Hi, I have a file with the following content. Now I want to count how many of them have 1 in the field -n2.
Bacteroides fragilis,0
Bacteroides fragilis,0
Salmonella enterica,1
Salmonella enterica,1
Salmonella enterica,1
Bacteroides fragilis,0
.................................
..................................
I used the following command :
cat f1.txt | awk {'$2 == 1'} | wc -l
But it doesn't give me the answer. Please help!
The weird format of your file (if indeed it is in this way) is out of anyone's understanding. But I ll explain how awk could work here provided a nicely formatted tab separated table
Consider your file (say file.txt) this way, the <tab> and <space> symbols are for representation, your actual file will have whitepspace (tabs and spaces) and corresponding positions shown in the file
Bacteroides<space>fragilis<tab>0
Bacteroides<space>fragilis<tab>0
Salmonella<space>enterica<tab>1
Salmonella<space>enterica<tab>1
Salmonella<space>enterica<tab>1
Bacteroides<space>fragilis<tab>0
Now if you say
awk '$2==1{print}' file.txt | wc -l
It may not work, because, by default the field separator which awk consider here is the first white space it encounters which in this case would be the space Bacteroides <space> fragilis
Hence, you must add a field separator -F
awk -F "\t" '$2==1{print}' file.txt | wc -l
set the field separator 'F' to 'comma' and increase a value 'N' each time column 2 is '1'. At the end print the value of N.
awk -F, '($2==1){N++;}END{print N;}' file.txt
but I think most people would use
cut -d, -f 2 file.txt | grep -c -w 1
Hi, Thanks. I have other related problem. My file like this:
10 Lachnoclostridium sp. 0 0 0 0 1
11 Haemophilus ducreyi 0 0 0 0 1
12 Clostridiales bacterium 0 0 0 0 1
13 Escherichia albertii 0 1 0 0 1
It has 8 fields. I want to just count the lines which value =1 in field 7 and field 8. How can I do that? I used the following, but it's not the exact output.
awk '$4 == 0; $5 == 0; $6 == 0; $7 == 1; $8 ==1' file.txt
Though OP wants solution in awk, here is datamash solution:
Species (organism) wide 0's and 1's count:
$ datamash -s -t "," -g 1,2 count 2 < test.txt | sed 's/,/\t/g'
Bacteroides fragilis 0 3
Salmonella enterica 1 3
Only 0's and 1's count:
$ datamash -s -t "," -g 2 count 2 < test.txt | sed 's/,/\t/g'
0 3
1 3
input (from OP):
$ cat test.txt
Bacteroides fragilis,0
Bacteroides fragilis,0
Salmonella enterica,1
Salmonella enterica,1
Salmonella enterica,1
Bacteroides fragilis,0
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I am not able to Understand input file format. You can use following command to count number of 1 in field 2