Related
I am trying to use awk to extract data using a conditional statement containing an array created using another awk script.
The awk script I use for creating the array is as follows:
array=($(awk 'NR>1 { print $1 }' < file.tsv))
Then, to use this array in the other awk script
awk var="${array[#]}" 'FNR==1{ for(i=1;i<=NF;i++){ heading[i]=$i } next } { for(i=2;i<=NF;i++){ if($i=="1" && heading[i] in var){ close(outFile); outFile=heading[i]".txt"; print ">kmer"NR-1"\n"$1 >> (outFile) }}}' < input.txt
However, when I run this, the following error occurs.
awk: fatal: cannot open file 'foo' for reading (No such file or directory)
I've already looked at multiple posts on why this error occurs and on how to correctly implement a shell variable in awk, but none of these have worked so far. However, when removing the shell variable and running the script it does work.
awk 'FNR==1{ for(i=1;i<=NF;i++){ heading[i]=$i } next } { for(i=2;i<=NF;i++){ if($i=="1"){ close(outFile); outFile=heading[i]".txt"; print ">kmer"NR-1"\n"$1 >> (outFile) }}}' < input.txt
I really need that conditional statement but don't know what I am doing wrong with implementing the bash variable in awk and would appreciate some help.
Thx in advance.
That specific error messages is because you forgot -v in front of var= (it should be awk -v var=, not just awk var=) but as others have pointed out, you can't set an array variable on the awk command line. Also note that array in your code is a shell array, not an awk array, and shell and awk are 2 completely different tools each with their own syntax, semantics, scopes, etc.
Here's how to really do what you're trying to do:
array=( "$(awk 'BEGIN{FS=OFS="\t"} NR>1 { print $1 }' < file.tsv)" )
awk -v xyz="${array[*]}" '
BEGIN{ split(xyz,tmp,RS); for (i in tmp) var[tmp[i]] }
... now use `var` as you were trying to ...
'
For example:
$ cat file.tsv
col1 col2
a b c d e
f g h i j
$ cat -T file.tsv
col1^Icol2
a b^Ic d e
f g h^Ii j
$ awk 'BEGIN{FS=OFS="\t"} NR>1 { print $1 }' < file.tsv
a b
f g h
$ array=( "$(awk 'BEGIN{FS=OFS="\t"} NR>1 { print $1 }' < file.tsv)" )
$ awk -v xyz="${array[*]}" '
BEGIN {
split(xyz,tmp,RS)
for (i in tmp) {
var[tmp[i]]
}
for (idx in var) {
print "<" idx ">"
}
}
'
<f g h>
<a b>
It's easier and more efficient to process both files in a single awk:
edit: fixed issues in comment, thanks #EdMorton
awk '
FNR == NR {
if ( FNR > 1 )
var[$1]
next
}
FNR == 1 {
for (i = 1; i <= NF; i++)
heading[i] = $i
next
}
{
for (i = 2; i <= NF; i++)
if ( $i == "1" && heading[i] in var) {
outFile = heading[i] ".txt"
print ">kmer" (NR-1) "\n" $1 >> (outFile)
close(outFile)
}
}
' file.tsv input.txt
You might store string in variable, then use split function to turn that into array, consider following simple example, let file1.txt content be
A B C
D E F
G H I
and file2.txt content be
1
3
2
then
var1=$(awk '{print $1}' file1.txt)
awk -v var1="$var1" 'BEGIN{split(var1,arr)}{print "First column value in line number",$1,"is",arr[$1]}' file2.txt
gives output
First column value in line number 1 is A
First column value in line number 3 is G
First column value in line number 2 is D
Explanation: I store output of 1st awk command, which is then used as 1st argument to split function in 2nd awk command. Disclaimer: this solutions assumes all files involved have delimiter compliant with default GNU AWK behavior, i.e. one-or-more whitespaces is always delimiter.
(tested in gawk 4.2.1)
I want to use awk to match all the occurrences of a pattern within a large file. For each match, I would like to print the row number and the starting position of the pattern along the row (sort of xy coordinates). There are several occurrences of the pattern in each line.
I found this somewhat related question.
So far, I managed to do it only for the first (leftmost) occurrence in each line. As an example:
echo xyzABCdefghiABCdefghiABCdef | awk 'match($0, /ABC/) {print NR, RSTART } '
The resulting output is :
1 4
But what I would expect is something like this:
1 4
1 13
1 22
I tried using split instead of match. I manage to identify all the occurrences, but the RSTART is lost and printed as "0".
echo xyzABCdefghiABCdefghiABCdef | awk ' { split($0,t, /ABC/,m) ; for (i=1; i in m; i++) print (NR, RSTART) } '
Output:
1 0
1 0
1 0
Any advice would be appreciated. I am not limited to using awk but a awk solution would be appreciated.
Also, in my case the pattern to match would be a regex (/A.C/).
Thank you
This may be what you're trying to do:
echo xyzABCdefghiABCdefghiABCdef |
awk '{ begpos=1
while (match(substr($0, begpos), /ABC/)) {
print NR, begpos + RSTART - 1
begpos += RLENGTH + RSTART - 1
}
}'
Another option using gnu awk could be using split with a regex.
Using the split function, the 3rd field is the fieldsep array and the 4th field is the seps array which you can both use to calculate the positions.
echo xyzABCdefghiABCdefghiABCdef |
awk ' {
n=split($0, a, /ABC/, seps); pos=1
for(i=1; i<n; i++){
pos += length(a[i])
print NR, pos
pos += length(seps[i])
}
}'
Output
1 4
1 13
1 22
With your shown samples, please try following awk code.
awk '
{
prev=0
while(match($0,/ABC/)){
$0=substr($0,RSTART+RLENGTH)
print FNR,prev+RSTART
prev+=RSTART+2
}
}
' Input_file
Explanation: Adding detailed explanation for above.
awk ' ##Starting awk program from here.
{
prev=0 ##Setting prev variable to 0 here.
while(match($0,/ABC/)){ ##Using while loop to match ABC string and it runs till ABC match is ture in current line.
$0=substr($0,RSTART+RLENGTH) ##Re-creating current line by assigning value of rest of line(which starts after match of ABC).
print FNR,prev+RSTART ##Printing line number along with prev+RSTART value here.
prev+=RSTART+2 ##Setting prev to prev+RSTART+2 here.
}
}
' Input_file ##Mentioning Input_file name here.
Determination of the coordinates of a string with awk:
echo "xyzABCdefghiABCdefghiABCdef" \
| awk -v s="ABC" 'BEGIN{ len=length(s) }
{
for(i=1; i<=length($0); i++){
if(substr($0, i, len)==s){
print NR, i
}
}
}'
Output:
1 4
1 13
1 22
As one line:
echo xyzABCdefghiABCdefghiABCdef | awk -v s="ABC" 'BEGIN{ len=length(s) } { for(i=1; i<=length($0); i++){ if(substr($0,i,len)==s) { print NR,i } } }'
Source: Find position of character with awk
One awk idea using split() and some slicing-n-dicing of length() results:
ptn='ABC'
echo xyzABCdefghiABCdefghiABCdef |
awk -v ptn="${ptn}" '
{ pos=-(length(ptn)-1)
n=split($0,arr,ptn)
for (i=1;i<n;i++) {
pos+=length(arr[i] ptn)
print NR,pos
}
}'
This generates:
1 4
1 13
1 22
I am trying to edit text in Bash, i got to point where i am no longer able to continue and i need help.
The text i need to edit:
Symbol Name Sector Market Cap, $K Last Links
AAPL
Apple Inc
Computers and Technology
2,006,722,560
118.03
AMGN
Amgen Inc
Medical
132,594,808
227.76
AXP
American Express Company
Finance
91,986,280
114.24
BA
Boeing Company
Aerospace
114,768,960
203.30
The text i need:
Symbol,Name,Sector,Market Cap $K,Last,Links
AAPL,Apple Inc,Computers and Technology,2,006,722,560,118.03
AMGN,Amgen Inc,Medical,132,594,808,227.76
AXP,American Express Company,Finance,91,986,280,114.24
BA,Boeing Company,Aerospace,114,768,960,203.30
I already tried :
sed 's/$/,/' BIPSukol.txt > BIPSukol1.txt | awk 'NR==1{print}' BIPSukol1.txt | awk '(NR-1)%5{printf "%s ", $0;next;}1' BIPSukol1.txt | sed 's/.$//'
But it doesnt quite do the job.
(BIPSukol1.txt is the name of the file i am editing)
The biggest problem you have is you do not have consistent delimiters between your fields. Some have commas, some don't and some are just a combination of 3-fields that happen to run together.
The tool you want is awk. It will allow you to treat the first line differently and then condition the output that follows with convenient counters you keep within the script. In awk you write rules (what comes between the outer {...} and then awk applies your rules in the order they are written. This allows you to "fix-up" your hap-hazard format and arrive at the desired output.
The first rule applied FNR==1 is applied to the 1st line. It loops over the fields and finds the problematic "Market Cap $K" field and considers it as one, skipping beyond it to output the remaining headings. It stores a counter count = NF - 3 as you only have 5 lines of data for each Symbol, and skips to the next record.
When count==n the next rule is triggered which just outputs the records stored in the a[] array, zeros count and deletes the a[] array for refilling.
The next rule is applied to every record (line) of input from the 2nd-on. It simply removes any whitespece from the fields by forcing awk to recalculate the fields with $1 = $1 and then stores the record in the array incrementing count.
The last rule, END is a special rule that runs after all records are processed (it lets you sum final tallies or output final lines of data) Here it is used to output the records that remain in a[] when the end of the file is reached.
Putting it altogether in another cut at awk:
awk '
FNR==1 {
for (i=1;i<=NF;i++)
if ($i == "Market") {
printf ",Market Cap $K"
i = i + 2
}
else
printf (i>1?",%s":"%s"), $i
print ""
n = NF-3
count = 0
next
}
count==n {
for (i=1;i<=n;i++)
printf (i>1?",%s":"%s"), a[i]
print ""
delete a
count = 0
}
{
$1 = $1
a[++count] = $0
}
END {
for (i=1;i<=count;i++)
printf (i>1?",%s":"%s"), a[i]
print ""
}
' file
Example Use/Output
Note: you can simply select-copy the script above and then middle-mouse-paste it into an xterm with the directory set so it contains file (you will need to rename file to whatever your input filename is)
$ awk '
> FNR==1 {
> for (i=1;i<=NF;i++)
> if ($i == "Market") {
> printf ",Market Cap $K"
> i = i + 2
> }
> else
> printf (i>1?",%s":"%s"), $i
> print ""
> n = NF-3
> count = 0
> next
> }
> count==n {
> for (i=1;i<=n;i++)
> printf (i>1?",%s":"%s"), a[i]
> print ""
> delete a
> count = 0
> }
> {
> $1 = $1
> a[++count] = $0
> }
> END {
> for (i=1;i<=count;i++)
> printf (i>1?",%s":"%s"), a[i]
> print ""
> }
> ' file
Symbol,Name,Sector,Market Cap $K,Last,Links
AAPL,Apple Inc,Computers and Technology,2,006,722,560,118.03
AMGN,Amgen Inc,Medical,132,594,808,227.76
AXP,American Express Company,Finance,91,986,280,114.24
BA,Boeing Company,Aerospace,114,768,960,203.30
(note: it is unclear why you want the "Links" heading included since there is no information for that field -- but that is how your desired output is specified)
More Efficient No Array
You always have afterthoughts that creep in after you post an answer, no different than remembering a better way to answer a question as you are walking out of an exam, or thinking about the one additional question you wished you would have asked after you excuse a witness or rest your case at trial. (there was some song that captured it -- a little bit ironic :)
The following does essentially the same thing, but without using arrays. Instead it simply outputs the information after formatting it rather than buffer it in an array for output all at once. It was one of those type afterthoughts:
awk '
FNR==1 {
for (i=1;i<=NF;i++)
if ($i == "Market") {
printf ",Market Cap $K"
i = i + 2
}
else
printf (i>1?",%s":"%s"), $i
print ""
n = NF-3
count = 0
next
}
count==n {
print ""
count = 0
}
{
$1 = $1
printf (++count>1?",%s":"%s"), $0
}
END { print "" }
' file
(same output)
With your shown samples, could you please try following(written and tested in GNU awk). Considering that(by seeing OP's attempts) after header of Input_file you want to make every 5 lines into a single line.
awk '
BEGIN{
OFS=","
}
FNR==1{
NF--
match($0,/Market.*\$K/)
matchedPart=substr($0,RSTART,RLENGTH)
firstPart=substr($0,1,RSTART-1)
lastPart=substr($0,RSTART+RLENGTH)
gsub(/,/,"",matchedPart)
gsub(/ +/,",",firstPart)
gsub(/ +/,",",lastPart)
print firstPart matchedPart lastPart
next
}
{
sub(/^ +/,"")
}
++count==5{
print val,$0
count=0
val=""
next
}
{
val=(val?val OFS:"")$0
}
' Input_file
OR if your awk doesn't support NF-- then try following.
awk '
BEGIN{
OFS=","
}
FNR==1{
match($0,/Market.*\$K/)
matchedPart=substr($0,RSTART,RLENGTH)
firstPart=substr($0,1,RSTART-1)
lastPart=substr($0,RSTART+RLENGTH)
gsub(/,/,"",matchedPart)
gsub(/ +/,",",firstPart)
gsub(/ +Links( +)?$/,"",lastPart)
gsub(/ +/,",",lastPart)
print firstPart matchedPart lastPart
next
}
{
sub(/^ +/,"")
}
++count==5{
print val,$0
count=0
val=""
next
}
{
val=(val?val OFS:"")$0
}
' Input_file
NOTE: Looks like your header/first line needed special manipulation because we can't simply set , for all spaces, so taken care of it in this solution as per shown samples.
With GNU awk. If your first line is always the same.
echo 'Symbol,Name,Sector,Market Cap $K,Last,Links'
awk 'NR>1 && NF=5' RS='\n ' ORS='\n' FS='\n' OFS=',' file
Output:
Symbol,Name,Sector,Market Cap $K,Last,Links
AAPL,Apple Inc,Computers and Technology,2,006,722,560,118.03
AMGN,Amgen Inc,Medical,132,594,808,227.76
AXP,American Express Company,Finance,91,986,280,114.24
BA,Boeing Company,Aerospace,114,768,960,203.30
See: 8 Powerful Awk Built-in Variables – FS, OFS, RS, ORS, NR, NF, FILENAME, FNR
I have a text file produced by some commercial software, looking like below. It consists in brackets delimited sections, each of which counts several million elements but the exact value changes from one case to another.
(1
2
3
...
)
(11
22
33
...
)
(111
222
333
...
)
I need to achieve an output like:
1; 11; 111
2; 22; 222
3; 33; 333
... ... ...
I found a complicated way that is:
perform sed operations to get
1
2
3
...
#
11
22
33
...
#
111
222
333
...
use awk as follows to split my file in several sub-files
awk -v RS="#" '{print > ("splitted-" NR ".txt")}'
remove white spaces from my subfiles again with sed
sed -i '/^[[:space:]]*$/d' splitted*.txt
join everything together:
paste splitted*.txt > out.txt
add a field separator (defined in my bash script)
awk -v sep=$my_sep 'BEGIN{OFS=sep}{$1=$1; print }' out.txt > formatted.txt
I feel this is crappy as I loop over million lines several time.
Even if the return time is quite OK (~80sec), I'd like to find a full awk solution but can't get to it.
Something like:
awk 'BEGIN{RS="(\\n)"; OFS=";"} { print something } '
I found some related questions, especially this one row to column conversion with awk, but it assumes a constant number of lines between brackets which I can't do.
Any help would be appreciated.
With GNU awk for multi-char RS and true multi dimensional arrays:
$ cat tst.awk
BEGIN {
RS = "(\\s*[()]\\s*)+"
OFS = ";"
}
NR>1 {
cell[NR][1]
split($0,cell[NR])
}
END {
for (rowNr=1; rowNr<=NF; rowNr++) {
for (colNr=2; colNr<=NR; colNr++) {
printf "%6s%s", cell[colNr][rowNr], (colNr<NR ? OFS : ORS)
}
}
}
$ awk -f tst.awk file
1; 11; 111
2; 22; 222
3; 33; 333
...; ...; ...
If you know you have 3 columns, you can do it in a very ugly way as following:
pr -3ts <file>
All that needs to be done then is to remove your brackets:
$ pr -3ts ~/tmp/f | awk 'BEGIN{OFS="; "}{gsub(/[()]/,"")}(NF){$1=$1; print}'
1; 11; 111
2; 22; 222
3; 33; 333
...; ...; ...
You can also do it in a single awk line, but it just complicates things. The above is quick and easy.
This awk program does the full generic version:
awk 'BEGIN{r=c=0}
/)/{r=0; c++; next}
{gsub(/[( ]/,"")}
(NF){a[r++,c]=$1; rm=rm>r?rm:r}
END{ for(i=0;i<rm;++i) {
printf a[i,0];
for(j=1;j<c;++j) printf "; " a[i,j];
print ""
}
}' <file>
Could you please try following once, considering that your actual Input_file is same as shown samples.
awk -v RS="" '
{
gsub(/\n|, /,",")
}
1' Input_file |
awk '
{
while(match($0,/\([^\)]*/)){
value=substr($0,RSTART+1,RLENGTH-2)
$0=substr($0,RSTART+RLENGTH)
num=split(value,array,",")
for(i=1;i<=num;i++){
val[i]=val[i]?val[i] OFS array[i]:array[i]
}
}
for(j=1;j<=num;j++){
print val[j]
}
delete val
delete array
value=""
}' OFS="; "
OR(above script is considering that numbers inside (...) will be constant, now adding script which will working even field numbers of not equal inside (....).
awk -v RS="" '
{
gsub(/\n/,",")
gsub(/, /,",")
}
1' Input_file |
awk '
{
while(match($0,/\([^\)]*/)){
value=substr($0,RSTART+1,RLENGTH-2)
$0=substr($0,RSTART+RLENGTH)
num=split(value,array,",")
for(i=1;i<=num;i++){
val[i]=val[i]?val[i] OFS array[i]:array[i]
max=num>max?num:max
}
}
for(j=1;j<=max;j++){
print val[j]
}
delete val
delete array
}' OFS="; "
Output will be as follows.
1; 11; 111
2; 22; 222
3; 33; 333
Explanation: Adding explanation for above code here.
awk -v RS="" ' ##Setting RS(record separator) as NULL here.
{ ##Starting BLOCK here.
gsub(/\n/,",") ##using gsub to substitute new line OR comma with space with comma here.
gsub(/, /,",")
}
1' Input_file | ##Mentioning 1 will be printing edited/non-edited line of Input_file. Using | means sending this output as Input to next awk program.
awk ' ##Starting another awk program here.
{
while(match($0,/\([^\)]*/)){ ##Using while loop which will run till a match is FOUND for (...) in lines.
value=substr($0,RSTART+1,RLENGTH-2) ##storing substring from RSTART+1 to till RLENGTH-1 value to variable value here.
$0=substr($0,RSTART+RLENGTH) ##Re-creating current line with substring valeu from RSTART+RLENGTH till last of line.
num=split(value,array,",") ##Splitting value variable into array named array whose delimiter is comma here.
for(i=1;i<=num;i++){ ##Using for loop which runs from i=1 to till value of num(length of array).
val[i]=val[i]?val[i] OFS array[i]:array[i] ##Creating array val whose index is value of variable i and concatinating its own values.
}
}
for(j=1;j<=num;j++){ ##Starting a for loop from j=1 to till value of num here.
print val[j] ##Printing value of val whose index is j here.
}
delete val ##Deleting val here.
delete array ##Deleting array here.
value="" ##Nullifying variable value here.
}' OFS="; " ##Making OFS value as ; with space here.
NOTE: This should work for more than 3 values inside (...) brackets also.
awk 'BEGIN { RS = "\\s*[()]\\s*"; FS = "\\s*" }
NF > 0 {
maxCol++
if (NF > maxRow)
maxRow = NF
for (row = 1; row <= NF; row++)
a[row,maxCol] = $row
}
END {
for (row = 1; row <= maxRow; row++) {
for (col = 1; col <= maxCol; col++)
printf "%s", a[row,col] ";"
print ""
}
}' yourFile
output
1;11;111;
2;22;222;
3;33;333;
...;...;...;
Change FS= "\\s*" to FS = "\n*" when you also want to allow spaces inside your fields.
This script supports columns of different lengths.
When benchmarking also consider replacing [i,j] with [i][j] for GNU awk. I'm unsure which one is faster and did not benchmark the script myself.
Here is the Perl one-liner solution
$ cat edouard2.txt
(1
2
3
a
)
(11
22
33
b
)
(111
222
333
c
)
$ perl -lne ' $x=0 if s/[)(]// ; if(/(\S+)/) { #t=#{$val[$x]};push(#t,$1);$val[$x++]=[#t] } END { print join(";",#{$val[$_]}) for(0..$#val) }' edouard2.txt
1;11;111
2;22;222
3;33;333
a;b;c
I would convert each section to a row and then transpose after, e.g. assuming you are using GNU awk:
<infile awk '{ gsub("[( )]", ""); $1=$1 } 1' RS='\\)\n\\(' OFS=';' |
datamash -t';' transpose
Output:
1;11;111
2;22;222
3;33;333
...;...;...
I have a dataset of the following structure:
1234 4334 8677 3753 3453 4554
4564 4834 3244 3656 2644 0474
...
I would like to:
1) search for a specific value, eg 4834
2) return the following field (3244)
I'm quite new to awk, but realize it is a simple operation. I have created a bash-script that asks the user for the input, and attempts to return the following field.
But I can't seem to get around scoping in AWK. How do I parse the input value to awk?
#!/bin/bash
read input
cat data.txt | awk '
for (i=1;i<=NF;i++) {
if ($i==input) {
print $(i+1)
}
}
}'
Cheers and thanks in advance!
UPDATE Sept. 8th 2011
Thanks for all the replies.
1) It will never happen that the last number of a row is picked - still I appreciate you pointing this out.
2) I have a more general problem with awk. Often I want to "do something" with the result found. In this case I would like to output it to xclip - an application which read from standard input and copies it to the clipboard. Eg:
$ echo Hi | xclip
Unfortunately, echo doesn't exist for awk, so I need to return the value and echo it. How would you go about this?
#!/bin/bash
read input
cat data.txt | awk '{
for (i=1;i<=NF;i++) {
if ($i=='$input') {
print $(i+1)
}
}
}'
Don't over think it!
You can create an array in awk with the split command:
split($0, ary)
This will split the line $0 into an array called ary. Now, you can use array syntax to find the particular fields:
awk '{
size = split($0, ary)
for (i=1; i < size ;i++) {
print ary[i]
}
print "---"
}' data.txt
Now, when you find ary[x] as the field, you can print out ary[x+1].
In your example:
awk -v input=$input '{
size = split($0, ary)
for (i=1; i<= size ;i++) {
if ($i == ary[i]) {
print ary[i+1]
}
}
}' data.txt
There is a way of doing this without creating an array, but it's simply much easier to work with arrays in situations like this.
By the way, you can eliminate the cat command by putting the file name after the awk statement and save creating an extraneous process. Everyone knows creating an extraneous process kills a kitten. Please don't kill a kitten.
You pass shell variable to awk using -v option. Its cleaner/nicer than having to put quotes.
awk -v input="$input" '
for(i=1;i<=NF;i++){
if ($i == input ){
print "Next value: " $(i+1)
}
}
' data.txt
And lose the useless cat.
Here is my solution: delete everything up to (and including) the search field, then the field you want to print out is field #1 ($1):
awk '/4834/ {sub(/^.* * 4834 /, ""); print $1}' data.txt