000456000001230000456 each digit can be separated by any delimeter I need to find out the starting point (index) of '123' and '456' I... (2 Replies)
Discussion started by: gjarms
2 Replies

9. Shell Programming and Scripting

Finding strings

Hi I made a post earlier but now my problem has become a lot more complicated. So I have a file that looks like this: Name 1 13 94 1 AGGTT Name 1 31 44 1 TTCCG Name 1 13 94 2 AAAAATTTT Name 1 41 47 2 GGGGGGGGGGG So the file is tab delimited and what I want to do is find... (8 Replies)
Discussion started by: kylle345
8 Replies

10. Shell Programming and Scripting

print 10 characters in series

suppose fileA kanika123ABC 1222222222222222 raciat5678ty 1221123333331121 jessica78ulllo 2233243223333333 so output shud be print only first 10 characters in series and rest remain same kanika123A 1222222222222222 raciat5678 1221123333331121 jessica78u ... (1 Reply)
Discussion started by: cdfd123
1 Replies
Login or Register to Ask a Question