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awk to print line(s) meeting condions

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# 1  
Old 05-10-2017
awk to print line(s) meeting condions
In the awk below which executes, but the out is empty, I am trying to print the line that meets both conditions below:
Code:
1. $7 = PASS
2.AF= > .03 or 3%
3. function = nonsense or frameshift

In the file below in the second line'function'is not present in the line and AF= < 3%.

I am close I think, but not able to get the script to work as desired. Thank you Smilie.

file tab-delimited
Code:
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
chr10 89624293 COSM86051 T G 341.74 PASS AF=0;AO=1;DP=4145;FAO=0;FDP=1995;FR=.;FRO=1995;FSAF=0;FSAR=0;FSRF=1008;FSRR=987;FWDB=0.0136548;FXX=0.00249999;HRUN=2;LEN=1;MLLD=151.799;OALT=G,G;OID=COSM86051,COSM86051;OMAPALT=G,G;OPOS=89624293,89624293;OREF=T,T;PB=.;PBP=.;QD=0.685192;RBI=0.0172428;REFB=4.38663E-6;REVB=0.010529;RO=4136;SAF=0;SAR=1;SRF=2077;SRR=2059;SSEN=0;SSEP=0;SSSB=-0.00528832;STB=0.5;STBP=1;TYPE=snp;VARB=0;HS;FUNC=[{'transcript':'NM_000314.4','gene':'PTEN','location':'exonic','exon':'1'}] GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/0:341:4145:1995:4136:1995:1:0:0:1:0:2077:2059:0:0:1008:987:0

awk
Code:
awk -F'\t' '{$7=="PASS" &&
                        if(/AF=[^;]*/+0 > .03 && "'function'" == "nonsense" || "'function'" == "frameshift"){
                                       print
      }
     }
' file > out

desired out tab-delimited --- only line that meets both conditions
Code:
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

# 2  
Old 05-10-2017
Hello cmccabe,

If your Input_file is same as shown sample Input_file then following may help you.
Code:
awk -F'[ ;=,:]' '$7=="PASS" && $9>.03 && $107 ~ /function/ && $108 ~ /nonsense/'   Input_file

In case your Input_file is NOT same as shown sample Input_file which means it's fields are NOT fixed then you need to traverse through the fields and check for these values like PASS,function etc etc and store their field number's value and then check your all conditions by using their field's values. I hope this helps.

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
cmccabe
# 3  
Old 05-10-2017
Hi,
You can try this:
Code:
awk -F'\t' '$7 == "PASS" && /AF=([1-9]|[0-9]\.[1-9]|0\.0[3-9])/ && /'"'"'function'"'"':'"'"'(nonsense|frameshift)'"'"'/' file

Regards.
This User Gave Thanks to disedorgue For This Post:
cmccabe
# 4  
Old 05-11-2017
Thank you both very much Smilie.
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