Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

Extracting data blocks from file

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Extracting data blocks from file
# 1  
Old 02-27-2012
Extracting data blocks from file
Hi all,

I want to extract blocks of data from a file depending on the contents of that block.
The input file(table) has several blocks each starting with 'gene' in the first column. I want to extract only those blocks which do not have the expression '_T02' in the second column.

Input file
Code:
gene f01
a t01
b t01
c t02
gene f02
a t01
b t01
c t01
gene f03
a t02
b t01
c t01
gene f04
a t01
b t01
c t01

Expected output
Code:
gene f02
a t01
b t01
c t01
gene f04
a t01
b t01
c t01

Many thanks
# 2  
Old 02-27-2012
Try:
Code:
perl -ln0e 'while (/gene.*?(?=gene|$)/sg){print $& if !($&=~/t02/)}' file

This User Gave Thanks to bartus11 For This Post:
newbie83
# 3  
Old 02-27-2012
Code:
$ cat gene.awk

/^gene/ {
        if(!T2) for(N=1; N<=L; N++) print LINE[N];

        L=0
        T2=0
}

$2 ~ /t02/ { T2=1 }

{ LINE[++L]=$0 }

END {   if(!T2) for(N=1; N<=L; N++) print LINE[N];      }

$ awk -f gene.awk input

gene f02
a t01
b t01
c t01
gene f04
a t01
b t01
c t01

$

Adjust /t02/ to taste, since you say _T02 in one place and t02 in another...
This User Gave Thanks to Corona688 For This Post:
newbie83
# 4  
Old 02-27-2012
Assuming 4 lines per block:
Code:
sed -n '
   N
   N
   N
   / t02$/p
 ' in_file >out_file

This User Gave Thanks to DGPickett For This Post:
newbie83
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Need Help in extracting data from XML File

Hi All My input file is an XML and it has some tags and data rows at end. Starting of data rows is <rs:data> and ending of data rows is </rs:data>. Within sample data rows (2 rows) shown below, I want to extract data value after equal to sign (until space or "/" sign). So if XML data... (7 Replies)
Discussion started by: vx04
7 Replies

2. UNIX for Dummies Questions & Answers

Extracting data from file

I am trying to compare the data in lines 3 & 5 to see if they match up to the '-S570' (see first code set, all proprietary information has been removed from code set) spawn telnet Trying ... Connected to CA-LOS1234-ASE-S570.cl . Escape character is '^]'. CA-LOS1234-ASE-S570 Username: ... (1 Reply)
Discussion started by: slipshft
1 Replies

3. Shell Programming and Scripting

Need help in extracting data from xml file

Hello, This is my first post in here, so excuse me if I sound too noob here! I need to extract the path "/apps/mp/installedApps/V61/HRO/hrms_01698_A_qa.ear" from the below xml extract. The path will always appear with the key "binariesURL" <deployedObject... (6 Replies)
Discussion started by: abhishek2386
6 Replies

4. Shell Programming and Scripting

Extracting specific lines of data from a file and related lines of data based on a grep value range?

Hi, I have one file, say file 1, that has data like below where 19900107 is the date, 19900107 12 144 129 0.7380047 19900108 12 168 129 0.3149017 19900109 12 192 129 3.2766666E-02 ... (3 Replies)
Discussion started by: Wynner
3 Replies

5. Shell Programming and Scripting

how to split this file into blocks and then send these blocks as input to the tool called Yices?

Hello, I have a file like this: FILE.TXT: (define argc :: int) (assert ( > argc 1)) (assert ( = argc 1)) <check> # (define c :: float) (assert ( > c 0)) (assert ( = c 0)) <check> # now, i want to separate each block('#' is the delimeter), make them separate files, and then send them as... (5 Replies)
Discussion started by: paramad
5 Replies

6. UNIX for Dummies Questions & Answers

Extracting data from an xml file

Hello, Please can someone assist. I have the following xml file: <?xml version="1.0" encoding="utf-8" ?> - <PUTTRIGGER xmlns:xsd="http://www.test.org/2001/XMLSchema" xmlns:xsi="http://www.test.org/2001/XMLSchema-instance" APPLICATIONNUMBER="0501160" ACCOUNTNAME="Mrs S Test"... (15 Replies)
Discussion started by: Dolph
15 Replies

7. Shell Programming and Scripting

extracting data from a .csv file

I have a .csv file equipment,bandtype abc,aws def,mmds ghi,umts jkl,mmds I can get the equipment from `hostname`. In my script i want to check what is the hostname. then see if it exists in the.csv file. if it does then i want to store the second parameter(bandtype) for the corresponding... (3 Replies)
Discussion started by: lassimanji
3 Replies

8. UNIX for Dummies Questions & Answers

Extracting Data from a File

Hi I need to calculate the number of occurrences of a item in a number of files using Perl. The item appears continually throughout the files but in each case I only want to calculate it in certain blocks of the file. Example - Calculalte the number of occurrences of a 'pass' in a block of... (0 Replies)
Discussion started by: oop
0 Replies

9. Shell Programming and Scripting

Extracting Data from xml file

Hi ppl out there... Can anyone help me with the shell script to extract data from an xml file. My xml file looks like : - <servlet> <servlet-name>FrontServlet</servlet-name> <display-name>FrontServlet</display-name> ... (3 Replies)
Discussion started by: nishana
3 Replies

10. UNIX for Dummies Questions & Answers

extracting recursive data file

Hi Gurus, Can awk be able to do this source file: 1|SPFE2027G1|1PFE-7000|T34801188|5066-0844| 2|T34801188|5066-0844|T35002355|5066-0845| 3|T35002355|5066-0845|T35203409|QFBR-7798| 1|SPFE2027H1|1PFE-7000|T34801198|5066-0844| 2|T34801198|5066-0844|T35002365|5066-0845| formatted into:... (1 Reply)
Discussion started by: bbeugie
1 Replies
Login or Register to Ask a Question