This question already has answers here:
Inner join on two text files
(5 answers)
Closed 6 years ago.
I have two file which I need to compare, and if the first column in file1 matches part of the fisrt columns in file2, then add them side by side in file3, below is an example:
File1:
123123,ABC,2016-08-18,18:53:53
456456,ABC,2016-08-18,18:53:53
789789,ABC,2016-08-18,18:53:53
123123,ABC,2016-02-15,12:46:22
File2
789789_TTT,567774,223452
123123_TTT,121212,343434
456456_TTT,323232,223344
output:
123123,ABC,2016-08-18,18:53:53,123123_TTT,121212,343434
456456,ABC,2016-08-18,18:53:53,456456_TTT,323232,223344
789789,ABC,2016-08-18,18:53:53,789789_TTT,567774,223452
123123,ABC,2016-02-15,18:53:53,123123_TTT,121212,343434
Thanks..
Usin Gnu AWK:
$ awk -F, 'NR==FNR{a[gensub(/([^_]*)_.*/,"\\1","g",$1)]=$0;next} $1 in a{print $0","a[$1]}' file2 file1
123123,ABC,2016-08-18,18:53:53 123123_TTT,121212,343434
456456,ABC,2016-08-18,18:53:53 456456_TTT,323232,223344
789789,ABC,2016-08-18,18:53:53 789789_TTT,567774,223452
123123,ABC,2016-02-15,12:46:22 123123_TTT,121212,343434
Explanation:
NR==FNR { # for the first file (file2)
a[gensub(/([^_]*)_.*/,"\\1","g",$1)]=$0 # store to array
next
}
$1 in a { # if the key from second file in array
print $0","a[$1] # output
}
awk solution matches keys formed from file2 against column 1 of file1 - should also work on Solaris using /usr/xpg4/bin/awk - I took the liberty of assuming the last line of OP output has a typo
file1=$1
file2=$2
AWK=awk
[[ $(uname) == SunOS ]] && AWK=/usr/xpg4/bin/awk
$AWK -F',' '
BEGIN{OFS=","}
# file2 key is part of $1 till underscore
FNR==NR{key=substr($1,1,index($1,"_")-1); f2[key]=$0; next}
$1 in f2 {print $0, f2[$1]}
' $file2 $file1
tested
123123,ABC,2016-08-18,18:53:53,123123_TTT,121212,343434
456456,ABC,2016-08-18,18:53:53,456456_TTT,323232,223344
789789,ABC,2016-08-18,18:53:53,789789_TTT,567774,223452
123123,ABC,2016-02-15,12:46:22,123123_TTT,121212,343434
Pure bash solution
file1=$1
file2=$2
while IFS= read -r line; do
key=${line%%_*}
f2[key]=$line
done <$file2
while IFS= read -r line; do
key=${line%%,*}
[[ -n ${f2[key]} ]] || continue
echo "$line,${f2[key]}"
done <$file1
Related
i have two files:
SCR_location - which has information about a SNP location in an ascending order.
19687
36075
n...
modi_VCF - a vcf table that has information about every SNP.
19687 G A xxx:255,0,195 xxx:255,0,206
20398 G C 0/0:0,255,255 0/0:0,208,255
n...
i want to save just the lines with the matching SNP location into a new file
i wrote the following script but it doesn't work
cat SCR_location |while read SCR_l; do
cat modi_VCF |while read line; do
if [ "$SCR_l" -eq "$line" ] ;
then echo "$line" >> file
else :
fi
done
done
Would you please try a bash solution:
declare -A seen
while read -r line; do
seen[$line]=1
done < SCR_location
while read -r line; do
read -ra ary <<< "$line"
if [[ ${seen[${ary[0]}]} ]]; then
echo "$line"
fi
done < modi_VCF > file
It first iterates over SCR_location and stores SNP locations in an associative array seen.
Next it scans modi_VCF and if the 1st column value is found in the associative array, then print the line.
If awk is your option, you can also say:
awk 'NR==FNR {seen[$1]++; next} {if (seen[$1]) print}' SCR_location modi_VCF > file
[Edit]
In order to filter out the unmached lines, just negate the logic as:
awk 'NR==FNR {seen[$1]++; next} {if (!seen[$1]) print}' SCR_location modi_VCF > file_unmatched
The code above outputs the unmatched lines only. If you want to sort the matched lines and the unmatched lines at once, please try:
awk 'NR==FNR {seen[$1]++; next} {if (seen[$1]) {print >> "file_matched"} else {print >> "file_unmatched"} }' SCR_location modi_VCF
Hope this helps.
I have a list of numbers in a file
cat to_delete.txt
2
3
6
9
11
and many txt files in one folder. Each file has tab delimited lines (can be more lines than this).
3 0.55667 0.66778 0.54321 0.12345
6 0.99999 0.44444 0.55555 0.66666
7 0.33333 0.34567 0.56789 0.34543
I want to remove the lines that the first number ($1 for awk) is in to_delete.txt and print only the lines that the first number is not in to_delete.txt. The change should be replacing the old file.
Expected output
7 0.33333 0.34567 0.56789 0.34543
This is what I got so far, which doesn't remove anything;
for file in *.txt; do awk '$1 != /2|3|6|9|11/' "$file" > "$tmp" && mv "$tmp" "$file"; done
I've looked through so many similar questions here but still cannot make it work. I also tried grep -v -f to_delete.txt and sed -n -i '/$to_delete/!p'
Any help is appreciated. Thanks!
In awk:
$ awk 'NR==FNR{a[$1];next}!($1 in a)' delete file
Output:
7 0.33333 0.34567 0.56789 0.34543
Explained:
$ awk '
NR==FNR { # hash records in delete file to a hash
a[$1]
next
}
!($1 in a) # if $1 not found in record in files after the first, output
' delete files* # mind the file order
My first idea was this:
printf "%s\n" *.txt | xargs -n1 sed -i "$(sed 's!.*!/& /d!' to_delete.txt)"
printf "%s\n" *.txt - outputs the *.txt files each on separate lines
| xargs -n1 execute the following command for each line passing the line content as the input
sed -i - edit file in place
$( ... ) - command substitution
sed 's!.*!/^& /d!' to_delete.txt - for each line in to_delete.txt, append the line with /^ and suffix with /d. That way from the list of numbers I get a list of regexes to delete, like:
/^2 /d
/^3 /d
/^6 /d
and so on. Which tells sed to delete lines matching the regex - line starting with the number followed by a space.
But I think awk would be simpler. You could do:
awk '$1 != 2 && $1 != 3 && $1 != 6 ... and so on ...`
but that would be longish, unreadable. It's easier to read the map from the file and then check if the number is in the array:
awk 'FNR==NR{ map[$1] } FNR!=NR && !($1 in map)' to_delete.txt "$file"
The FNR==NR is true only for the first file. So when we read it, we set the map[$1] (we "set" it, just so such element exists). Then FNR!=NR is true for the second file, for which we check if the first element is the key in the map. If it is not, the expression is true and the line gets printed out.
all together:
for file in *.txt; do awk 'FNR==NR{ map[$1] } FNR!=NR && !($1 in map)' to_delete.txt "$file" > "$tmp"; mv "$tmp" "$file"; done
This question already has answers here:
Sort keys and Sum their values in bash
(4 answers)
sum of column in text file using shell script
(4 answers)
How can I sum values in column based on the value in another column?
(5 answers)
Closed 4 years ago.
I have a file with below records:
$ cat sample.txt
ABC,100
XYZ,50
ABC,150
QWE,100
ABC,50
XYZ,100
Expecting the output to be:
$ cat output.txt
ABC,300
XYZ,150
QWE,100
I tried the below script:
PREVVAL1=0
SUM1=0
cat sam.txt | sort > /tmp/Pos.part
while read line
do
VAL1=$(echo $line | awk -F, '{print $1}')
VAL2=$(echo $line | awk -F, '{print $2}')
if [ $VAL1 == $PREVVAL1 ]
then
SUM1=` expr $SUM + $VAL2`
PREVVAL1=$VAL1
echo $VAL1 $SUM1
else
SUM1=$VAL2
PREVVAL1=$VAL1
fi
done < /tmp/Pos.part
I want to get some one liner command to get the required output. Wanted to avoid the while loop concept. I want to just add the numbers where the first column is same and show it in a single line.
awk -F, '{a[$1]+=$2} END{for (i in a) print i FS a[i]}' sample.txt
Output
QWE,100
XYZ,150
ABC,300
The first part is executed for each line and creates an associative array. The END part prints this array.
It's an awk one-liner:
awk -F, -v OFS=, '{sum[$1]+=$2} END {for (key in sum) print key, sum[key]}' sample.txt > output.txt
sum[$1] += $2 creates an associative array whose keys are the first field and values are the corresponding sums.
This can also be done easily enough in native bash. The following uses no external tools, no subshells and no pipelines, and is thus far faster (I'd place money on 100x the throughput on a typical/reasonable system) than your original code:
declare -A sums=( )
while IFS=, read -r name val; do
sums[$name]=$(( ${sums[$name]:-0} + val ))
done
for key in "${!sums[#]}"; do
printf '%s,%s\n' "$key" "${sums[$key]}"
done
If you want to, you can make this a one-liner:
declare -A sums=( ); while IFS=, read -r name val; do sums[$name]=$(( ${sums[$name]:-0} + val )); done; for key in "${!sums[#]}"; do printf '%s,%s\n' "$key" "${sums[$key]}"; done
#!/bin/bash
function compare {
for file1 in /dir1/*.csv
do
file2=/dir2/$(basename "$file1")
if [[ -e "$file2" ]] ### loop only if the file2 with same filename as file1 is present ###
then
awk 'BEGIN {FS==","} NR == FNR{arr[$0];next} ! ($0 in arr)' $file1 $file2 > /dirDiff/`echo $(basename "$file1")_diff`
fi
done
}
function removeNULL {
for i in /dirDiff/*_diff
do
if [[ ! -s "$i" ]] ### if file exists with zero size ###
then
\rm -- "$i"
fi
done
}
compare
removeNULL
file1 and file2 are the formatted files from two different sources. Source1 is inducing an arbitrary newLine character making one record to split into two records, causing script to fail and generate wrong diff o/p.
I want my script to compare b/w file1 and file2 by ignoring the induced newLine character by Source1. But, I am not sure how my script will identify b/w an actual new record and the manually induced newLine.
file1:-
11447438218480362,6005560623,6005560623,11447438218480362,5,20160130103044,100,195031,,1,0,00,49256,0
,195031_5_00_6,0.1,6;
11447691224860640,6997557634,6997557634,11447691224860640,601511,20160130103457,500,195035,,2,0,00,45394,0
,195035_601511_00_6,0.5,6;
file2:-
11447438218480362,6005560623,6005560623,11447438218480362,5,20160130103044,100,195031,,1,0,00,49256,0,195031_5_00_6,0.1,6;
11447691224860640,6997557634,6997557634,11447691224860640,601511,20160130103457,500,195035,,2,0,00,45394,0,195035_601511_00_6,0.5,6;
Appreciate your support.
You could preprocess your file1 joining lines not ending in ; with the next line:
sed -r ":again; /;$/! { N; s/(.+)[\r\n]+(.+)/\1\2/g; b again; }" file1
so that file1 and file2 are comparable.
I want a unix command to find the lines between first & last occurence of a word
For example:
let's imagine we have 1000 lines. Tenth line contains word "stackoverflow", thirty fifth line also contains word "stackoverflow".
I want to print lines between 10 and 35 and write it to a new file.
You can make it in two steps. The basic idea is to:
1) get the line number of the first and last match.
2) print the range of lines in between these range.
$ read first last <<< $(grep -n stackoverflow your_file | awk -F: 'NR==1 {printf "%d ", $1}; END{print $1}')
$ awk -v f=$first -v l=$last 'NR>=f && NR<=l' your_file
Explanation
read first last reads two values and stores them in $first and $last.
grep -n stackoverflow your_file greps and shows the output like this: number_of_line:output
awk -F: 'NR==1 {printf "%d ", $1}; END{print $1}') prints the number of line of the first and last match of stackoverflow in the file.
And
awk -v f=$first -v l=$last 'NR>=f && NR<=l' your_file prints all lines from $first line number till $last line number.
Test
$ cat a
here we
have some text
stackoverflow
and other things
bla
bla
bla bla
stackoverflow
and whatever else
stackoverflow
to make more fun
blablabla
$ read first last <<< $(grep -n stackoverflow a | awk -F: 'NR==1 {printf "%d ", $1}; END{print $1}')
$ awk -v f=$first -v l=$last 'NR>=f && NR<=l' a
stackoverflow
and other things
bla
bla
bla bla
stackoverflow
and whatever else
stackoverflow
By steps:
$ grep -n stackoverflow a
3:stackoverflow
9:stackoverflow
11:stackoverflow
$ grep -n stackoverflow a | awk -F: 'NR==1 {printf "%d ", $1}; END{print $1}'
3 11
$ read first last <<< $(grep -n stackoverflow a | awk -F: 'NR==1 {printf "%d ", $1}; END{print $1}')
$ echo "first=$first, last=$last"
first=3, last=11
If you know an upper bound of how many lines there can be (say, a million), then you can use this simple abusive script:
(grep -A 100000 stackoverflow | grep -B 1000000 stackoverflow) < file
You can append | tail -n +2 | head -n -1 to strip the border lines as well:
(grep -A 100000 stackoverflow | grep -B 1000000 stackoverflow
| tail -n +2 | head -n -1) < file
I'm not 100% sure from the question whether the output should be inclusive of the first and last matching lines, so I'm assuming it is. But this can be easily changed if we want exclusive instead.
This pure-bash solution does it all in one step - i.e. the file (or pipe) is only read once:
#!/bin/bash
function midgrep {
while read ln; do
[ "$saveline" ] && linea[$((i++))]=$ln
if [[ $ln =~ $1 ]]; then
if [ "$saveline" ]; then
for ((j=0; j<i; j++)); do echo ${linea[$j]}; done
i=0
else
saveline=1
linea[$((i++))]=$ln
fi
fi
done
}
midgrep "$1"
Save this as a script (e.g. midgrep.sh) and pipe whatever output you like to it as follows:
$ cat input.txt | ./midgrep.sh stackoverflow
This works as follows:
find the first matching line and buffer in the first element of an array
continue reading lines until the next match, buffering to the array as we go
on each subsequent matches, flush the buffer array to output
continue reading file to the end. If there are no more matches, then the last buffer is simply discarded.
The advantage of this approach is that we only read through the input one time only. The disadvantage is that we buffer everything between each match - if there are many lines between each match, then these are all buffered to memory, until we hit the next match.
Also this uses the bash =~ regular expression operator to keep this pure bash. But you could replace this with a grep instead, if you are more comfortable with that.
Using perl :
perl -00 -lne '
chomp(my #arr = split /stackoverflow/);
print join "\nstackoverflow", #arr[1 .. $#arr -1 ]
' file.txt | tee newfile.txt
The idea behind this is to feed an array of the whole input file in to chunks using "stackoverflow" string to split. Next, we print the 2nd occurrences to the last -1 with join "stackoverflow".