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I am trying to add a prefix to a field in awk if it is not already present. That is if chr isn't present before the number it is inserted. However, if it is there it is skipped.
The first awk adds the prefix to each $2 even if it is present and the senond awk does skip the $2 with chr in them, but does print chr in the $2 without. Thank you :).
file
ASPA,17:3483575-3483585
ATM,11:108289609-108289613
ATP7B,13:51937469-51937480
ATR,chr3:142562768-142562773
BAG3,chr10:119670120-119670123
desired
ASPA,chr17:3483575-3483585
ATM,chr11:108289609-108289613
ATP7B,chr13:51937469-51937480
ATR,chr3:142562768-142562773
BAG3,chr10:119670120-119670123
awk
awk -F, '{$2="chr"$2; print}' file
awk 2
awk -F, '$2 !~/chr/{gsub("chr","chr",$2)}1' file
You can use:
awk 'BEGIN {FS=OFS=","} $2 !~ /^chr/ {$2="chr" $2} 1' file
ASPA,chr17:3483575-3483585
ATM,chr11:108289609-108289613
ATP7B,chr13:51937469-51937480
ATR,chr3:142562768-142562773
BAG3,chr10:119670120-119670123
Or without using any regex:
awk 'BEGIN {FS=OFS=","} index($2 , "chr") != 1 {$2="chr" $2} 1' file
Another solution that might be shortest of all:
awk '{sub(/,(chr)?/, ",chr")} 1' file
1st solution: With your shown samples, please try following awk code.
awk '
BEGIN{FS=OFS=":"}
{
split($1,arr,",")
if(int(arr[2]) || arr[2]==0){
$1=arr[1] ",chr" arr[2]
}
}
1
' Input_file
2nd solution: With GNU awk using its match function which captures values into an array from capturing groups try following code.
awk '
match($0,/^([^,]*,)([^:]*)(:.*)/,arr){
if(int(arr[2]) || arr[2]==0){
arr[2]="chr" arr[2]
}
print arr[1] arr[2] arr[3]
}
' Input_file
3rd solution(Bonus one): Just in case your 2nd field is having Negative values(integers) and you want to change it Eg: from -11 to -chr11 then you can try following GNU awk code.
awk '
match($0,/^([^,]*,)(-)?([^:]*)(:.*)/,arr){
if(int(arr[3]) || arr[3]==0){
if(arr[2]=="-"){
arr[3]="-chr" arr[3]
}
else{
arr[3]="chr" arr[3]
}
$0=arr[1] arr[3] arr[4]
}
print
}
' Input_file
mawk NF=NF FS=',(chr)?' OFS=',chr'
ASPA,chr17:3483575-3483585
ATM,chr11:108289609-108289613
ATP7B,chr13:51937469-51937480
ATR,chr3:142562768-142562773
BAG3,chr10:119670120-119670123
I have a file file like this :
k_1_1
k_1_3
k_1_6
...
I have a file file2 :
0,1,2,3,...
k_1_1,17,16,15,...
k_1_2,17,89,15,...
k_1_3,10,26,45,...
k_1_4,17,16,15,...
k_1_5,10,26,45,...
k_1_6,17,16,15,...
...
I want to print lines of file2 that is matched with fileThe desired output is :
0,1,2,3,...
k_1_1,17,16,15,...
k_1_3,10,26,45,...
k_1_6,17,16,15,...
I tried
awk 'BEGIN{FS=OFS=","}NR==FNR{a[$1];next}$1 in a {print $0}' file file2 > result
But the header line is gone in result like this :
k_1_1,17,16,15,...
k_1_3,10,26,45,...
k_1_6,17,16,15,...
How can a maintain it? Thank you.
Always print the first line, unconditionally.
awk 'BEGIN{FS=OFS=","}
NR==FNR{a[$1];next}
FNR==1 || $1 in a' file file2 > result
Notice also how { print $0 } is not necessary because it's the default action.
A very ad-hoc solution to your problem could be to compose the output in a command group:
{ head -1 file2; awk 'BEGIN{FS=OFS=","}NR==FNR{a[$1];next}$1 in a {print $0}' file file2; } > result
Could you please try following.
awk -F, 'FNR==NR{a[$1]=$0;next} FNR==1 && ++count==1{print;next} a[$1]' Input_file Input_file2
OR
awk -F, 'FNR==NR{a[$1]=$0;next} FNR==1{print;next} a[$1]' Input_file Input_file2
Would like to print unique lines based on first field , keep the first occurrence of that line and remove duplicate other occurrences.
Input.csv
10,15-10-2014,abc
20,12-10-2014,bcd
10,09-10-2014,def
40,06-10-2014,ghi
10,15-10-2014,abc
Desired Output:
10,15-10-2014,abc
20,12-10-2014,bcd
40,06-10-2014,ghi
Have tried below command and in-complete
awk 'BEGIN { FS = OFS = "," } { !seen[$1]++ } END { for ( i in seen) print $0}' Input.csv
Looking for your suggestions ...
You put your test for "seen" in the action part of the script instead of the condition part. Change it to:
awk -F, '!seen[$1]++' Input.csv
Yes, that's the whole script:
$ cat Input.csv
10,15-10-2014,abc
20,12-10-2014,bcd
10,09-10-2014,def
40,06-10-2014,ghi
10,15-10-2014,abc
$
$ awk -F, '!seen[$1]++' Input.csv
10,15-10-2014,abc
20,12-10-2014,bcd
40,06-10-2014,ghi
This should give you what you want:
awk -F, '{ if (!($1 in a)) a[$1] = $0; } END '{ for (i in a) print a[i]}' input.csv
typo there in syntax.
awk '{ if (!($1 in a)) a[$1] = $0; } END { for (i in a) print a[i]}'
I am learning AWK and was trying some exercises on built-in string functions.
Here's my exercise:
I have a file containing as below
RecordType:83
1,2,3,a|x|y|z,4,5
And my desired output is as below:
RecordType:83
1,2,3,a,4,5
1,0,0,x,4,5
1,0,0,y,4,5
1,0,0,z,4,5
I wrote an awk command for the above output.
awk -F',' '$1 ~ /RecordType:83/{print $0}
$1 == 1{
split($4,splt,"|")
for(i in splt)
{
if(i==1)
print $1,$2,$3,splt[i],$5,$6
else
print $1,0,0,splt[i],$5,$6
}
}' OFS=, file_name
The above command looks so clumsy. Is there any way minimizing the command?
Thanks in advance
The shortest possible one-liner I could manage:
awk -F, 'NR>1{n=split($4,a,"|");for(;i++<n;){$4=a[i];print;$2=$3=0}}NR==1' OFS=, file
RecordType:83
1,2,3,a,4,5
1,0,0,x,4,5
1,0,0,y,4,5
1,0,0,z,4,5
The much more readable script (recommended):
BEGIN {
FS=OFS="," # Comma delimiter
}
NR==1 { # If the first line in file
print $0 # Print the whole line
next # Skip to next line
}
{
n=split($4,a,"|") # Split field four on |
for(i=1;i<=n;i++) # For each sub-field
print $1,i==1?$2OFS$3:"0"OFS"0",a[i],$5,$6 # Print the output
}
another shorter one-liner
awk -F, -v OFS="," 'NR>1{n=split($4,a,"|");while(++i<=n){$4=a[i];print;$2=$3=0}}NR==1' file
with your example:
kent$ awk -F, -v OFS="," 'NR>1{n=split($4,a,"|");while(++i<=n){$4=a[i];print;$2=$3=0}}NR==1' file
RecordType:83
1,2,3,a,4,5
1,0,0,x,4,5
1,0,0,y,4,5
1,0,0,z,4,5
A very simple question, which a found no answer to. How do I print out a specific field in awk?
awk '/word1/', will print out the whole sentence, when I need just a word1. Or I need a chain of patterns (word1 + word2) to be printed out only from a text.
Well if the pattern is a single word (which you want to print and can't contaion FS (input field separator)) why not:
awk -v MYPATTERN="INSERT_YOUR_PATTERN" '$0 ~ MYPATTERN { print MYPATTERN }' INPUTFILE
If your pattern is a regex:
awk -v MYPATTERN="INSERT_YOUR_PATTERN" '$0 ~ MYPATTERN { print gensub(".*(" MYPATTERN ").*","\\1","1",$0) }' INPUTFILE
If your pattern must be checked in every single field:
awk -v MYPATTERN="INSERT_YOUR_PATTERN" '$0 ~ MYPATTERN {
for (i=1;i<=NF;i++) {
if ($i ~ MYPATTERN) { print "Field " i " in " NR " row matches: " MYPATTERN }
}
}' INPUTFILE
Modify any of the above to your taste.
The fields in awk are represented by $1, $2, etc:
$ echo this is a string | awk '{ print $2 }'
is
$0 is the whole line, $1 is the first field, $2 is the next field ( or blank ),
$NF is the last field, $( NF - 1 ) is the 2nd to last field, etc.
EDIT (in response to comment).
You could try:
awk '/crazy/{ print substr( $0, match( $0, "crazy" ), RLENGTH )}'
i know you can do this with awk :
an alternative would be :
sed -nr "s/.*(PATTERN_TO_MATCH).*/\1/p" file
or you can use grep -o
Something like this perhaps:
awk '{split("bla1 bla2 bla3",a," "); print a[1], a[2], a[3]}'