Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

Extract text between two character positions

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Extract text between two character positions
# 1  
Old 01-31-2012
Extract text between two character positions
Greetings.

I need to extract text between two character positions, e.g: all text between character 4921 and 6534.

The text blocks are FASTA-format sequence of whole chromosomes, so basically a million A, T, G, C, combinations. E.g:
Code:
>Chr_1
ACCTGTTCAACTCTCAGGACTCTCAGGTCAACTCTCAG
CAACTCTCAGGAACTCTCAGGTCAACTCTCACTCTCAG
GTCAACTCTCCAGGAACTCTCCACTCTCAGAGGTCAAC
.......

I need to extract a region of genes, I know the character positions that are the boundaries.

I need the equivalent of what this does for lines:
Code:
sed -n 'line1,line2p" > new_file.txt

But for character positions.

Thanks!
Moderator's Comments:
Mod Comment Please use next time code tags for your code and data
Last edited by vbe; 01-31-2012 at 11:39 AM..
# 2  
Old 01-31-2012
See if this works:
Code:
awk 'NR>1{p=$0;sub($1 ORS,x,p);sub(ORS,x,p); print RS $1 ORS substr(p, 4921,6534-4921+1)}' RS=\> OFS= infile

This User Gave Thanks to Scrutinizer For This Post:
Twinklefingers
# 3  
Old 01-31-2012
Perfect! Het werkt! Bedankt!

Moderator's Comments:
Mod Comment Please use ONLY english language. Thank you.
Last edited by DukeNuke2; 01-31-2012 at 12:17 PM..
# 4  
Old 01-31-2012
Nothing to thank Smilie
Login or Register to Ask a Question

Previous Thread | Next Thread

9 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

Extracting strings at various positions of text file

Hi Team - I hope everyone has been well! I export a file from one of our source systems that gives me more information than I need. The way the file outputs, I need to extract certain strings at different positions on the file and echo them to another file. I can do this in batch easily,... (2 Replies)
Discussion started by: SIMMS7400
2 Replies

2. Shell Programming and Scripting

seds to extract fields based on positions

Hi My file has a series of rows up to 160 characters in length. There are 7 columns for each row. In each row, column 1 starts at position 4 column 2 starts at position 12 column 3 starts at position 43 column 4 starts at position 82 column 5 starts at... (7 Replies)
Discussion started by: malts18
7 Replies

3. Shell Programming and Scripting

Insert text with Sed (in various positions)

Hello. I'm trying to insert text in various positions and I could only do that using pipes for each position. Example: cat file | sed -e 's#\(.\{5\}\)\(.*\)#\1:\2#g' | sed -e 's#\(.\{26\}\)\(.*\)#\1:\2#g' Insert ":" at position 5 and 26. it can be done in the same sentence, without using... (4 Replies)
Discussion started by: </kida>
4 Replies

4. UNIX for Dummies Questions & Answers

find positions of a letter in a text file

Hi, I would like to know how can I get all the positions of a letter, let say letter C in a text file. sample input file: hcck pgog hlhhc desired output file: 2 3 13 Many thanks! (2 Replies)
Discussion started by: fadista
2 Replies

5. Shell Programming and Scripting

awk script replace positions if certain positions equal prescribed value

I am attempting to replace positions 44-46 with YYY if positions 48-50 = XXX. awk -F "" '{if (substr($0,48,3)=="XXX") $44="YYY"}1' OFS="" $filename > $tempfile But this is not working, 44-46 is still spaces in my tempfile instead of YYY. Any suggestions would be greatly appreciated. (9 Replies)
Discussion started by: halplessProblem
9 Replies

6. Shell Programming and Scripting

Filling positions based on consensus character

I have files with hundreds of sequences with missing characters represented by a dash ("-"), something like this I need to go sequence by sequence and if a dash is found, it should be replaced with the most common character in that particular position. Thus, in my example the dash in the second... (6 Replies)
Discussion started by: Xterra
6 Replies

7. Shell Programming and Scripting

read the text file and print the content character by character..

hello all i request you to give the solution for the following problem.. I want read the text file.and print the contents character by character..like if the text file contains google means..i want to print g go goo goog googl google like this Using unix Shell scripting... without using... (1 Reply)
Discussion started by: samupnl
1 Replies

8. Shell Programming and Scripting

Replace 9-16 positions of a text file.

Hi i am having text file like this 40000201040005200213072009000000700000050744820906904421 40069300240005200713072009000000067400098543630000920442 i want to replace 9-16 positions of my txt file...by 1234567...in a single line command i.e 0400052....should be replaced by... (2 Replies)
Discussion started by: suryanarayana
2 Replies

9. Shell Programming and Scripting

extract character + 1

Hi, I would like extract from a file a character or pattern after ( n + 1) a specific pattern (n) . ( i supposed with awk) how could i do ? Thanks in advance. (1 Reply)
Discussion started by: francis_tom
1 Replies
Login or Register to Ask a Question