Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Search field in text file and replace value
Top Forums Shell Programming and Scripting Search field in text file and replace value Post 302769878 by doom4 on Wednesday 13th of February 2013 06:41:13 PM
Old 02-13-2013
Search field in text file and replace value
Hi there,

First of all this is my first post here. Thank you in advance for your help.

What I am trying to do is the following. I have a text file where each field of each row is separated by a tabulator.

Looks like this:
Code:
ATOM      1  N   HSE A  26       3.033 -10.429  -2.262  1.00 17.07           N1+
ATOM      2  CA  HSE A  26       3.226 -11.674  -3.040  1.00 14.73           C  
ATOM      3  CB  HSE A  26       4.705 -11.978  -3.127  1.00 15.52           C  
ATOM      4  CG  HSE A  26       5.055 -13.031  -4.057  1.00 15.51           C  
ATOM      5  ND1 HSE A  26       4.959 -14.364  -3.715  1.00 15.39           N  
ATOM      6  CE1 HSE A  26       5.349 -15.091  -4.746  1.00 17.55           C  
ATOM      7  NE2 HSE A  26       5.765 -14.285  -5.726  1.00 21.97           N  
ATOM      8  CD2 HSE A  26       5.577 -12.980  -5.296  1.00 18.48           C  
ATOM      9  C   HSE A  26       2.538 -12.795  -2.235  1.00 13.15           C  
ATOM     10  O   HSE A  26       2.537 -12.755  -1.031  1.00 13.11           O  
ATOM     11  H1  HSE A  26       3.422 -10.546  -1.337  1.00 17.07           H  
ATOM     12  H2  HSE A  26       2.046 -10.227  -2.189  1.00 17.07           H  
ATOM     13  H3  HSE A  26       3.499  -9.664  -2.729  1.00 17.07           H  
ATOM     14  HA  HSE A  26       2.818 -11.585  -4.047  1.00 14.73           H  
ATOM     15  HB2 HSE A  26       5.049 -12.273  -2.136  1.00 15.52           H  
ATOM     16  HB3 HSE A  26       5.221 -11.068  -3.435  1.00 15.52           H  
ATOM     17  HD2 HSE A  26       5.808 -12.085  -5.855  1.00 18.48           H  
ATOM     18  HE2 HSE A  26       6.146 -14.573  -6.616  1.00 21.97           H  
ATOM     19  HE1 HSE A  26       5.334 -16.170  -4.790  1.00 17.55           H  
ATOM     20  N   PRO A  27       1.965 -13.801  -2.950  1.00 14.19           N  
ATOM     21  CA  PRO A  27       1.227 -14.887  -2.217  1.00 14.75           C  
ATOM     22  CB  PRO A  27       0.797 -15.859  -3.316  1.00 17.54           C  
ATOM     23  CG  PRO A  27       0.763 -15.036  -4.490  1.00 19.69           C  
ATOM     24  CD  PRO A  27       1.755 -13.904  -4.376  1.00 16.62           C  
ATOM     25  C   PRO A  27       2.086 -15.623  -1.216  1.00 13.14           C  
ATOM     26  O   PRO A  27       1.601 -16.109  -0.212  1.00 13.57           O  
ATOM     27  HA  PRO A  27       0.404 -14.463  -1.642  1.00 14.75           H  
ATOM     28  HB2 PRO A  27      -0.187 -16.278  -3.104  1.00 17.54           H  
ATOM     29  HB3 PRO A  27       1.520 -16.668  -3.427  1.00 17.54           H  
ATOM     30  HG2 PRO A  27      -0.239 -14.623  -4.609  1.00 19.69           H  
ATOM     31  HG3 PRO A  27       1.011 -15.643  -5.360  1.00 19.69           H  
ATOM     32  HD2 PRO A  27       2.684 -14.143  -4.893  1.00 16.62           H  
ATOM     33  HD3 PRO A  27       1.343 -12.979  -4.779  1.00 16.62           H

First what I do is find the last row which starts with ATOM and save the field value of the 6th column in this row:
Code:
last=$[$(grep 'ATOM' test.pdb | tail -n1 | awk '{ print $6 }')+1]

Then I want to search for a value I define in 6th column and replace this value by another value. This should be done until I reach the last row which starts with ATOM. Can you somehow use AWK or SED to search specifically for the row? I am new to shell scripting so sorry if the question is too trivial.

Thanks for help,

Max

---------- Post updated at 06:41 PM ---------- Previous update was at 06:18 PM ----------

Sorry the fields are not separated by tabs it is:

Code:
COLUMNS        DATA  TYPE    FIELD        DEFINITION
-------------------------------------------------------------------------------------
 1 -  6        Record name   "ATOM  "
 7 - 11        Integer       serial       Atom  serial number.
13 - 16        Atom          name         Atom name.
17             Character     altLoc       Alternate location indicator.
18 - 20        Residue name  resName      Residue name.
22             Character     chainID      Chain identifier.
23 - 26        Integer       resSeq       Residue sequence number.
27             AChar         iCode        Code for insertion of residues.
31 - 38        Real(8.3)     x            Orthogonal coordinates for X in Angstroms.
39 - 46        Real(8.3)     y            Orthogonal coordinates for Y in Angstroms.
47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
55 - 60        Real(6.2)     occupancy    Occupancy.
61 - 66        Real(6.2)     tempFactor   Temperature  factor.
77 - 78        LString(2)    element      Element symbol, right-justified.
79 - 80        LString(2)    charge       Charge  on the atom.

I am interested in the row 23 - 26 (Residue sequence number)
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

automating file search and replace text

Hi, I am trying something like this: Let's say I have a file called File1 with contents: x=-0.3 y=2.1 z=9.0 I have another file, File2, with contents: xx= yy= zz= (nothing after "="). What I want to do is get the value of x in File1 and set it to xx in File2, i.e., xx=-0.3. And the... (3 Replies)
Discussion started by: ommatidia
3 Replies

2. Shell Programming and Scripting

How to search and replace text in same file

script is as below v_process_run=5 typeset -i p_cnt=0 pdata=/home/proc_data.log while do # execute script in background dummy_test.sh "a1" "a2" & p_cnt=$p_cnt+1 echo "data : $p_cnt : Y" >> $pdata done file created with following data in... (1 Reply)
Discussion started by: Vrgurav
1 Replies

3. UNIX for Dummies Questions & Answers

search and replace a specific text in text file?

I have a text file with following content (3 lines) filename : output.txt first line:12/12/2008 second line:12/12/2008 third line:Y I would like to know how we can replace 'Y' with 'N' in the 3rd line keeping 1st and 2nd lines same as what it was before. I tried using cat output.txt... (4 Replies)
Discussion started by: santosham
4 Replies

4. Shell Programming and Scripting

search and replace a text in a file

Hi all, I have a requirement where i have to search data between strings 'SELECT' and ';' and replace this text as "SELECT.....;" so that i can export this extracted string into a excel cell. Please suggest on this. (5 Replies)
Discussion started by: goutam_igate
5 Replies

5. Shell Programming and Scripting

text file search and replace with awk

hello all greeting for the day i have a text file as the following text.xml abcd<FIELD>123.456</FIELD>efgh i need to replace the value between <FIELD> and </FIELD> by using awk command. please throw some light on this. thank you very very much Erik (5 Replies)
Discussion started by: erikshek
5 Replies

6. Shell Programming and Scripting

replace 3rd field of space delimited text file

how to replace the 3rd colum? Each line begins similarly, but they all ends variously. XX YY 03 variable text here XX YY 03 more variable text here XX YY 03 even more variable text here really long setence XX YY 03 variable numbers also appear 03 11. 123 456 XX YY 03 the occasional comma,... (4 Replies)
Discussion started by: ajp7701
4 Replies

7. Shell Programming and Scripting

Search replace strings between single quotes in a text file

Hi There... I need to serach and replace a strings in a text file. My file has; books.amazon='Let me read' and the output needed is books.amazon=NONFOUND pls if anybody know this can be done in script sed or awk.. i have a list of different strings to be repced by NONFOUND.... (7 Replies)
Discussion started by: Hiano
7 Replies

8. Shell Programming and Scripting

Awk Search text string in field, not all in field.

Hello, I am using awk to match text in a tab separated field and am able to do so when matching the exact word. My problem is that I would like to match any sequence of text in the tab-separated field without having to match it all. Any help will be appreciated. Please see the code below. awk... (3 Replies)
Discussion started by: rocket_dog
3 Replies

9. Emergency UNIX and Linux Support

Search and replace in text file

Hi, I have gigabytes of text files that I need to search for "&" and replace with "&amp". Is there a way to do this efficiently (like sed command)? Hope you could help. Thanks. (17 Replies)
Discussion started by: daytripper1021
17 Replies

10. Shell Programming and Scripting

awk search/replace specific field, using variables for regexp & subsitution then overwrite file

Hello, I'm trying the solve the following problem. I have a file which I intend to use as a csv called master.csv The columns are separated by commas. I want to change the text on a specific row in either column 3,4,5 or 6 from xxx to yyy depending upon if column 1 matches a specified pattern.... (3 Replies)
Discussion started by: cyphex
3 Replies
All times are GMT -4. The time now is 12:49 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy