Parse input of two files to be the same in awk


 
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# 1  
Old 01-12-2016
Parse input of two files to be the same in awk

I have two files that I am going to use diff to find the differences but need to parse them before I do that. I have include the format of each file1 and file2 with the desired output of each (the first 5 fields in each file). The first file has a "chr" before the # that needs to be removed. I have included an awk for file2 that I think will work but not sure about file1. Thank you Smilie.

file1
Code:
chr1    977330    .    T    C    1442.18    PASS    AF=1;AO=150;DP=150;FAO=151;FDP=151;FR=.;FRO=0;FSAF=86;FSAR=65;FSRF=0;FSRR=0;FWDB=0.0177391;FXX=0;HRUN=1;
LEN=1;MLLD=104.329;OALT=C;OID=.;OMAPALT=C;OPOS=977330;OREF=T;PB=0.5;PBP=1;QD=38.2033;RBI=0.0302247;REFB=0;REVB=-0.0244715;RO=0;SAF=85;SAR=65;
SRF=0;SRR=0;SSEN=0;SSEP=0;SSSB=3.81633e-08;STB=0.5;STBP=1;TYPE=snp;VARB=-1.50479e-05    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:
FSRR    1/1:68:150:151:0:0:150:151:1:65:85:0:0:65:86:0:0
chr1    981931    .    A    G    773.354    PASS

desired output of file1
Code:
1    977330    .    T    C

file2
Code:
1    955597    .    G    G    256.13    PASS    AC=0;AN=2;SF=8;GENE=AGRN    
GT:MQRS:FS:DPF:RPRS:QD:BQRS:MQR:AD:GQ:MQ0:VAL:PL:ROI    0/0:.:.:.:.:.:.:.:.:.:.:1:.:1  
  ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0  
  ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    0/0:0.252:0.000:94:-0.100:8.83:1.930:59.78:38,0:99:0:1:985,985,985:1  
  ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0  
  ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0  
  ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    0/0:.:.:.:.:.:.:.:.:.:.:1:.:1 
   ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    ./.:.:.:.:.:.:.:.:.:.:.:.:.:0    0/0:.:.:.:.:.:.:.:.:.:.:1:.:1

desired output of file2
Code:
1    955597    .    G    G

Code:
awk '{print $1}' file1
awk '{print $1}' file1
awk '{print $1}' file1
awk '{print$1, $2, $3, $4, $5}' file2


Last edited by cmccabe; 01-12-2016 at 04:29 PM.. Reason: fixed format
# 2  
Old 01-12-2016
Code:
awk '{sub (/chr/, "", $1); print$1, $2, $3, $4, $5}' file1

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