I wish you you all a very happy New Year.
I have a file that looks like this(example): There is no header and this file has about 10000 such rows
123 345 676 58 1
464 222 0 0 1
555 22 888 555 1
777 333 676 0 1
555 444 0 58 1
PROBLEM: I only want those rows where both field 3 and 4 have a non zero value i.e. in the above example row 1 & row 3 should be included and rest should be excluded. How can I do this?
The output should look like this:
123 345 676 58 1
555 22 888 555 1
Thanks.
awk is perfect for this kind of stuff:
awk '$3 && $4' input.txt
This will give you the output that you want.
$3 && $4 is a filter. $3 is the value of the 3rd field, $4 is the value of the forth. 0 values will be evaluated as false, anything else will be evaluated as true. If there can be negative values, than you need to write more precisely:
awk '$3 > 0 && $4 > 0' input.txt
Related
I have two files that I need to merge together based on what string they contain in a specific column.
File 1 looks like this:
1 1655 1552 189
1 1433 1552 185
1 1623 1553 175
1 691 1554 182
1 1770 1554 184
1 1923 1554 182
1 1336 1554 181
1 660 1592 179
1 743 1597 179
File 2 looks like this:
1 1552 0 0 2 -9 G A A A
1 1553 0 0 2 -9 A A G A
1 1554 0 751 2 -9 A A A A
1 1592 0 577 1 -9 G A A A
1 1597 0 749 2 -9 A A G A
1 1598 0 420 1 -9 A A A A
1 1600 0 0 1 -9 A A G G
1 1604 0 1583 1 -9 A A A A
1 1605 0 1080 2 -9 G A A A
I am wanting to match column 3 from file 1 to column 2 on file 2, with my output looking like:
1 1655 1552 189 0 0 2 -9 G A A A
1 1433 1552 185 0 0 2 -9 G A A A
1 1623 1553 175 0 0 2 -9 A A G A
1 691 1554 182 0 751 2 -9 A A A A
1 1770 1554 184 0 751 2 -9 A A A A
1 1923 1554 182 0 751 2 -9 A A A A
1 1336 1554 181 0 751 2 -9 A A A A
1 660 1592 179 0 577 1 -9 G A A A
1 743 1597 179 0 749 2 -9 A A G A
I am not interested in keeping any lines in file 2 that are not in file 1. Thanks in advance!
Thanks to #Abelisto I managed to figure something out 4 hours later!
sort -k 3,3 File1.txt > Pheno1.txt
awk '($2 >0)' File2.ped > Ped1.ped
sort -k 2,2 Ped1.ped > Ped2.ped
join -1 3 -2 2 Pheno1.txt Ped2.ped > Ped3.txt
cut -d ' ' -f 1,4,5 --complement Ped3.txt > Output.ped
My real File2 actually contained negative values in the 2nd column (thankfully my real File1 didn't have any negatives) hence the use of awk to remove those rows
Using awk:
awk 'NR == FNR { arr[$2]=$3" "$4" "$5" "$6" "$7" "$8" "$9" "$10 } NR != FNR { print $1" "$2" "$3" "$4" "arr[$3] }' file2 file1
Process file2 first (NR==FNR) Set up an array called arr with the 3rd space delimited field as the index and the 3rd to 10th fields as values separated with a space. Then when processing the first file (NR!=FNR) print the 1st to the 4th space delimited fields followed by the contents of arr, index field 3.
Since $1 seems like constant 1 and I have no idea about rowcounts of either file (800,000 columns in file2 sounded a lot) I'm hashing file1 instead:
$ awk '
NR==FNR {
a[$3]=a[$3] (a[$3]==""?"":ORS) $2 OFS $3 OFS $4
next
}
($2 in a) {
n=split(a[$2],t,ORS)
for(i=1;i<=n;i++) {
$2=t[i]
print
}
}' file1 file2
Output:
1 1655 1552 189 0 0 2 -9 G A A A
1 1433 1552 185 0 0 2 -9 G A A A
1 1623 1553 175 0 0 2 -9 A A G A
1 691 1554 182 0 751 2 -9 A A A A
1 1770 1554 184 0 751 2 -9 A A A A
1 1923 1554 182 0 751 2 -9 A A A A
1 1336 1554 181 0 751 2 -9 A A A A
1 660 1592 179 0 577 1 -9 G A A A
1 743 1597 179 0 749 2 -9 A A G A
When posting a question, please add details such as row and column counts to it. Better requirements yield better answers.
I'm trying to create a table based on the ASCII bellow. What I need is to arrange the numbers from the 2nd column in a matrix. The first and third columns of the ASCII give columns and rows in the new matrix. The new matrix needs to be fully populated, so it is necessary to complete missing positions on the new table with NA (or -999).
This is what I have
$ cat infile.txt
1 68 2
1 182 3
1 797 4
2 4 1
2 70 2
2 339 3
2 1396 4
3 12 1
3 355 3
3 1854 4
4 7 1
4 85 2
4 333 3
5 9 1
5 68 2
5 182 3
5 922 4
6 10 1
6 70 2
and what I would like to have:
NA 4 12 7 9 10
68 70 NA 85 68 70
182 339 355 333 182 NA
797 1396 1854 NA 922 NA
I can only use standard UNIX commands (e.g. awk, sed, grep, etc).
So What I have so far...
I can mimic a 2d array in bash
irows=(`awk '{print $1 }' infile.txt`) # rows positions
jcols=(`awk '{print $3 }' infile.txt`) # columns positions
values=(`awk '{print $2 }' infile.txt`) # values
declare -A matrix # the new matrix
nrows=(`sort -k3 -n in.txt | tail -1 | awk '{print $3}'`) # numbers of rows
ncols=(`sort -k1 -n in.txt | tail -1 | awk '{print $1}'`) # numbers of columns
nelem=(`echo "${#values[#]}"`) # number of elements I want to pass to the new matrix
# Creating a matrix (i,j) with -999
for ((i=0;i<=$((nrows-1));i++)) do
for ((j=0;j<=$((ncols-1));j++)) do
matrix[$i,$j]=-999
done
done
and even print on the screen
for ((i=0;i<=$((nrows-1));i++)) do
for ((j=0;j<=$((ncols-1));j++)) do
printf " %i" ${matrix[$i,$j]}
done
echo
done
But when I tried to assign the elements, something gets wrong
for ((i=0;i<=$((nelem-1));i++)) do
matrix[${irows[$i]},${jcols[$i]}]=${values[$i]}
done
Thanks in advance for any help with this, really.
A solution in plain bash by simulating a 2D array with an associative array could be something like that (Notice that row and column counts are not hard coded and the code works with any permutation of input lines provided that each line has the format specified in the question):
$ cat printmat
#!/bin/bash
declare -A mat
nrow=0
ncol=0
while read -r col elem row; do
mat[$row,$col]=$elem
if ((row > nrow)); then nrow=$row; fi
if ((col > ncol)); then ncol=$col; fi
done
for ((row = 1; row <= nrow; ++row)); do
for ((col = 1; col <= ncol; ++col)); do
elem=${mat[$row,$col]}
if [[ -z $elem ]]; then elem=NA; fi
if ((col == ncol)); then elem+=$'\n'; else elem+=$'\t'; fi
printf "%s" "$elem"
done
done
$ ./printmat < infile.txt prints out
NA 4 12 7 9 10
68 70 NA 85 68 70
182 339 355 333 182 NA
797 1396 1854 NA 922 NA
Any time you find yourself writing a loop in shell just to manipulate text you have the wrong approcah. See why-is-using-a-shell-loop-to-process-text-considered-bad-practice for many of the reasons why.
Using any awk in any shell on every UNIX box:
$ cat tst.awk
{
vals[$3,$1] = $2
numRows = ($3 > numRows ? $3 : numRows)
numCols = $1
}
END {
OFS = "\t"
for (rowNr=1; rowNr<=numRows; rowNr++) {
for (colNr=1; colNr<=numCols; colNr++) {
val = ((rowNr,colNr) in vals ? vals[rowNr,colNr] : "NA")
printf "%s%s", val, (colNr < numCols ? OFS : ORS)
}
}
}
.
$ awk -f tst.awk infile.txt
NA 4 12 7 9 10
68 70 NA 85 68 70
182 339 355 333 182 NA
797 1396 1854 NA 922 NA
here is one way to get you started. Note that this is not intended to be "the" answer but to encourage you to try to learn the toolkit.
$ join -a1 -e NA -o2.2 <(printf "%s\n" {1..4}"_"{1..6}) \
<(awk '{print $3"_"$1,$2}' file | sort -n) |
pr -6at
NA 4 12 7 9 10
68 70 NA 85 68 70
182 339 355 333 182 NA
797 1396 1854 NA 922 NA
works, however, row and column counts are hard coded, which is not the proper way to do it.
Preferred solution will be filling up an awk 2D array with the data and print it in matrix form at the end.
Good nigt. I have this two files:
File 1 - with phenotype informations, the first column are the Ids, the orinal file has 400 rows:
ID a b c d
215 2 25 13.8354303 15.2841303
222 2 25.2 15.8507278 17.2994278
216 2 28.2 13.0482192 14.4969192
223 11 15.4 9.2714745 11.6494745
File 2 - with SNPs information, the original file has 400 lines and 42,000 characters per line.
ID t u j l
215 2 0 2 1
222 2 0 1 1
216 2 0 2 1
223 2 0 2 2
217 2 0 2 1
218 0 2 0 2
And I need to remove from file 2 individuals that do not appear in the file 1, for example:
ID t u j l
215 2 0 2 1
222 2 0 1 1
216 2 0 2 1
223 2 0 2 2
I used this code:
awk 'NR==FNR{a[$1]; next}$1 in a{print $0}' file2 file1 > file3
and I can get this output(file 3):
215 2 0 2 1
222 2 0 1 1
216 2 0 2 1
223 2 0 2 2
but I lose the header, how do I not lose the header?
To keep the header of the second file, add a condition{action} like this:
awk 'NR==FNR {a[$1]; next}
FNR==1 {print $0; next} # <= this will print the header of file2.
$1 in a {print $0}' file1 file2
NR holds the total record number while FNR is the file record number, it counts the records of the file currently being processed. Also the next statements are important, so that to continue with the next record and don't try the rest of the actions.
I have following 2 files file1.txt and file2.txt with the data as given below-
Data in file1.txt
125
125
295
295
355
355
355
Data in file2.txt
125
125
295
355
I did below operation over the files and got following output-
Operation1-
sort file1.txt | uniq -c
2 125
2 295
3 355
Operation2-
sort file2.txt | uniq -c
2 125
1 295
1 355
Now, I want following output using the result of Operation1 and Operation2 -
I want to compare the result of Operation1 and Operation2 and get the output which will show the difference of values from column 1 of both the files, and it will show the column 2 as it is as given below-
0 125
1 295
2 355
redirect output of operation 1 and operation 2 in some files. Let say
file1
and
file2
, then write like this:-
paste file1 file2 | awk '{print $1-$3,$2}'
you will have output
0 125
1 295
2 355
These are my two imput files:
file1.txt
1 34
2 55
3 44
6 77
file2.txt
1 12
2 7
5 32
And I wish my output to be:
1 34 12
2 55 0
3 44 0
5 0 32
6 77 0
I need to do this in awk and although I was able to merge files, I do not know how to do it without losing info...
awk -F"\t" 'NR==FNR {h[$1] = $2; next }{print $1,$2,h[$2]}' file1.txt file2.txt > try.txt
awk '{ if ($3 !="") print $1,$2,$3; else print $1,$2,"0";}' try.txt > output.txt
And the output is:
1 34 12
2 55 7
3 44 0
6 77 0
Sorry, I know this must be very easy, but I am quite new in this world! Please I need help!!! Thanks in advance!!
this command gives you the desired output:
awk 'NR==FNR{a[$1]=$2;next}
{if($1 in a){print $0,a[$1];delete a[$1]}
else print $0,"0"}
END{for(x in a)print x,"0",a[x]}' file2 file1|sort -n|column -t
note that I used sort and column to sort & format the output.
output: (note I guess the 2 55 0 was a typo in your expected output)
1 34 12
2 55 7
3 44 0
5 0 32
6 77 0
Here is another way using join and awk:
join -a1 -a2 -o1.1 2.1 1.2 2.2 -e0 file1 file2 | awk '{print ($1?$1:$2),$3,$4}' OFS='\t'
1 34 12
2 55 7
3 44 0
5 0 32
6 77 0
-a switch allows to join on un-pairable lines.
-o builds our output format
-e allows to specify what should be printed for values that do not exist
awk just completes the final formatting.