I am looking for a way of counting the number of times a value in a field appears in a range of fields in a csv file much the same as countif in excel although I would like to use an awk command if possible.
So column 6 should have the range of values and column 7 would have the times the value appears in column 7, as per below
>awk -F, '{print $0}' file3
f1,f2,f3,f4,f5,test
row1_1,row1_2,row1_3,SBCDE,row1_5,SBCD
row2_1,row2_2,row2_3,AWERF,row2_5,AWER
row3_1,row3_2,row3_3,ASDFG,row3_5,ASDF
row4_1,row4_2,row4_3,PRE-ASDQG,row4_5,ASDQ
row4_1,row4_2,row4_3,PRE-ASDQF,row4_5,ASDQ
>awk -F, '{print $6}' file3
test
SBCD
AWER
ASDF
ASDQ
ASDQ
What i want is:
f1,f2,f3,f4,f5,test,count
row1_1,row1_2,row1_3,SBCDE,row1_5,SBCD,1
row2_1,row2_2,row2_3,AWERF,row2_5,AWER,1
row3_1,row3_2,row3_3,ASDFG,row3_5,ASDF,1
row4_1,row4_2,row4_3,PRE-ASDQG,row4_5,ASDQ,2
row4_1,row4_2,row4_3,PRE-ASDQF,row4_5,ASDQ,2
#adds field name count that I want:
awk -F, -v OFS=, 'NR==1{ print $0, "count"}
NR>1{ print $0}' file3
Ho do I get the output I want?
I have tried this from previous/similar question but no joy,
>awk -F, 'NR>1{c[$6]++;l[NR>1]=$0}END{for(i=0;i++<NR;){split(l[i],s,",");print l[i]","c[s[1]]}}' file3
row4_1,row4_2,row4_3,PRE-ASDQF,row4_5,ASDQ,
,
,
,
,
,
very similar question to this one
similar python related Q, for my ref
I would harness GNU AWK for this task following way, let file.txt content be
f1,f2,f3,f4,f5,test
row1_1,row1_2,row1_3,SBCDE,row1_5,SBCD
row2_1,row2_2,row2_3,AWERF,row2_5,AWER
row3_1,row3_2,row3_3,ASDFG,row3_5,ASDF
row4_1,row4_2,row4_3,PRE-ASDQG,row4_5,ASDQ
row4_1,row4_2,row4_3,PRE-ASDQF,row4_5,ASDQ
then
awk 'BEGIN{FS=OFS=","}NR==1{print $0,"count";next}FNR==NR{arr[$6]+=1;next}FNR>1{print $0,arr[$6]}' file.txt file.txt
gives output
f1,f2,f3,f4,f5,test,count
row1_1,row1_2,row1_3,SBCDE,row1_5,SBCD,1
row2_1,row2_2,row2_3,AWERF,row2_5,AWER,1
row3_1,row3_2,row3_3,ASDFG,row3_5,ASDF,1
row4_1,row4_2,row4_3,PRE-ASDQG,row4_5,ASDQ,2
row4_1,row4_2,row4_3,PRE-ASDQF,row4_5,ASDQ,2
Explanation: this is two-pass approach, hence file.txt appears twice. I inform GNU AWK that , is both field separator (FS) and output field separator (OFS), then for first line (header) I print it followed by count and instruct GNU AWK to go to next line, so nothing other is done regarding 1st line, then for first pass, i.e. where global number of line (NR) is equal to number of line in file (FNR) I count number of occurences of values in 6th field and store them as values in array arr, then instruct GNU AWK to get to next line, so onthing other is done in this pass. During second pass for all lines after 1st (FNR>1) I print whole line ($0) followed by corresponding value from array arr
(tested in GNU Awk 5.0.1)
You did not copy the code from the linked question properly. Why change l[NR] to l[NR>1] at all? On the other hand, you should change s[1] to s[6] since it's the sixth field that has the key you're counting:
awk -F, 'NR>1{c[$6]++;l[NR]=$0}END{for(i=0;i++<NR;){split(l[i],s,",");print l[i]","c[s[6]]}}'
You can also output the header with the new field name:
awk -F, -vOFS=, 'NR==1{print $0,"count"}NR>1{c[$6]++;l[NR]=$0}END{for(i=0;i++<NR;){split(l[i],s,",");print l[i],c[s[6]]}}'
One awk idea:
awk '
BEGIN { FS=OFS="," } # define input/output field delimiters as comma
{ lines[NR]=$0
if (NR==1) next
col6[NR]=$6 # copy field 6 so we do not have to parse the contents of lines[] in the END block
cnt[$6]++
}
END { for (i=1;i<=NR;i++)
print lines[i], (i==1 ? "count" : cnt[col6[i]] )
}
' file3
This generates:
f1,f2,f3,f4,f5,test,count
row1_1,row1_2,row1_3,SBCDE,row1_5,SBCD,1
row2_1,row2_2,row2_3,AWERF,row2_5,AWER,1
row3_1,row3_2,row3_3,ASDFG,row3_5,ASDF,1
row4_1,row4_2,row4_3,PRE-ASDQG,row4_5,ASDQ,2
row4_1,row4_2,row4_3,PRE-ASDQF,row4_5,ASDQ,2
I have a tab delimited text file:
#CHROM
POS
ID
REF
ALT
1
188277
rs434
C
T
20
54183975
rs5321
CTAAA
C
and I try to replace the "ID" column with specific patern $CHROM_$POS_$REF_$ALT with sed or awk
#CHROM
POS
ID
REF
ALT
1
188277
1_188277_C_T
C
T
20
54183975
20_54183975_CTAAA_C
CTAAA
C
unfortunately, I managed only to delete this ID column with:
sed -i -r 's/\S+//3'
and all patterns I try do not work in all cases. To be honest I am lost in the documentation and I am looking for examples which could help me solve this problem.
Using awk, you can set the value of the 3rd field concatenating field 1,2,4 and 5 with an underscore except for the first line. Using column -t to present the output as a table:
awk '
BEGIN{FS=OFS="\t"}
NR>1 {
$3 = $1"_"$2"_"$4"_"$5
}1' file | column -t
Output
#CHROM POS ID REF ALT
1 188277 1_188277_C_T C T
20 54183975 20_54183975_CTAAA_C CTAAA C
Or writing all fields, with a custom value for the 3rd field:
awk '
BEGIN{FS=OFS="\t"}
NR==1{print;next}
{print $1, $2, $1"_"$2"_"$4"_"$5, $4, $5}
' file | column -t
GNU sed solution
sed '2,$s/\(\S*\)\t\(\S*\)\t\(\S*\)\t\(\S*\)\t\(\S*\)/\1\t\2\t\1_\2_\3_\4_\5\t\4\t\5/' file.txt
Explanation: from line 2 to last line, do following replace: put 5 \t-sheared columns (holding zero or more non-whitespace) into groups. Then replace it with these column joined using \t excluding third one, which is replace by _-join of 1st, 2nd, 3rd, 4th, 5th column.
(tested in sed (GNU sed) 4.2.2)
awk -v OFS='\t' 'NR==1 {print $0}; NR>1 {print $1, $2, $1"_"$2"_"$4"_"$5, $4, $5}' inputfile.txt
I need 7th column of a csv file to be converted from float to decimal. It's a huge file and I don't want to use while read for conversion. Any shortcuts with awk?
Input:
"xx","x","xxxxxx","xxx","xx","xx"," 00000001.0000"
"xx","x","xxxxxx","xxx","xx","xx"," 00000002.0000"
"xx","x","xxxxxx","xxx","xx","xx"," 00000005.0000"
"xx","x","xxxxxx","xxx","xx","xx"," 00000011.0000"
Output:
"xx","x","xxxxxx","xxx","xx","xx","1"
"xx","x","xxxxxx","xxx","xx","xx","2"
"xx","x","xxxxxx","xxx","xx","xx","5"
"xx","x","xxxxxx","xxx","xx","xx","11"
Tried these, worked. But anything simpler ?
awk 'BEGIN {FS=OFS="\",\""} {$7 = sprintf("%.0f", $7)} 1' $test > $test1
awk '{printf("%s\"\n", $0)}' $test1
With your shown samples, please try following awk program.
awk -v s1="\"" -v OFS="," '{$NF = s1 ($NF + 0) s1} 1' Input_file
Explanation: Simple explanation would be, setting OFS as , then in main program; in each line's last field keeping only digits and covering last field with ", re-shuffle the fields and printing edited/non-edited all lines.
Another simple awk solution:
awk 'BEGIN {FS=OFS="\",\""} {$NF = $NF+0 "\""} 1' file
"xx","x","xxxxxx","xxx","xx","xx","1"
"xx","x","xxxxxx","xxx","xx","xx","2"
"xx","x","xxxxxx","xxx","xx","xx","5"
"xx","x","xxxxxx","xxx","xx","xx","11"
awk 'BEGIN{FS=OFS=","} {gsub(/"/, "", $7); $7="\"" $7+0 "\""; print}' file
Output:
"xx","x","xxxxxx","xxx","xx","xx","1"
"xx","x","xxxxxx","xxx","xx","xx","2"
"xx","x","xxxxxx","xxx","xx","xx","5"
"xx","x","xxxxxx","xxx","xx","xx","11"
gsub(/"/, "", $7): removes all " from $7
$7+0: Reduces the number in $7 to minimal representation