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Compare two column in file and extract complate line

 
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# 1  
Old 05-03-2013
Compare two column in file and extract complate line
Code:
No Chr   Pos              Qual     GT_1   GT_2
1. chr1   478493       595     A/G     G/G
2. chr1    879243     700       A/T      T/T
3. chr2    889922     1300    C/C     C/C
4. chr2    1926372    300     T/A     T/A 
5. chr3     237474     500      G/C       C/C
6. chr3      575757    700      A/T       T/T
7. chr3    6666874    746       T/T       T/T

I have one file with six column file is tab delimited. I like to check if column GT_1 and GT_2 did not match, print complete line and at the end It also count how many A/G converted to G/G , AT converted to T/T . It has to skip all lines in which GT_1 column has same value in GT_2 for example both column has T/T and t/A value in line 7 and 4 respectively. I don't know We can compare text value like T/A in unix or not because I don't have numeric values in my problem. Thanks for your time for my question
Last edited by radoulov; 05-03-2013 at 12:53 PM..
# 2  
Old 05-03-2013
A start...
Code:
$ cat sample32.txt
No Chr   Pos              Qual     GT_1   GT_2
1. chr1   478493       595     A/G     G/G
2. chr1    879243     700       A/T      T/T
3. chr2    889922     1300    C/C     C/C
4. chr2    1926372    300     T/A     T/A
5. chr3     237474     500      G/C       C/C
6. chr3      575757    700      A/T       T/T
7. chr3    6666874    746       T/T       T/T

$ awk '{if ($5!=$6) {print $0}}' <sample32.txt
No Chr   Pos              Qual     GT_1   GT_2
1. chr1   478493       595     A/G     G/G
2. chr1    879243     700       A/T      T/T
5. chr3     237474     500      G/C       C/C
6. chr3      575757    700      A/T       T/T

# 3  
Old 05-03-2013
I think the complete answer now...
Code:
$ awk '($5!=$6) {print $0}; ($5=="A/G")&&($6=="G/G") {++cnt1} ; ($5=="A/T")&&($6=="T/T") {++cnt2} ; END { print "Counts="cnt1" & "cnt2 }' <sample32.txt
No Chr   Pos              Qual     GT_1   GT_2
1. chr1   478493       595     A/G     G/G
2. chr1    879243     700       A/T      T/T
5. chr3     237474     500      G/C       C/C
6. chr3      575757    700      A/T       T/T
Counts=1 & 2

 
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