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Full Discussion: Parse input of two files to be the same in awk
Top Forums Shell Programming and Scripting Parse input of two files to be the same in awk Post 302964234 by cmccabe on Tuesday 12th of January 2016 02:25:41 PM
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 03:29 PM.. Reason: fixed format
 

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