#file test.txt
a b c 5
d e f g h 7
gg jj 2
Say X = 3 I need the output like this:
#file out.txt
a b c 5
d e f 7
gg jj 2
NOT this:
a b c 5
d e f 7
gg jj 2 2 <--- WRONG
I've gotten to this stage:
cat test.txt | awk ' { print $1" "$2" "$3" "NF } '
If you're unsure of the total number of fields, then one option would be to use a loop:
awk '{ for (i = 1; i <= 3 && i < NF; ++i) printf "%s ", $i; print $NF }' file
The loop can be avoided by using a ternary:
awk '{ print $1, $2, (NF > 3 ? $3 OFS $NF : $3) }' file
This is slightly more verbose than the approach suggested by 123 but means that you aren't left with trailing white space on the lines with three fields. OFS is the Output Field Separator, a space by default, which is what print inserts between fields when you use a ,.
Use a $ combined with NF :
cat test.txt | awk ' { print $1" "$2" "$3" "$NF } '
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)
Suppose I have a file A contains the column numbers need to be removed (I really have over 500 columns in my input file fileB),
fileA:
2
5
And I want to remove those columns(2 and 5) from fileB:
a b c d e f
g h i j k l
in Linux to get:
a c d f
g i j l
what should I do? I found out that I could eliminate printing those columns with the code:
awk '{$2=$5="";print $0}' fileB
however, there are two problems in this way, first it does not really remove those columns, it just using empty string to replace them; second, instead of manually typing in those column numbers, how can I get these column numbers by reading from another file.
Original Question:
Suppose I have a file A contains the column numbers need to be removed,
file A:
223
345
346
567
And I want to remove those columns(223, 345,567) from file B in Linux, what should I do?
If your cut have the --complement option then you can do:
cut --complement -d ' ' -f "$(echo $(<FileA))" fileB
$ cat tst.awk
NR==FNR {
badFldNrs[$1]
next
}
FNR == 1 {
for (inFldNr=1; inFldNr<=NF; inFldNr++) {
if ( !(inFldNr in badFldNrs) ) {
out2in[++numOutFlds] = inFldNr
}
}
}
{
for (outFldNr=1; outFldNr<=numOutFlds; outFldNr++) {
inFldNr = out2in[outFldNr]
printf "%s%s", $inFldNr, (outFldNr<numOutFlds ? OFS : ORS)
}
}
$ awk -f tst.awk fileA fileB
a c d f
g i j l
One awk idea:
awk '
FNR==NR { skip[$1] ; next } # store field #s to be skipped
{ line="" # initialize output variable
pfx="" # first prefix will be ""
for (i=1;i<=NF;i++) # loop through the fields in this input line ...
if ( !(i in skip) ) { # if field # not mentioned in the skip[] array then ...
line=line pfx $i # add to our output variable
pfx=OFS # prefix = OFS for 2nd-nth fields to be added to output variable
}
if ( pfx == OFS ) # if we have something to print ...
print line # print output variable to stdout
}
' fileA fileB
NOTE: OP hasn't provided the input/output field delimiters; OP can add the appropriate FS/OFS assignments as needed
This generates:
a c d f
g i j l
Using awk
$ awk 'NR==FNR {col[$1]=$1;next} {for(i=1;i<=NF;++i) if (i != col[i]) printf("%s ", $i); printf("\n")}' fileA fileB
a c d f
g i j l
I have file with following format :
Qil
Lop
A D E
a 1 10
b 2 21
c 3 22
d 4 5
3 5 9
I need to skip lines that start with pattern 'Qil' or 'Lop' or 'A D E' and ones where the third column has a value greater than 10 and save the entire thing in 2 different files with formats as shown below.
Example output files :
Output file 1
Qil
Lop
A D E
a 1 10
d 4 5
3 5 9
Output file 2
a
d
3
My code :
while read -r line; if [[ $line == "A" ]] ||[[ $line == "Q" ]]||[[ $line == "L" ]] ; then
awk '$2 < "11" { print $0 }' test.txt
awk '$2 < "11" { print $1 }' test1.txt
done < input.file
Could you please try following.
awk '
/^Qil$|^Lop$|^A D E$/{
val=(val?val ORS:"")$0
next
}
$3<=10{
if(!flag){
print val > "file1"
flag=1
}
print > "file1"
if(!a[$1]++){
print $1> "file2"
}
}' Input_file
This will create 2 output files named file1 and file2 as per OP's requirements.
This can be done in a single awk:
awk '$1 !~ /^[QLA]/ && $2 <= 10' file
1 10
4 5
5 9
If you want to print only first column then use:
awk '$1 !~ /^[QLA]/ && $2 <= 10 { print $1 }' file
1
4
5
I have a tab-separated file and want to extract a few columns with cut.
Two example line
(...)
0 0 1 0 AB=1,2,3;CD=4,5,6;EF=7,8,9 0 0
1 1 0 0 AB=2,1,3;CD=1,1,2;EF=5,3,4 0 1
(...)
What I want to achieve is to select columns 2,3,5 and 7, however from column 5 only CD=4,5,6.
So my expected result is
0 1 CD=4,5,6; 0
1 0 CD=1,1,2; 1
How can I use cut for this problem and run grep on one of the extracted columns? Any other one-liner is of course also fine.
here is another awk
$ awk -F'\t|;' -v OFS='\t' '{print $2,$3,$6,$NF}' file
0 1 CD=4,5,6 0
1 0 CD=1,1,2 1
or with cut/paste
$ paste <(cut -f2,3 file) <(cut -d';' -f2 file) <(cut -f7 file)
0 1 CD=4,5,6 0
1 0 CD=1,1,2 1
Easier done with awk. Split the 5th field using ; as the separator, and then print the second subfield.
awk 'BEGIN {FS="\t"; OFS="\t"}
{split($5, a, ";"); print $2, $3, a[2]";", $7 }' inputfile > outputfile
If you want to print whichever subfield begins with CD=, use a loop:
awk 'BEGIN {FS="\t"; OFS="\t"}
{n = split($5, a, ";");
for (i = 1; i <= n; i++) {
if (a[i] ~ /^CD=/) subfield = a[i];
}
print $2, $3, subfield";", $7}' < inputfile > outputfile
I think awk is the best tool for this kind of task and the other two answers give you good short solutions.
I want to point out that you can use awk's built-in splitting facility to gain more flexibility when parsing input. Here is an example script that uses implicit splitting:
parse.awk
# Remember second, third and seventh columns
{
a = $2
b = $3
d = $7
}
# Split the fifth column on ";". After this the positional variables
# (e.g. $1, # $2, ..., $NF) contain the fields from the previous
# fifth column
{
oldFS = FS
FS = ";"
$0 = $5
}
# For example to test if the second elemnt starts with "CD", do
# something like this
$2 ~ /^CD/ {
c = $2
}
# Print the selected elements
{
print a, b, c, d
}
# Restore FS
{
FS = oldFS
}
Run it like this:
awk -f parse.awk FS='\t' OFS='\t' infile
Output:
0 1 CD=4,5,6 0
1 0 CD=1,1,2 1
I have the following awk command within a "for" loop in bash:
awk -v pdb="$pdb" 'BEGIN {file = 1; filename = pdb"_" file ".pdb"}
/ENDMDL/ {getline; file ++; filename = pdb"_" file ".pdb"}
{print $0 > filename}' < ${pdb}.pdb
This reads a series of files with the name $pdb.pdb and splits them in files called $pdb_1.pdb, $pdb_2.pdb, ..., $pdb_21.pdb, etc. However, I would like to produce files with names like $pdb_01.pdb, $pdb_02.pdb, ..., $pdb_21.pdb, i.e., to add padding zeros to the "file" variable.
I have tried without success using printf in different ways. Help would be much appreciated.
Here's how to create leading zeros with awk:
# echo 1 | awk '{ printf("%02d\n", $1) }'
01
# echo 21 | awk '{ printf("%02d\n", $1) }'
21
Replace %02 with the total number of digits you need (including zeros).
Replace file on output with sprintf("%02d", file).
Or even the whole assigment with filename = sprintf("%s_%02d.pdb", pdb, file);.
This does it without resort of printf, which is expensive. The first parameter is the string to pad, the second is the total length after padding.
echo 722 8 | awk '{ for(c = 0; c < $2; c++) s = s"0"; s = s$1; print substr(s, 1 + length(s) - $2); }'
If you know in advance the length of the result string, you can use a simplified version (say 8 is your limit):
echo 722 | awk '{ s = "00000000"$1; print substr(s, 1 + length(s) - 8); }'
The result in both cases is 00000722.
Here is a function that left or right-pads values with zeroes depending on the parameters: zeropad(value, count, direction)
function zeropad(s,c,d) {
if(d!="r")
d="l" # l is the default and fallback value
return sprintf("%" (d=="l"? "0" c:"") "d" (d=="r"?"%0" c-length(s) "d":""), s,"")
}
{ # test main
print zeropad($1,$2,$3)
}
Some tests:
$ cat test
2 3 l
2 4 r
2 5
a 6 r
The test:
$ awk -f program.awk test
002
2000
00002
000000
It's not fully battlefield tested so strange parameters may yield strange results.