awk to combine lines if fields match in lines Post: 302997389

Sponsored Content

Top Forums Shell Programming and Scripting awk to combine lines if fields match in lines Post 302997389 by RavinderSingh13 on Friday 12th of May 2017 11:57:50 AM

05-12-2017

Moderator

Hello cmccabe,

Could you please check if following may help you in same.

Code:

awk '/SVTYPE=Fusion/{match($5,/].*]/);sub(/.COS.*/,"",$3);sub(/-/,"",$3);sub(/\./,"-",$3);VAL=substr($5,RSTART+1,RLENGTH-2);num=split($8, array,";");for(i=1;i<=num;i++){if(array[i] ~  /SVTYPE/){sub(/.*=/,"",array[i]);svtype=array[i]};if(array[i] ~ /READ_COUNT/){sub(/.*=/,"",array[i]);read_count=array[i]}};match($0,/oncomineGeneClass.*,/);print $1":"$2 "-" VAL OFS svtype OFS substr($0,RSTART+20,RLENGTH-22) OFS $3 OFS read_count;}'  Input_file

EDIT: Adding a non-one liner form of solution too now.

Code:

awk '/SVTYPE=Fusion/{
                        match($5,/].*]/);
                        sub(/.COS.*/,"",$3);
                        sub(/-/,"",$3);
                        sub(/\./,"-",$3);
                        VAL=substr($5,RSTART+1,RLENGTH-2);
                        num=split($8, array,";");
                        for(i=1;i<=num;i++){
                                                if(array[i] ~  /SVTYPE/){
                                                sub(/.*=/,"",array[i]);
                                                svtype=array[i]
                                                                        };
                                                if(array[i] ~ /READ_COUNT/){
                                                sub(/.*=/,"",array[i]);
                                                read_count=array[i]
                                                                           }
                                           };
                        match($0,/oncomineGeneClass.*,/);
                        print $1":"$2 "-" VAL OFS svtype OFS substr($0,RSTART+20,RLENGTH-22) OFS $3 OFS read_count;
                    }
    '   Input_file

Thanks,
R. Singh

This User Gave Thanks to RavinderSingh13 For This Post:

RavinderSingh13

View Public Profile for RavinderSingh13

Find all posts by RavinderSingh13

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

SImple HELP! how to combine two lines together using sed or awk..

hi..im new to UNIX... ok i have this information in the normal shell... there are 2 lines display like this: h@hotmail.com k@hotmail.com i want it to display like this with a space betweem them h@hotmail.com k@hotmail.com the information is stored in a text file.... anyone...

2. Shell Programming and Scripting

search and combine lines in awk

Hi All, I have 1 "keyword" file like this: 00-1F-FB-00-04-18 00-19-CB-8E-66-DF 00-1F-FB-00-48-9C 00-1F-FB-00-AA-4F .... and the 2nd "details" file like this: Wed Feb 11 00:00:02 2009 NAS-IP-Address = xxxxxxxxxxxxxxxxxx Class = "P1-SHT-AAA01;1233704662;4886720" ...

3. UNIX for Dummies Questions & Answers

awk display the match and 2 lines after the match is found.

Hello, can someone help me how to find a word and 2 lines after it and then send the output to another file. For example, here is myfile1.txt. I want to search for "Error" and 2 lines below it and send it to myfile2.txt I tried with grep -A but it's not supported on my system. I tried with awk,...

4. Shell Programming and Scripting

Print only lines where fields concatenated match strings

Hello everyone, Maybe somebody could help me with an awk script. I have this input (field separator is comma ","): 547894982,M|N|J,U|Q|P,98,101,0,1,1 234900027,M|N|J,U|Q|P,98,101,0,1,1 234900023,M|N|J,U|Q|P,98,54,3,1,1 234900028,M|H|J,S|Q|P,98,101,0,1,1 234900030,M|N|J,U|F|P,98,101,0,1,1...

5. UNIX for Dummies Questions & Answers

awk - (URGENT!) Print lines sort and move lines if match found

URGENT HELP IS NEEDED!! I am looking to move matching lines (01 - 07) from File1 and 77 tab the matching string from File2, to File3.txt. I am almost done but - Currently, script is not printing lines to File3.txt in order. - Also the matching lines are not moving out of File1.txt ...

6. Shell Programming and Scripting

Awk: Combine multiple lines based on number of fields

If a file has following kind of data, comma delimited 1,2,3,4 1 1 1,2,3,4 1,2 2 2,3,4 My required output must have only 4 columns with comma delimited 1,2,3,4 111,2,3,4 1,222,3,4 I have tried many awk command using ORS="" but couldnt progress

7. Shell Programming and Scripting

awk to combine lines from line with pattern match to a line that ends in a pattern

I am trying to combine lines with these conditions: 1. First line starts with text of "libname VALUE db2 datasrc" where VALUE can be any text. 2. If condition1 is met then continue to combine lines through a line that ends with a semicolon. 3. Ignore case when matching patterns and remove any...

8. UNIX for Beginners Questions & Answers

How to count lines of CSV file where 2 fields match variables?

I'm trying to use awk to count the occurrences of two matching fields of a CSV file. For instance, for data that looks like this... Joe,Blue,Yes,No,High Mike,Blue,Yes,Yes,Low Joe,Red,No,No,Low Joe,Red,Yes,Yes,Low I've been trying to use code like this... countvar=`awk ' $2~/$color/...

9. Shell Programming and Scripting

awk to combine matching lines in file

I am trying to combine all matching lines in the tab-delimited using awk. The below runs but no output results. Thank you :). input chrX 110925349 110925532 ALG13 chrX 110925349 110925532 ALG13 chrX 110925349 110925532 ALG13 chrX 47433390 47433999 SYN1...

10. Shell Programming and Scripting

awk to remove lines that do not start with digit and combine line or lines

I have been searching and trying to come up with an awk that will perform the following on a converted text file (original is a pdf). 1. Since the first two lines are (begin with) text they are removed 2. if $1 is a number then all text is merged (combined) into one line until the next...

LEARN ABOUT MINIX

grep

GREP(1) 						      General Commands Manual							   GREP(1)

NAME

       grep - search a file for lines containing a given pattern

SYNOPSIS

       grep [-elnsv] pattern [file] ...

OPTIONS

       -e     -e pattern is the same as pattern

       -c     Print a count of lines matched

       -i     Ignore case

       -l     Print file names, no lines

       -n     Print line numbers

       -s     Status only, no printed output

       -v     Select lines that do not match

EXAMPLES

       grep mouse file	   # Find lines in file containing mouse

       grep [0-9] file	   # Print lines containing a digit

DESCRIPTION

       Grep  searches  one  or	more  files (by default, stdin) and selects out all the lines that match the pattern.  All the regular expressions
       accepted by ed and mined are allowed.  In addition, + can be used instead of * to mean 1 or more occurrences, ? can be used to mean 0 or  1
       occurrences,  and  |  can  be used between two regular expressions to mean either one of them.  Parentheses can be used for grouping.  If a
       match is found, exit status 0 is returned.  If no match is found, exit status 1 is returned.  If an error is detected,  exit  status  2	is
       returned.

SEE ALSO

       cgrep(1), fgrep(1), sed(1), awk(9).

																	   GREP(1)