CODEWITHSUNDEEP
shellunixawk
Jan Shamsani
Jan Shamsani

Reputation: 321

sum up counts in shell

I would like to sum up integers per line. I have a data file where I extract information.

I use this command to extract 7th information in column 10 that has value more than 0.25 . I would like to get the total number of integers having more than 0.25 value. But I'm getting a list of integers that are more than 0.25

awk -F"\t" 'NR>1{split($10,a,":"); count10[a[7]]++} END {for (i in count10) if (i>0.25) print i, count10[i]}' mygene.vcf

sample output that I'm getting now :

0.689 7
0.648 9
0.607 83
0.279 26

what I require:

125

sample data (10th column)

1/1:27:0,27:0,37:0:0,0.741:1.0:0:98:0,59.0
1/0:26:15,11:35,37:0:0.733,0.727:0.423:0:28:56.9,60.0
1/1:55:0,55:0,38:0:0,0.527:1.0:0:183:0,59.6
1/0:49:26,23:36,36:0:0.615,0.739:0.469:0:47:60.0,58.5

Upvotes: 1

Views: 39

Answers (1)

jas
jas

Reputation: 10865

You basically already have it. Instead of doing a print for each iteration of the for loop, accumulate into a sum and print that:

awk -F"\t" 'NR>1 {split($10,a,":"); 
                  count10[a[7]]++} 
            END  {for (i in count10) 
                    if (i>0.25) 
                      sum += count10[i];
                  print sum }' mygene.vcf

Upvotes: 1

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