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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snp

SNP(4)							   BSD Kernel Interfaces Manual 						    SNP(4)

NAME

     snp -- tty snoop interface

SYNOPSIS

     #include <sys/snoop.h>

     int
     ioctl(fd, SNPSTTY, &dev);

     int
     ioctl(fd, SNPGTTY, &dev);

     int
     ioctl(fd, FIONREAD, &result);

DESCRIPTION

     /dev/snp is a snoop device which allows users to attach to any tty and watch activities on it.  The kernel must be compiled with device snp,
     or the snp module must be loaded, for these devices to be available.

     To associate a given snp device with a tty to be observed, open the snp device and a tty device, and then issue the SNPSTTY ioctl on snp
     device.  The argument passed to the ioctl(2) is the address of a variable of type int, holding the file descriptor of a tty device.  To
     detach the snp device from a tty use a pointer to a value of -1.

     The SNPGTTY ioctl returns information about the current tty attached to the open snp device.

     The FIONREAD ioctl returns a positive value equal to the number of characters in a read buffer.  Special values defined are:

     SNP_OFLOW	   device overflow occurred, device detached.

     SNP_TTYCLOSE  tty not attached.

     SNP_DETACH    snp device has been detached by user or tty device has been closed and detached.

SEE ALSO

     pty(4), sio(4), kldload(8), watch(8)

HISTORY

     The snp device first appeared in FreeBSD 2.1.  In FreeBSD 8.0 the snp driver was rewritten to work with the replaced TTY subsystem.

AUTHORS

     The author of the current implementation is Ed Schouten <ed@FreeBSD.org>.	Previous versions of snp were based on code written by
     Ugen J.S. Antsilevich <ugen@NetVision.net.il>.

BUGS

     This version of snp does not return proper error codes when calling FIONREAD.  It also does not allow SNPSTTY to detach itself from the TTY.

BSD
								 November 5, 2008							       BSD