In the perl below I am trying to extract and print specic values from patterns using multiple regex . One of the patterns AF= may be a whole number or a decimal but I can not seem
to capture both. I think it is the regex .*AF=(\d+\.\d+); as it is expecting a #.#### and it may only be a #. I tried changing it to ^\d*\.?\d*$ but that returned all four lines as is with
the last 8 fields empty. Thank you :).
file
##INFO=<ID=OREF,Number=.,Type=String,Description="List of original reference bases">
##INFO=<ID=OALT,Number=.,Type=String,Description="List of original variant bases">
##INFO=<ID=OMAPALT,Number=.,Type=String,Description="Maps OID,OPOS,OREF,OALT entries to specific ALT alleles">
##deamination_metric=0.184377
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT xxxxx
chr1 10327407 . A T 447.753 PASS AF=0.56962;AO=90;DP=158;FAO=90;FDP=158;FR=.;FRO=68;FSAF=46;FSAR=44;FSRF=29;FSRR=39;FWDB=0.0102227;FXX=0;HRUN=1;LEN=1;MLLD=75.1519;OALT=T;OID=.;OMAPALT=T;OPOS=10327407;OREF=A;PB=.;PBP=.;QD=11.3355;RBI=0.0341128;REFB=-0.00773916;REVB=0.032545;RO=67;SAF=46;SAR=44;SRF=28;SRR=39;SSEN=0;SSEP=0;SSSB=0.0730222;STB=0.536379;STBP=0.323;TYPE=snp;VARB=0.00446437 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/1:246:158:158:67:68:90:90:0.56962:44:46:28:39:44:46:29:39:1
chr1 948846 . T TA 786.915 PASS AF=1;AO=139;DP=159;FAO=152;FDP=152;FR=.;FRO=0;FSAF=79;FSAR=73;FSRF=0;FSRR=0;FWDB=-0.0705752;FXX=0.0256394;HRUN=1;LEN=1;MLLD=19.5287;OALT=A;OID=.;OMAPALT=TA;OPOS=948847;OREF=-;PB=.;PBP=.;QD=20.7083;RBI=0.0969354;REFB=0.149002;REVB=0.0664501;RO=11;SAF=67;SAR=72;SRF=9;SRR=2;SSEN=0;SSEP=0;SSSB=-0.0467166;STB=0.5;STBP=1;TYPE=ins;VARB=-0.00147685 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 1/1:153:159:152:11:0:139:152:1:72:67:9:2:73:79:0:0:1
chr1 9162051 . C T 1642.03 PASS AF=1;AO=172;DP=172;FAO=172;FDP=172;FR=.;FRO=0;FSAF=87;FSAR=85;FSRF=0;FSRR=0;FWDB=0.00602093;FXX=0;HRUN=1;LEN=1;MLLD=174.212;OALT=T;OID=.;OMAPALT=T;OPOS=9162051;OREF=C;PB=.;PBP=.;QD=38.1868;RBI=0.0184042;REFB=0;REVB=-0.0173914;RO=0;SAF=87;SAR=85;SRF=0;SRR=0;SSEN=0;SSEP=0;SSSB=5.71345e-08;STB=0.5;STBP=1;TYPE=snp;VARB=-9.55704e-06 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 1/1:78:172:172:0:0:172:172:1:85:87:0:0:85:87:0:0:1
chr1 9305445 . A C 911.07 PASS AF=0.5175;AO=302;DP=574;FAO=207;FDP=400;FR=.,REALIGNEDx0.5175;FRO=193;FSAF=102;FSAR=105;FSRF=109;FSRR=84;FWDB=0.00317233;FXX=0;HRUN=1;LEN=1;MLLD=73.0922;OALT=C;OID=.;OMAPALT=C;OPOS=9305445;OREF=A;PB=.;PBP=.;QD=9.1107;RBI=0.00738387;REFB=0.00272197;REVB=0.00666767;RO=269;SAF=157;SAR=145;SRF=153;SRR=116;SSEN=0;SSEP=0;SSSB=-0.0424848;STB=0.534715;STBP=0.145;TYPE=snp;VARB=-0.00235714 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/1:782:574:400:269:193:302:207:0.5175:145:157:153:116:105:102:109:84:1
perl
perl -plae '
BEGIN{ %h = qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom) } /^[^#].*AF=(\d+\.\d+);.*FDP=(\d+);.*FSAF=(\d+);.*FSAR=(\d+);.*HRUN=(\d+);.*STB=(\d+\.\d+)[,;].*([0-2]\/[0-2])/ and $_ .= join "\t", ("", sprintf("%1.3f",$1),$3,$4,$5, ($6 >= 0.8 ? "STRANDBIAS" : "GOOD"), $2, $h{$7}, int($F[5]/33+0.5))' file
current output
##INFO=<ID=OREF,Number=.,Type=String,Description="List of original reference bases">
##INFO=<ID=OALT,Number=.,Type=String,Description="List of original variant bases">
##INFO=<ID=OMAPALT,Number=.,Type=String,Description="Maps OID,OPOS,OREF,OALT entries to specific ALT alleles">
##deamination_metric=0.184377
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT xxxxx
chr1 10327407 . A T 447.753 PASS AF=0.56962;AO=90;DP=158;FAO=90;FDP=158;FR=.;FRO=68;FSAF=46;FSAR=44;FSRF=29;FSRR=39;FWDB=0.0102227;FXX=0;HRUN=1;LEN=1;MLLD=75.1519;OALT=T;OID=.;OMAPALT=T;OPOS=10327407;OREF=A;PB=.;PBP=.;QD=11.3355;RBI=0.0341128;REFB=-0.00773916;REVB=0.032545;RO=67;SAF=46;SAR=44;SRF=28;SRR=39;SSEN=0;SSEP=0;SSSB=0.0730222;STB=0.536379;STBP=0.323;TYPE=snp;VARB=0.00446437 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/1:246:158:158:67:68:90:90:0.56962:44:46:28:39:44:46:29:39:1 0.570 46 44 1 GOOD 158 het 14
chr1 948846 . T TA 786.915 PASS AF=1;AO=139;DP=159;FAO=152;FDP=152;FR=.;FRO=0;FSAF=79;FSAR=73;FSRF=0;FSRR=0;FWDB=-0.0705752;FXX=0.0256394;HRUN=1;LEN=1;MLLD=19.5287;OALT=A;OID=.;OMAPALT=TA;OPOS=948847;OREF=-;PB=.;PBP=.;QD=20.7083;RBI=0.0969354;REFB=0.149002;REVB=0.0664501;RO=11;SAF=67;SAR=72;SRF=9;SRR=2;SSEN=0;SSEP=0;SSSB=-0.0467166;STB=0.5;STBP=1;TYPE=ins;VARB=-0.00147685 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 1/1:153:159:152:11:0:139:152:1:72:67:9:2:73:79:0:0:1
chr1 9162051 . C T 1642.03 PASS AF=1;AO=172;DP=172;FAO=172;FDP=172;FR=.;FRO=0;FSAF=87;FSAR=85;FSRF=0;FSRR=0;FWDB=0.00602093;FXX=0;HRUN=1;LEN=1;MLLD=174.212;OALT=T;OID=.;OMAPALT=T;OPOS=9162051;OREF=C;PB=.;PBP=.;QD=38.1868;RBI=0.0184042;REFB=0;REVB=-0.0173914;RO=0;SAF=87;SAR=85;SRF=0;SRR=0;SSEN=0;SSEP=0;SSSB=5.71345e-08;STB=0.5;STBP=1;TYPE=snp;VARB=-9.55704e-06 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 1/1:78:172:172:0:0:172:172:1:85:87:0:0:85:87:0:0:1
chr1 9305445 . A C 911.07 PASS AF=0.5175;AO=302;DP=574;FAO=207;FDP=400;FR=.,REALIGNEDx0.5175;FRO=193;FSAF=102;FSAR=105;FSRF=109;FSRR=84;FWDB=0.00317233;FXX=0;HRUN=1;LEN=1;MLLD=73.0922;OALT=C;OID=.;OMAPALT=C;OPOS=9305445;OREF=A;PB=.;PBP=.;QD=9.1107;RBI=0.00738387;REFB=0.00272197;REVB=0.00666767;RO=269;SAF=157;SAR=145;SRF=153;SRR=116;SSEN=0;SSEP=0;SSSB=-0.0424848;STB=0.534715;STBP=0.145;TYPE=snp;VARB=-0.00235714 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/1:782:574:400:269:193:302:207:0.5175:145:157:153:116:105:102:109:84:1 0.517 102 105 1 GOOD 400 het 28
desired result
##INFO=<ID=OREF,Number=.,Type=String,Description="List of original reference bases">
##INFO=<ID=OALT,Number=.,Type=String,Description="List of original variant bases">
##INFO=<ID=OMAPALT,Number=.,Type=String,Description="Maps OID,OPOS,OREF,OALT entries to specific ALT alleles">
##deamination_metric=0.184377
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT xxxxx
chr1 10327407 . A T 447.753 PASS AF=0.56962;AO=90;DP=158;FAO=90;FDP=158;FR=.;FRO=68;FSAF=46;FSAR=44;FSRF=29;FSRR=39;FWDB=0.0102227;FXX=0;HRUN=1;LEN=1;MLLD=75.1519;OALT=T;OID=.;OMAPALT=T;OPOS=10327407;OREF=A;PB=.;PBP=.;QD=11.3355;RBI=0.0341128;REFB=-0.00773916;REVB=0.032545;RO=67;SAF=46;SAR=44;SRF=28;SRR=39;SSEN=0;SSEP=0;SSSB=0.0730222;STB=0.536379;STBP=0.323;TYPE=snp;VARB=0.00446437 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/1:246:158:158:67:68:90:90:0.56962:44:46:28:39:44:46:29:39:1 0.570 46 44 1 GOOD 158 het 14
chr1 948846 . T TA 786.915 PASS AF=1;AO=139;DP=159;FAO=152;FDP=152;FR=.;FRO=0;FSAF=79;FSAR=73;FSRF=0;FSRR=0;FWDB=-0.0705752;FXX=0.0256394;HRUN=1;LEN=1;MLLD=19.5287;OALT=A;OID=.;OMAPALT=TA;OPOS=948847;OREF=-;PB=.;PBP=.;QD=20.7083;RBI=0.0969354;REFB=0.149002;REVB=0.0664501;RO=11;SAF=67;SAR=72;SRF=9;SRR=2;SSEN=0;SSEP=0;SSSB=-0.0467166;STB=0.5;STBP=1;TYPE=ins;VARB=-0.00147685 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 1/1:153:159:152:11:0:139:152:1:72:67:9:2:73:79:0:0:1 1 79 73 1 GOOD 152 hom 24
chr1 9162051 . C T 1642.03 PASS AF=1;AO=172;DP=172;FAO=172;FDP=172;FR=.;FRO=0;FSAF=87;FSAR=85;FSRF=0;FSRR=0;FWDB=0.00602093;FXX=0;HRUN=1;LEN=1;MLLD=174.212;OALT=T;OID=.;OMAPALT=T;OPOS=9162051;OREF=C;PB=.;PBP=.;QD=38.1868;RBI=0.0184042;REFB=0;REVB=-0.0173914;RO=0;SAF=87;SAR=85;SRF=0;SRR=0;SSEN=0;SSEP=0;SSSB=5.71345e-08;STB=0.5;STBP=1;TYPE=snp;VARB=-9.55704e-06 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 1/1:78:172:172:0:0:172:172:1:85:87:0:0:85:87:0:0:1 1 87 85 1 GOOD 172 hom 50
chr1 9305445 . A C 911.07 PASS AF=0.5175;AO=302;DP=574;FAO=207;FDP=400;FR=.,REALIGNEDx0.5175;FRO=193;FSAF=102;FSAR=105;FSRF=109;FSRR=84;FWDB=0.00317233;FXX=0;HRUN=1;LEN=1;MLLD=73.0922;OALT=C;OID=.;OMAPALT=C;OPOS=9305445;OREF=A;PB=.;PBP=.;QD=9.1107;RBI=0.00738387;REFB=0.00272197;REVB=0.00666767;RO=269;SAF=157;SAR=145;SRF=153;SRR=116;SSEN=0;SSEP=0;SSSB=-0.0424848;STB=0.534715;STBP=0.145;TYPE=snp;VARB=-0.00235714 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR:QT 0/1:782:574:400:269:193:302:207:0.5175:145:157:153:116:105:102:109:84:1 0.517 102 105 1 GOOD 400 het 28