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How to count a string in a line and report it?

 
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# 8  
Old 05-24-2013
Hi Yoda,
I have one more question. How should I change the code if I want it to count "0/1" and "1/1"?
Thanks
# 9  
Old 05-24-2013
Assuming you want to count "0/1" & "1/1" separately for each record:
Code:
awk '{i=gsub("0/1","&");j=gsub("1/1","&");print $0,"0/1 count: " i, "1/1 count: ", j}' file

# 10  
Old 05-24-2013
No, actually, I want to count both together and report it in the last column.
# 11  
Old 05-24-2013
Quote:
Originally Posted by a_bahreini
No, actually, I want to count both together and report it in the last column.
Code:
awk '{n=gsub(/0\/1|1\/1/,"&");print $0,n}' file

This User Gave Thanks to Yoda For This Post:
a_bahreini
# 12  
Old 05-24-2013
Sorry again, it turned out that I also have "./." strings in my text which I need to count. However, when I replace it with previous ones, it only counts all the "/" instead of "./."
Could you please help me fix this?
Thanks
# 13  
Old 05-24-2013
Period . is a metacharacter, hence it has to be escaped to preserve its literal meaning:
Code:
awk '{n=gsub(/0\/1|1\/1|\.\/\./,"&");print $0,n}' file

# 14  
Old 05-24-2013
Sorry, but it doesn't count it. Try on the following section:
Code:
AC=21;AF=0.256;AN=82;BaseQRankSum=-2.712;DB;DP=369;Dels=0.00;FS=1.862;HaplotypeScore=0.4505;InbreedingCoeff=0.2067;MLEAC=20;MLEAF=0.244;MQ=49.76;MQ0=0;MQRankSum=-0.555;QD=8.10;ReadPosRankSum=0.944    GT:AD:DP:GQ:PL  0/0:6,0:6:15:0,15,159   0/1:2,5:7:15:107,0,15   0/1:8,11:20:99:154,0,141        0/0:9,0:9:15:0,15,170   0/0:4,1:5:9:0,9,105     0/1:12,6:18:99:99,0,205 0/1:2,3:5:50:50,0,54    0/1:18,3:20:9:9,0,437   0/0:16,0:16:33:0,33,3700/0:12,0:12:24:0,24,260  0/0:6,0:7:12:0,12,118   0/0:11,0:11:27:0,27,280 0/0:8,0:8:21:0,21,227   1/1:0,4:4:12:127,12,0   0/0:5,0:5:9:0,9,98      0/0:9,0:9:21:0,21,222  1/1:0,1:1:3:34,3,0       0/0:5,0:5:15:0,15,165   ./.     0/1:4,3:9:50:50,0,86    0/1:6,5:11:85:85,0,143  0/0:9,0:9:18:0,18,204   0/0:12,0:12:27:0,27,291 1/1:0,5:5:15:151,15,0   1/1:1,5:7:12:123,12,0   0/0:10,0:10:24:0,24,265 0/0:5,0:5:6:0,6,58      1/1:0,7:7:18:181,18,0   0/0:3,0:3:6:0,6,67      0/0:7,0:7:18:0,18,186   0/0:12,0:12:24:0,24,245 0/1:4,1:6:20:20,0,85    ./.     ./.     0/1:5,2:7:28:28,0,37    0/1:4,4:8:52:79,0,52    0/0:13,0:13:30:0,30,318 0/0:3,0:3:6:0,6,67      0/0:5,0:5:12:0,12,128  0/0:8,0:8:18:0,18,191    0/0:2,0:2:6:0,6,64      0/1:10,8:18:99:125,0,182        0/0:11,0:12:21:0,21,250 0/0:11,0:12:27:0,27,281 ./.

 
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