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Help with file manipulation

 
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Top Forums UNIX for Dummies Questions & Answers Help with file manipulation
# 1  
Old 04-12-2011
Lightbulb Help with file manipulation
Dear All,
I have a question. So for the following sample file I would like to collect information about entries in $F[0], $F[1] & $F[4] so as to acheive the following output as shown below
Code:
SK1.chr01    854    levure5    A    G    225    .    DP=407;AF1=0.5;CI95=0.5,0.5;DP4=142,103,72,68;MQ=31;FQ=225;PV4=0.24,1,1,1    GT:PL:GQ;telomere;ID=TEL01L;Name=TEL01L
SK1.chr01    854    levure6    A    G    199    .    DP=360;AF1=0.5;CI95=0.5,0.5;DP4=138,80,70,48;MQ=31;FQ=202;PV4=0.48,1,1,1    GT:PL:GQ;telomere;ID=TEL01L;Name=TEL01L
SK1.chr01    854    levure7    A    G    225    .    DP=163;AF1=0.5;CI95=0.5,0.5;DP4=60,30,37,19;MQ=31;FQ=225;PV4=1,0.26,1,1    GT:PL:GQ;telomere;ID=TEL01L;Name=TEL01L
SK1.chr01    854    levure8    A    G    225    .    DP=194;AF1=0.5;CI95=0.5,0.5;DP4=66,46,40,28;MQ=31;FQ=225;PV4=1,1,1,1    GT:PL:GQ;telomere;ID=TEL01L;Name=TEL01L
SK1.chr01    12745    levure5    C    G    185    .    DP=125;AF1=0.5;CI95=0.5,0.5;DP4=45,21,25,20;MQ=23;FQ=155;PV4=0.23,1,1,1    GT:PL:GQ
SK1.chr01    12745    levure6    C    G    197    .    DP=85;AF1=0.5;CI95=0.5,0.5;DP4=30,15,18,18;MQ=23;FQ=153;PV4=0.17,1,1,1    GT:PL:GQ
SK1.chr01    12745    levure7    C    G    152    .    DP=36;AF1=0.5;CI95=0.5,0.5;DP4=10,7,11,6;MQ=22;FQ=42;PV4=1,1,1,1    GT:PL:GQ
SK1.chr01    12745    levure8    C    G    173    .    DP=63;AF1=0.5;CI95=0.5,0.5;DP4=21,16,12,14;MQ=23;FQ=98;PV4=0.45,1,1,1    GT:PL:GQ
SK1.chr02    16511    levure5    G    A    148    .    DP=43;AF1=1;CI95=1,1;DP4=2,1,16,19;MQ=24;FQ=-85;PV4=0.59,5.9e-05,1,1    GT:PL:GQ
SK1.chr02    16511    levure6    G    A    127    .    DP=35;AF1=0.5;CI95=0.5,0.5;DP4=4,3,7,16;MQ=25;FQ=30;PV4=0.37,0.0035,0.24,1    GT:PL:GQ

Expected output:
Code:
chr01    854     AAAA     GGGG
chr01    12745   CCCC     GGGG
chr02    16511   GG       AA

Could someone help me figure out a way to do this?
Cheers and hv a nice daySmilie
# 2  
Old 04-12-2011
Code:
nawk '{x=$1;sub(".*[.]","",x);A[$2]=x;B[$2]=B[$2]$4""}END{for(i in A) print A[i],i,B[i]}' inputfile

Ooops, i missed the $5 here you go :

Code:
nawk '{x=$1;sub(".*[.]","",x);A[$2]=x;B[$2]=B[$2]$4"";C[$2]=C[$2]$5""}END{for(i in A) print A[i],i,B[i],C[i]}' inputfile

This User Gave Thanks to ctsgnb For This Post:
pawannoel
# 3  
Old 04-12-2011
Thanks ctsgnb
nawk was not supported but awk version worked Smilie
Cheers

---------- Post updated at 10:28 AM ---------- Previous update was at 10:25 AM ----------

Could you comment on the code please and if you have a Perl version I'll appreciate that too Smilie
# 4  
Old 04-12-2011
Perl solution:
Code:
perl -alne '$F[0]=~s/.*\.//;push @{$a{$F[1]}},$F[3];push @{$b{$F[1]}},$F[4];$c{$F[1]}=$F[0];END{for $i (keys %a){print "$c{$i}\t$i\t",@{$a{$i}},"\t",@{$b{$i}}}}' file

This User Gave Thanks to bartus11 For This Post:
pawannoel
# 5  
Old 04-13-2011
Thanks Bartus Smilie
Hv a nice day
# 6  
Old 04-13-2011
nawk '{ call nawk
x=$1store 1rst field in variable x
sub(".*[.]","",x)replace the string followed by the dot by nothing (extract only the chr<nn> part) into the x variable
A[$2]=xcreate associative array indexed by field 2 and store the value of x
B[$2]=B[$2]$4""concatenate field 4 into an associative array indexed by field 2 (the trailing "" force the element to be considered as strings.)
C[$2]=C[$2]$5""concatenate field 5 into an associative array indexed by field 2
}END{when th whole file has been scanned so that the array have been built
for(i in A)for i taking the values of the index of the associative array A (in fact it will go through the $2 value previously found)
print A[i],i,B[i],C[i]}' inputfileprint the wanted output
This User Gave Thanks to ctsgnb For This Post:
pawannoel
# 7  
Old 04-13-2011
Thanks for the comments ctsgnb
Hv a nice daySmilie
 
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