In the awk below which executes as is, I am trying to add a condition that will extract the text or
value after the FR= for the lines in each line of file1 compared
to file2. As is the lines between the two files are either a match, Missing in file 1, or Missing in file2,
but I can not add the condition to extract FR= up to the ; (semi-colon). There may
not always be text after the FR=, but it always ends with a ;. Thank you .
file1
Code:
chr1 43814978 COSM27286 G A 86.92679999999999 PASS AF=0;AO=1;DP=5535;FAO=0;FDP=2000;FR=.,REALIGNEDx0.008;FRO=2000;FSAF=0;FSAR=0;FSRF=1213;FSRR=787;FWDB=0.0456208;FXX=0;HRUN=1;LEN=1;MLLD=67.7782;OALT=A;OID=COSM27286;OMAPALT=A;OPOS=43814979;OREF=G;PB=.;PBP=.;QD=0.173854;RBI=0.0521772;REFB=2.05804E-5;REVB=0.0253221;RO=5523;SAF=1;SAR=0;SRF=3401;SRR=2122;SSEN=0;SSEP=0;SSSB=0.00321242;STB=0.5;STBP=1;TYPE=snp;VARB=0;HS;FUNC=[{'transcript':'NM_005373.2','gene':'MPL','location':'exonic','exon':'10'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/0:86:5535:2000:5523:2000:1:0:0:0:1:3401:2122:0:0:1213:787:0
chr1 43814981 COSM27287 G A 86.83350000000002 PASS AF=0;AO=2;DP=5556;FAO=0;FDP=1999;FR=.;FRO=1999;FSAF=0;FSAR=0;FSRF=1239;FSRR=760;FWDB=-0.0139666;FXX=4.99998E-4;HRUN=1;LEN=1;MLLD=230.086;OALT=A;OID=COSM27287;OMAPALT=A;OPOS=43814981;OREF=G;PB=.;PBP=.;QD=0.173754;RBI=0.0152778;REFB=-9.34219E-7;REVB=-0.00619229;RO=5525;SAF=2;SAR=0;SRF=3391;SRR=2134;SSEN=0;SSEP=0;SSSB=0.00642119;STB=0.5;STBP=1;TYPE=snp;VARB=0;HS;FUNC=[{'transcript':'NM_005373.2','gene':'MPL','location':'exonic','exon':'10'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/0:86:5556:1999:5525:1999:2:0:0:0:2:3391:2134:0:0:1239:760:0
chr1 43815008 COSM29008;COSM43212;COSM19193;COSM27289;COSM28487 TGG AAA,AAG,AGG,CGG,GCG 70.3099 PASS AF=0,0,0,0,0;AO=0,0,1,3,0;DP=5528;FAO=0,0,0,0,0;FDP=1675;FR=.,.,.,.,.;FRO=1675;FSAF=0,0,0,0,0;FSAR=0,0,0,0,0;FSRF=1010;FSRR=665;FWDB=-0.0326268,-0.0568148,-0.0658984,-0.0526516,-0.0545445;FXX=0.162499;HRUN=1,1,1,1,1;LEN=3,2,1,1,2;MLLD=155.105,120.652,107.82,60.137,93.9951;OALT=AAA,AA,A,C,GC;OID=COSM28487,COSM19193,COSM29008,COSM43212,COSM27289;OMAPALT=AAA,AAG,AGG,CGG,GCG;OPOS=43815008,43815008,43815008,43815008,43815008;OREF=TGG,TG,T,T,TG;PB=.,.,.,.,.;PBP=.,.,.,.,.;QD=0.167904;RBI=0.0432053,0.0581938,0.0673244,0.0594109,0.0551872;REFB=0.00195961,3.64629E-5,0.00186523,0.00842498,0.00169447;REVB=-0.028323,-0.0125932,-0.0137832,-0.0275221,-0.00839827;RO=4345;SAF=0,0,1,0,0;SAR=0,0,0,3,0;SRF=2598;SRR=1747;SSEN=0,0,0,0,0;SSEP=0,0,0,0,0;SSSB=-6.91127E-8,-6.91127E-8,0.00419704,-0.0184325,-6.91127E-8;STB=0.5,0.5,0.5,0.5,0.5;STBP=1,1,1,1,1;TYPE=mnp,mnp,snp,snp,mnp;VARB=0,0,0,0,0;HS;FUNC=[{'transcript':'NM_005373.2','gene':'MPL','location':'exonic','exon':'10'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/0:73:5528:1675:4345:1675:0,0,1,3,0:0,0,0,0,0:0,0,0,0,0:0,0,0,3,0:0,0,1,0,0:2598:1747:0,0,0,0,0:0,0,0,0,0:1010:665:0
file2
Code:
chr1 43814979 COSM27286 G A 86.92679999999999 PASS AF=0;AO=1;DP=5535;FAO=0;FDP=2000;FR=.,REALIGNEDx0.004;FRO=2000;FSAF=0;FSAR=0;FSRF=1213;FSRR=787;FWDB=0.0456208;FXX=0;HRUN=1;LEN=1;MLLD=67.7782;OALT=A;OID=COSM27286;OMAPALT=A;OPOS=43814979;OREF=G;PB=.;PBP=.;QD=0.173854;RBI=0.0521772;REFB=2.05804E-5;REVB=0.0253221;RO=5523;SAF=1;SAR=0;SRF=3401;SRR=2122;SSEN=0;SSEP=0;SSSB=0.00321242;STB=0.5;STBP=1;TYPE=snp;VARB=0;HS;FUNC=[{'transcript':'NM_005373.2','gene':'MPL','location':'exonic','exon':'10'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/0:86:5535:2000:5523:2000:1:0:0:0:1:3401:2122:0:0:1213:787:0
chr1 43814981 COSM27287 G A 86.83350000000002 PASS AF=0;AO=2;DP=5556;FAO=0;FDP=1999;FR=.;FRO=1999;FSAF=0;FSAR=0;FSRF=1239;FSRR=760;FWDB=-0.0139666;FXX=4.99998E-4;HRUN=1;LEN=1;MLLD=230.086;OALT=A;OID=COSM27287;OMAPALT=A;OPOS=43814981;OREF=G;PB=.;PBP=.;QD=0.173754;RBI=0.0152778;REFB=-9.34219E-7;REVB=-0.00619229;RO=5525;SAF=2;SAR=0;SRF=3391;SRR=2134;SSEN=0;SSEP=0;SSSB=0.00642119;STB=0.5;STBP=1;TYPE=snp;VARB=0;HS;FUNC=[{'transcript':'NM_005373.2','gene':'MPL','location':'exonic','exon':'10'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/0:86:5556:1999:5525:1999:2:0:0:0:2:3391:2134:0:0:1239:760:0
chr1 43815008 COSM29008;COSM43212;COSM19193;COSM27289;COSM28487 TGG AAA,AAG,AGG,CGG,GCG 70.3099 PASS AF=0,0,0,0,0;AO=0,0,1,3,0;DP=5528;FAO=0,0,0,0,0;FDP=1675;FR=.,.,.,.,.;FRO=1675;FSAF=0,0,0,0,0;FSAR=0,0,0,0,0;FSRF=1010;FSRR=665;FWDB=-0.0326268,-0.0568148,-0.0658984,-0.0526516,-0.0545445;FXX=0.162499;HRUN=1,1,1,1,1;LEN=3,2,1,1,2;MLLD=155.105,120.652,107.82,60.137,93.9951;OALT=AAA,AA,A,C,GC;OID=COSM28487,COSM19193,COSM29008,COSM43212,COSM27289;OMAPALT=AAA,AAG,AGG,CGG,GCG;OPOS=43815008,43815008,43815008,43815008,43815008;OREF=TGG,TG,T,T,TG;PB=.,.,.,.,.;PBP=.,.,.,.,.;QD=0.167904;RBI=0.0432053,0.0581938,0.0673244,0.0594109,0.0551872;REFB=0.00195961,3.64629E-5,0.00186523,0.00842498,0.00169447;REVB=-0.028323,-0.0125932,-0.0137832,-0.0275221,-0.00839827;RO=4345;SAF=0,0,1,0,0;SAR=0,0,0,3,0;SRF=2598;SRR=1747;SSEN=0,0,0,0,0;SSEP=0,0,0,0,0;SSSB=-6.91127E-8,-6.91127E-8,0.00419704,-0.0184325,-6.91127E-8;STB=0.5,0.5,0.5,0.5,0.5;STBP=1,1,1,1,1;TYPE=mnp,mnp,snp,snp,mnp;VARB=0,0,0,0,0;HS;FUNC=[{'transcript':'NM_005373.2','gene':'MPL','location':'exonic','exon':'10'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/0:73:5528:1675:4345:1675:0,0,1,3,0:0,0,0,0,0:0,0,0,0,0:0,0,0,3,0:0,0,1,0,0:2598:1747:0,0,0,0,0:0,0,0,0,0:1010:665:0
awk
Code:
awk 'FNR==1 { next }
FNR == NR { file1[$1,$2,$7] = $1 " " $2 " " $6 " "$7 }
FNR != NR { file2[$1,$2,$7] = $1 " " $2 " " $6 " "$7 }
END { print "Match:"; for (k in file1) if (k in file2) print file1[k] # Or file2[k]
print "Missing in file1:"; for (k in file2) if (!(k in file1)) print file2[k]
print "Missing in file2:"; for (k in file1) if (!(k in file2)) print file1[k]
}' file1 file2 > out
Hello ,
I need your help to extract a line in a big file , and this line is always 11 lines
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Thanks in advance
npn35 (17 Replies)
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07-25-2017
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