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Full Discussion: awk to combine lines if fields match in lines
Top Forums Shell Programming and Scripting awk to combine lines if fields match in lines Post 302997468 by cmccabe on Sunday 14th of May 2017 10:46:43 AM
Old 05-14-2017
I have added two lines to add a header and remove duplicates based on $4. The portion of code in bold below was an attempt to print the two lines (in this example, there may be more). If the SVTYPE=Fusion is not true then the entire line is printed in the output. Thank you Smilie.

Code:
awk -v OFS="\t" '/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 "Locus\tType\tFunction\tGene\tReads" ### add header
                        print $1":"$2 "-" VAL OFS svtype OFS substr($0,RSTART+20,RLENGTH-22) OFS $3 OFS read_count;
                        ' $8 != "\"SVTYPE=Fusion\"" {print;}'
                    }
' input | awk -F'\t' '!seen[$4]++'### remove duplicates based on $4

awk: cmd. line:21:                         
awk: cmd. line:21:                         ^ unexpected newline or end of string

current output
Code:
chr12:12006495-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E4N15 1868
chr12:12022903-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E5N15 414833

desired output
Code:
chr12:12006495-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E4N15 1868
chr12:12022903-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E5N15 414833
chr17 entire line.... (this line does not have the keyword in it so is printed in the output)
chr10 entire line...   (this line does not have the keyword in it so is printed in the output

Last edited by cmccabe; 05-14-2017 at 11:48 AM.. Reason: added current output
 

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LEARN ABOUT PLAN9

grep

GREP(1) 						      General Commands Manual							   GREP(1)

NAME

       grep - search a file for a pattern

SYNOPSIS

       grep [ option ...  ] pattern [ file ...	]

DESCRIPTION

       Grep  searches  the input files (standard input default) for lines (with newlines excluded) that match the pattern, a regular expression as
       defined in regexp(6).  Normally, each line matching the pattern is `selected', and each selected line is copied	to  the  standard  output.
       The options are

       -c     Print only a count of matching lines.
       -h     Do not print file name tags (headers) with output lines.
       -i     Ignore alphabetic case distinctions.  The implementation folds into lower case all letters in the pattern and input before interpre-
	      tation.  Matched lines are printed in their original form.
       -l     (ell) Print the names of files with selected lines; don't print the lines.
       -L     Print the names of files with no selected lines; the converse of -l.
       -n     Mark each printed line with its line number counted in its file.
       -s     Produce no output, but return status.
       -v     Reverse: print lines that do not match the pattern.

       Output lines are tagged by file name when there is more than one input file.  (To force this tagging, include  /dev/null  as  a	file  name
       argument.)

       Care should be taken when using the shell metacharacters $*[^|()= and newline in pattern; it is safest to enclose the entire expression in
       single quotes '...'.

SOURCE

       /sys/src/cmd/grep.c

SEE ALSO

       ed(1), awk(1), sed(1), sam(1), regexp(6)

DIAGNOSTICS

       Exit status is null if any lines are selected, or non-null when no lines are selected or an error occurs.

																	   GREP(1)
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