awk to combine lines if fields match in lines Post: 302997474

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Top Forums Shell Programming and Scripting awk to combine lines if fields match in lines Post 302997474 by RavinderSingh13 on Sunday 14th of May 2017 12:27:31 PM

05-14-2017

Moderator

Hello cmccabe,

When I run my script I got following output. Where 4 lines in which string Fusion is there is coming to output.

Code:

chr12:12006495-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E4N15 1868
chr15:88483984-chr12:12006495 Fusion Gain-of-Function ETV6NTRK3-E4N15 1868
chr12:12022903-chr15:88483984 Fusion Gain-of-Function ETV6NTRK3-E5N15 414833
chr15:88483984-chr12:12022903 Fusion Gain-of-Function ETV6NTRK3-E5N15 414833
chr17    7577108    COSM10749;COSM43737    C    A,T    149.594    PASS    AF=0.0830415,0.0;AO=372,2;DP=4420;FAO=166,0;FDP=1999;FR=.,.,REALIGNEDx0.0865;FRO=1833;FSAF=82,0;FSAR=84,0;FSRF=952;FSRR=881;FWDB=0.0072184,-0.0207142;FXX=4.99998E-4;HRUN=1,1;LEN=1,1;MLLD=293.795,80.5366;OALT=A,T;OID=COSM10749,COSM43737;OMAPALT=A,T;OPOS=7577108,7577108;OREF=C,C;PB=.,.;PBP=.,.;QD=0.299338;RBI=0.00721997,0.02565;REFB=1.40155E-4,-7.81395E-4;REVB=1.50579E-4,0.0151276;RO=4043;SAF=187,1;SAR=185,1;SRF=2118;SRR=1925;SSEN=0,0;SSEP=0,0;SSSB=-0.0251826,-5.12306E-4;STB=0.52327,0.5;STBP=0.541,1.0;TYPE=snp,snp;VARB=-0.00153404,0.0;HS;FUNC=[{'origPos':'7577108','origRef':'C','normalizedRef':'C','gene':'TP53','normalizedPos':'7577108','normalizedAlt':'A','polyphen':'1.0','gt':'pos','codon':'TTT','coding':'c.830G>T','sift':'0.0','grantham':'205.0','transcript':'NM_000546.5','function':'missense','protein':'p.Cys277Phe','location':'exonic','origAlt':'A','exon':'8','oncomineGeneClass':'Loss-of-Function','oncomineVariantClass':'Hotspot'}]    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT    0/1:149:4420:1999:4043:1833:372,2:166,0:0.0830415,0.0:185,1:187,1:2118:1925:84,0:82,0:952:881:1
chr10    89624278    .    G    T    62.8836    PASS    AF=0.0785393;AO=297;DP=4155;FAO=157;FDP=1999;FR=.;FRO=1842;FSAF=77;FSAR=80;FSRF=908;FSRR=934;FWDB=0.0113997;FXX=4.99998E-4;HRUN=1;LEN=1;MLLD=117.237;OALT=T;OID=.;OMAPALT=T;OPOS=89624278;OREF=G;PB=.;PBP=.;QD=0.12583;RBI=0.040843;REFB=5.39678E-4;REVB=-0.0392199;RO=3844;SAF=150;SAR=147;SRF=1936;SRR=1908;SSEN=0;SSEP=0;SSSB=0.00159791;STB=0.502301;STBP=0.96;TYPE=snp;VARB=-0.00676678;FUNC=[{'origPos':'89624278','origRef':'G','normalizedRef':'G','gene':'PTEN','normalizedPos':'89624278','normalizedAlt':'T','gt':'pos','codon':'TAG','coding':'c.52G>T','transcript':'NM_000314.4','function':'nonsense','protein':'p.Glu18Ter','location':'exonic','origAlt':'T','exon':'1'}]    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT    0/1:62:4155:1999:3844:1842:297:157:0.0785393:147:150:1936:1908:80:77:908:934:1

Thanks,
R. Singh

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igawk

IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME

       igawk - gawk with include files

SYNOPSIS

       igawk [ all gawk options ] -f program-file [ -- ] file ...
       igawk [ all gawk options ] [ -- ] program-text file ...

DESCRIPTION

       Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1).

       AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like

	      @include getopt.awk

       in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path.

OPTIONS

       See gawk(1) for a full description of the AWK language and the options that gawk supports.

EXAMPLES

       cat << EOF > test.awk
       @include getopt.awk

       BEGIN {
	    while (getopt(ARGC, ARGV, "am:q") != -1)
		 ...
       }
       EOF

       igawk -f test.awk

SEE ALSO

       gawk(1)

       Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995.

AUTHOR

       Arnold Robbins (arnold@skeeve.com).

Free Software Foundation					    Nov 3 1999								  IGAWK(1)