Comparing values in two files - bash

I am comparing two files, each having one column and n number of rows.
file 1
vincy
alex
robin
file 2
Allen
Alex
Aaron
ralph
robin
if the data of file 1 is present in file 2 it should return 1 or else 0, in a tab seprated file.
Something like this
vincy 0
alex 1
robin 1
What I am doing is
#!/bin/bash
for i in `cat file1 `
do
cat file2 | awk '{ if ($1=="'$i'") print 1 ; else print 0 }'>>binary
done
the above code is not giving me the output which I am looking for.
Kindly have a look and suggest correction.
Thank you

The simple awk solution:
awk 'NR==FNR{ seen[$0]=1 } NR!=FNR{ print $0 " " seen[$0] + 0}' file2 file1
A simple explanation: for the lines in file2, NR==FNR, so the first action is executed and we simply record that a line has been seen. In file1, the 2nd action is taken and the line is printed, followed by a space, followed by a "0" or a "1", depending on if the line was seen in file2.

AWK loves to do this kind of thing.
awk 'FNR == NR {a[tolower($1)]; next} {f = 0; if (tolower($1) in a) {f = 1}; print $1, f}' file2 file1
Swap the positions of file2 and file1 in the argument list to make file1 the dictionary instead of file2.
When FNR (the record number in the current file) and NR (the record number of all records so far) are equal, then the first file is the one being processed. Simply referencing an array element brings it into existence. This sets up the dictionary. The next instruction reads the next record.
Once FNR and NR aren't equal, subsequent file(s) are being processed and their data is looked up in the dictionary array.

The following code should do it.
Take a close look to the BEGIN and END sections.
#!/bin/bash
rm -f binary
for i in $(cat file1); do
awk 'BEGIN {isthere=0;} { if ($1=="'$i'") isthere=1;} END { print "'$i'",isthere}' < file2 >> binary
done

There are several decent approaches. You can simply use line-by-line set math:
{
grep -xF -f file1 file2 | sed $'s/$/\t1/'
grep -vxF -f file1 file2 | sed $'s/$/\t0/'
} > somefile.txt
Another approach would be to simply combine the files and use uniq -c, then just swap the numeric column with something like awk:
sort file1 file2 | uniq -c | awk '{ print $2"\t"$1 }'

The comm command exists to do this kind of comparison for you.
The following approach does only one pass and scales well to very large input lists:
#!/bin/bash
while read; do
if [[ $REPLY = $'\t'* ]] ; then
printf "%s\t0\n" "${REPLY#?}"
else
printf "%s\t1\n" "${REPLY}"
fi
done < <(comm -2 <(tr '[A-Z]' '[a-z]' <file1 | sort) <(tr '[A-Z]' '[a-z]' <file2 | sort))
See also BashFAQ #36, which is directly on-point.

Another solution, if you have python installed.
If you're familiar with Python and are interested in the solution, you only need a bit of formatting.
#/bin/python
f1 = open('file1').readlines()
f2 = open('file2').readlines()
f1_in_f2 = [int(x in f2) for x in f1]
for n,c in zip(f1, f1_in_f2):
print n,c

Related

Write specific columns of files into another files, Who can give me a more concise solution?

I have a troublesome problem about writing specific columns of the file into another file, more details are I have the file1 like below, I need to write the first columns exclude the first row to file2 with one line and separated with '|' sign. And now I have a solution by sed and awk, this missing last step inserts into the top of file2, even though I still believe there should be some more concise solution on account of powerful of awk、sed, etc. So, Who can offer me another more concise script?
sed '1d;s/ .//' ./file1 | awk '{printf "%s|", $1; }' | awk '{if (NR != 0) {print substr($1, 1, length($1) - 1)}}'
file1:
col_name data_type comment
aaa string null
bbb int null
ccc int null
file2:
xxx ccc(whatever is this)
The result of file2 should be this :
aaa|bbb|ccc
xxx ccc(whatever is this)
Assuming there's no whitespace in the column 1 data, in increasing length:
sed -i "1i$(awk 'NR > 1 {print $1}' file1 | paste -sd '|')" file2
or
ed file2 <<END
1i
$(awk 'NR > 1 {print $1}' file1 | paste -sd '|')
.
wq
END
or
{ awk 'NR > 1 {print $1}' file1 | paste -sd '|'; cat file2; } | sponge file2
or
mapfile -t lines < <(tail -n +2 file1)
col1=( "${lines[#]%%[[:blank:]]*}" )
new=$(IFS='|'; echo "${col1[*]}"; cat file2)
echo "$new" > file2
This might work for you (GNU sed):
sed -z 's/[^\n]*\n//;s/\(\S*\).*/\1/mg;y/\n/|/;s/|$/\n/;r file2' file1
Process file1 "wholemeal" by using the -z command line option.
Remove the first line.
Remove all columns other than the first.
Replace newlines by |'s
Replace the last | by a newline.
Append file2.
Alternative using just command line utils:
tail +2 file1 | cut -d' ' -f1 | paste -s -d'|' | cat - file2
Tail file1 from line 2 onwards.
Using the results from the tail command, isolate the first column using a space as the column delimiter.
Using the results from the cut command, serialize each line into one, delimited by |',s.
Using the results from the paste, append file2 using the cat command.
I'm learning awk at the moment.
awk 'BEGIN{a=""} {if(NR>1) a = a $1 "|"} END{a=substr(a, 1, length(a)-1); print a}' file1
Edit: Here's another version that uses an array:
awk 'NR > 1 {a[++n]=$1} END{for(i=1; i<=n; ++i){if(i>1) printf("|"); printf("%s", a[i])} printf("\n")}' file1
Here is a simple Awk script to merge the files as per your spec.
awk '# From the first file, merge all lines except the first
NR == FNR { if (FNR > 1) { printf "%s%s", sep, $1; sep = "|"; } next }
# We are in the second file; add a newline after data from first file
FNR == 1 { printf "\n" }
# Simply print all lines from file2
1' file1 file2
The NR==FNR condition is true when we are reading the first input file: The overall line number NR is equal to the line number within the current file FNR. The final 1 is a common idiom for printing all input lines which make it this far into the script (the next in the first block prevent lines from the first file to reaching this far).
For conciseness, you can remove the comments.
awk 'NR == FNR { if (FNR > 1) { printf "%s%s", sep, $1; sep = "|"; } next }
FNR == 1 { printf "\n" } 1' file1 file2
Generally speaking, Awk can do everything sed can do, so piping sed into Awk (or vice versa) is nearly always a useless use of sed.

Extracting unique values between 2 files with awk

I need to get uniq lines when comparing 2 files. These files containing field separator ":" which should be treated as the end of line while comparing strings.
The file1 contains these lines
apple:tasty
apple:red
orange:nice
kiwi:awesome
kiwi:expensive
banana:big
grape:green
orange:oval
banana:long
The file2 contains these lines
orange:nice
banana:long
The output file should be (2 occurrences of orange and 2 occurrences of banana deleted)
apple:tasty
apple:red
kiwi:awesome
kiwi:expensive
grape:green
So the only strings before : should be compared
Is it possible to complete this task in 1 command ?
I tried to complete the task in such way but field separator does not work in that situation.
awk -F: 'FNR==NR {a[$0]++; next} !a[$0]' file1 file2 > outputfile
You basically had it, but $0 refers to the whole line when you want to deal with only the first field, which is $1.
Also you need to take care with the order of the input files. To use the values from file2 for deciding which lines to include from file1, process file2 first:
$ awk -F: 'FNR==NR {a[$1]++; next} !a[$1]' file2 file1
apple:tasty
apple:red
kiwi:awesome
kiwi:expensive
grape:green
One comment: awk is very ineffective with arrays. In real life with big files, better use something like:
comm -3 <(cut -d : -f 1 f1 | sort -u) <(cut -d : -f 1 f2 | sort -u) | grep -h -f /dev/stdin f1 f2

awk or shell command to count occurence of value in 1st column based on values in 4th column

I have a large file with records like below :
jon,1,2,apple
jon,1,2,oranges
jon,1,2,pineaaple
fred,1,2,apple
tom,1,2,apple
tom,1,2,oranges
mary,1,2,apple
I want to find the no of person (names in col 1) have apple and oranges both. And the command should take as less memory as possible and should be fast. Any help appreciated!
Output :
awk/sed file => 2 (jon and tom)
Using awk is pretty easy:
awk -F, \
'$4 == "apple" { apple[$1]++ }
$4 == "oranges" { orange[$1]++ }
END { for (name in apple) if (orange[name]) print name }' data
It produces the required output on the sample data file:
jon
tom
Yes, you could squish all the code onto a single line, and shorten the names, and otherwise obfuscate the code.
Another way to do this avoids the END block:
awk -F, \
'$4 == "apple" { if (apple[$1]++ == 0 && orange[$1]) print $1 }
$4 == "oranges" { if (orange[$1]++ == 0 && apple[$1]) print $1 }' data
When it encounters an apple entry for the first time for a given name, it checks to see if the name also (already) has an entry for oranges and prints it if it has; likewise and symmetrically, if it encounters an orange entry for the first time for a given name, it checks to see if the name also has an entry for apple and prints it if it has.
As noted by Sundeep in a comment, it could use in:
awk -F, \
'$4 == "apple" { if (apple[$1]++ == 0 && $1 in orange) print $1 }
$4 == "oranges" { if (orange[$1]++ == 0 && $1 in apple) print $1 }' data
The first answer could also use in in the END loop.
Note that all these solutions could be embedded in a script that would accept data from standard input (a pipe or a redirected file) — they have no need to read the input file twice. You'd replace data with "$#" to process file names if they're given, or standard input if no file names are specified. This flexibility is worth preserving when possible.
With awk
$ awk -F, 'NR==FNR{if($NF=="apple") a[$1]; next}
$NF=="oranges" && ($1 in a){print $1}' ip.txt ip.txt
jon
tom
This processes the input twice
In first pass, add key to an array if last field is apple (-F, would set , as input field separator)
In second pass, check if last field is oranges and if first field is a key of array a
To print only number of matches:
$ awk -F, 'NR==FNR{if($NF=="apple") a[$1]; next}
$NF=="oranges" && ($1 in a){c++} END{print c}' ip.txt ip.txt
2
Further reading: idiomatic awk for details on two file processing and awk idioms
I did a work around and used only grep and comm commands.
grep "apple" file | cut -d"," -f1 | sort > file1
grep "orange" file | cut -d"," -f1 | sort > file2
comm -12 file1 file2 > names.having.both.apple&orange
comm -12 shows only the common names between the 2 files.
Solution from Jonathan also worked.
For the input:
jon,1,2,apple
jon,1,2,oranges
jon,1,2,pineaaple
fred,1,2,apple
tom,1,2,apple
tom,1,2,oranges
mary,1,2,apple
the command:
sed -n "/apple\|oranges/p" inputfile | cut -d"," -f1 | uniq -d
will output a list of people with both apples and oranges:
jon
tom
Edit after comment: For an for input file where lines are not ordered by 1st column and where each person can have two or more repeated fruits, like:
jon,1,2,apple
fred,1,2,apple
fred,1,2,apple
jon,1,2,oranges
jon,1,2,pineaaple
jon,1,2,oranges
tom,1,2,apple
mary,1,2,apple
tom,1,2,oranges
This command will work:
sed -n "/\(apple\|oranges\)$/ s/,.*,/,/p" inputfile | sort -u | cut -d, -f1 | uniq -d

Printing numerous specific lines from file using awk or sed command loop

I've got this big txt file with ID names. It has 2500 lines, one column. Let's call it file.txt
H3430
H3467
H9805
Also, I've got another file, index.txt, which has 390 numbers:
1
4
9
13
15
Those numbers are the number of lines (of IDs) I have to extract from file.txt. I need to generate another file, newfile.txt let's call it, with only the 390 IDs that are in the specific lines that index.txt demands (the first ID of the list, the fourth, the ninth, and so on).
So, I tried to do the following loop, but it didn't work.
num=$'index.txt'
for i in num
do
awk 'NR==i' "file.txt" > newfile.txt
done
I'm a noob regarding this matters... so, I need some help. Even if it is with my loop or with a new solution suggested by you. Thank you :)
Lets create an example file that simulates your 2500 line file with seq:
$ seq 2500 > /tmp/2500
And use the example you have for the line numbers to print in a file called 390:
$ echo "1
4
9
13
15" > /tmp/390
You can print line N in the file 2500 by reading the line numbers into an array and printing the lines if in that array:
$ awk 'NR==FNR{ a[$1]++; next} a[FNR]' /tmp/390 /tmp/2500
You can also use a sed command file:
$ sed 's/$/p/' /tmp/390 > /tmp/sed_cmd
$ sed -n -f /tmp/sed_cmd /tmp/2500
With GNU sed, you can do sed 's/$/p/' /tmp/390 | sed -n -f - /tmp/2500 but that does not work on OS X :-(
You can do this tho:
$ sed -n -f <(sed 's/$/p/' /tmp/390) /tmp/2500
You can read the index.txt file in to a map and then compare it with the line number of file.txt. Redirect the output to another file.
awk 'NR==FNR{line[$1]; next}(FNR in line){print $1}' index.txt file.txt > newfile.txt
When you work with two files, using FNR is necessary as it gets reset to 1 when new file starts (on the contrary NR will continue to increment).
As Ed Morton suggests in the comments. The command could then be refined to further remove {print $1} since awk prints by default on truth.
awk 'NR==FNR{line[$1]; next} FNR in line' index.txt file.txt > newfile.txt
If index.txt is sorted, we could walk file.txt in order.
That reduces the number of actions to the very minimum (faster script):
awk 'BEGIN
{ indexfile="index.txt"
if ( (getline ind < indexfile) <= 0)
{ printf("Empty %s\n; exiting",indexfile);exit }
}
{ if ( FNR < ind ) next
if ( FNR == ind ) printf("%s %s\n",ind,$0)
if ( (getline ind < indexfile) <= 0) {exit}
}' file.txt
If the file is not actually sorted, get it quickly sorted with sort:
sort -n index.txt > temp.index.txt
rm index.txt
mv temp.index.txt index.txt

Replacing a specific field using awk, sed or any POSIX tool

I have a huge file1, which has values as follows:
a 1
b 2
c 3
d 4
e 5
I have another huge file2, which is colon delimited with seven fields as follows:
a:2543:2524:2542:252:536365:54654
c:5454:5454:654:54:87:54
d:87:65:1:98:32:87
I want to search the lines for the variables of file1 and replace its value in the 7th column in file2 so the output should be as follows:
a:2543:2524:2542:252:536365:1
c:5454:5454:654:54:87:3
d:87:65:1:98:32:4
Maybe this awk will work, assuming the files are as posted
awk -F: 'NR==FNR{a[$1]=$0;next;}a[$1]{$0=a[$1]}1' file1 file2
a:2543:2524:2542:252:536365:1
c:5454:5454:654:54:87:3
d:87:65:1:98:32:4
So I came up with a solution; ended up with a couple of lines of code. Maybe there is a better way to do it.But this works !
while read line ; do
var1=`echo $line| awk '{print $1}'`
var2=`echo $line| awk '{print $2}'`
awk -v var1="$var1" -v var2="$var2" -F ':' 'BEGIN { OFS = ":"} $1==var1 {sub(".*",var2,$7)}{print}' file2 > file2.tmp
mv file2.tmp file2
done < file1
cat file2
This should work - it assumes both files are sorted on the first column - I'd be very interested in any performance comparisons with your solution for very large files - both speed and memory - --complement is linux-specific but easily replaced if not available
file0=$1 #file with single value
file1=$2 #file with 6th value to be replaced
# normalize on colon delimiter
tr ' ' : <$file0|
# join on first field
join -t: $file1 -|
# delete column 7
cut --complement -d: -f7

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