as you can read in the title Im dealing with two files. Her is the example how the look like.
file1:
Name (additional info separated by a tab from the name)
Peter Schwarzer<tab>Best friend of mine
file2:
Name (followed by a float separated by a tab from the name)
Peter Schwarzer<tab>1456
So what i want to do is use file1 one as an index for searching file2. If the Names match it should be written in file3 which should contain the Name followed by the float from file2 followed by the additional info from file1.
So file3 should look like:
Peter Schwarzer<tab>1456<tab>Best friend of mine
(everything separated by tab)
I tried grep -f to read a pattern from a file and without the additional information it works. So is there any way to get the desired result with grep or is AWK the answer?
Thanks in advance,
Julian
give this line a try, I didn't test, but should go:
awk -F'\t' -v OFS="\t" 'NR==FNR{n[$1]=$2;next}$1 in n{print $0,n[$1]}' file1 file2 > file3
Try this awk one liner!
awk -v FS="\t" -v OFS="\t" 'FNR==NR{ A[$1]=$2; next}$1 in A{print $0,A[$1];}' file1.txt file2.txt > file3.txt
To me this looks like a job for join:
join -t '\t' file1 file2
This assumes file1 and file2 are sorted. If not, sort them first:
sort -o file1 file1
sort -o file2 file2
join -t '\t' file1 file2
If you can't modify file1 and file2 (if you need to leave them in their original, unsorted state), use a temporary file:
tmpfile=/tmp/tf$$
sort file1 > $tmpfile
sort file2 | join -t '\t' $tmpfile -
If join says "illegal tab character specification" you'll have to use join -t ' ' where you type an actual tab between the single quotes (and depending on your shell, you may have to use control-V before that tab).
Related
I have two files, file1 and file2, where the target_id compose the first column in both.
I want to compare file1 to file2, and only keep the rows of file1 which match the target_id in file2.
file2:
target_id
ENSMUST00000128641.2
ENSMUST00000185334.7
ENSMUST00000170213.2
ENSMUST00000232944.2
Any help would be appreciated.
% grep -x -f file1 file2 resulted in no output in my terminal
Sample data that actually shows overlaps between the files.
file1.csv:
target_id,KO_1D_7dpi,KO_2D_7dpi
ENSMUST00000178537.2,0,0
ENSMUST00000178862.2,0,0
ENSMUST00000196221.2,0,0
ENSMUST00000179664.2,0,0
ENSMUST00000177564.2,0,0
file2.csv
target_id
ENSMUST00000178537.2
ENSMUST00000196221.2
ENSMUST00000177564.2
Your grep command, but swapped:
$ grep -F -f file2.csv file1.csv
target_id,KO_1D_7dpi,KO_2D_7dpi
ENSMUST00000178537.2,0,0
ENSMUST00000196221.2,0,0
ENSMUST00000177564.2,0,0
Edit: we can add the -F argument since it is a fixed-string search. Plus it adds protection against the . matching something else as a regex. Thanks to #Sundeep for the recommendation.
I want to find matching lines from file 2 when compared to file 1.
file2 contains multiple columns and column one contains information that could match file1.
I tried below commands and they didn't give any matching results (contents in file1 are definitely in file2) . I have used these commands previously to compare between different files and they worked.
grep -f file1 file2
grep -Fwf file1 file2
When i tried to grep whatever that's not matching, i get results
grep -vf file1 file2
file1 contains list of genes (754 genes) , one line each
ATM
ATP5B
ATR
ATRIP
ATRX
I have a feeling the problem is with my file1. When I tried to type several items manually in my file1 just to test, and do grep with file2, I get the matching lines from file2.
When I copied the contents of file1 (originally in excel) into notepad making a .txt file, I didn't get any matching results.
I can't see any problem with my file1. Any suggestion?
You said,
I copied the contents of file1 (originally in excel) into notepad making a .txt file
It's likely that the txt file contains carriage-return/linefeed pairs which are screwing up the grep. As I suggested in a comment, try this:
tr -d '\015' < file1 > file1a
grep -Fwf file1a file2
The tr invocation deletes all the carriage returns, giving you a proper Unix/Linux text file with only newlines (\n) as line terminators.
You said:
I can't see any problem with my file1.
Here's how to see the extra-carriage-return problem:
cat -v test1
Those little ^M markers at the end of each line are cat -v's way of showing you the carriage return control codes.
Addendum:
Carriage Return (CR) is decimal 13, hex 0x0d, octal 015, \r in C.
Line Feed (LF) is decimal 10, hex 0x0a, octal 012, \n in C.
Because it's an old-school utility, tr accepts octal (base 8) notation for control characters.
(I think in some versions tr -d '\r' would work, but I'm not sure, and anyway I'm not sure what version you have. tr -d '\015' should be universal.)
Simple shell script that performs grep for every input in file1.txt
#!/bin/bash
while read content; do
grep -q "$content" file2.txt
if [ $? -eq "0" ]; then
echo "$content" was found in file2 >> results.txt
fi
done < file1.txt
Let's suppose this is file2:
$ cat file2
a b ATM
c d e
f ATR g
Using grep and process substitution
We can get lines from file1 that match any of the columns in file2 via:
$ grep -wFf <(sed 's/[[:space:]]/\n/g' file2) file1
ATM
ATR
This works because it converts file2 to a form that grep understands:
$ sed 's/[[:space:]]/\n/g' file2
a
b
ATM
c
d
e
f
ATR
g
Using awk
$ awk 'FNR==NR{for (i=1;i<=NF;i++) seen[$i]; next} $0 in seen' file2 file1
ATM
ATR
Here, awk keeps track of every column that it sees in file2 and then print only those lines in file1 that match one of those columns
Try to use command
comm
it is a reversed version of diff
I want to compare two files and redirect the difference between the two files to third one.
file1:
/opt/a/a.sql
/opt/b/b.sql
/opt/c/c.sql
In case any file has # before /opt/c/c.sql, it should skip #
file2:
/opt/c/c.sql
/opt/a/a.sql
I want to get the difference between the two files. In this case, /opt/b/b.sql should be stored in a different file. Can anyone help me to achieve the above scenarios?
file1
$ cat file1 #both file1 and file2 may contain spaces which are ignored
/opt/a/a.sql
/opt/b/b.sql
/opt/c/c.sql
/opt/h/m.sql
file2
$ cat file2
/opt/c/c.sql
/opt/a/a.sql
Do
awk 'NR==FNR{line[$1];next}
{if(!($1 in line)){if($0!=""){print}}}
' file2 file1 > file3
file3
$ cat file3
/opt/b/b.sql
/opt/h/m.sql
Notes:
The order of files passed to awk is important here, pass the file to check - file2 here - first followed by the master file -file1.
Check awk documentation to understand what is done here.
You can use some tools like cat, sed, sort and uniq.
The main observation is this: if the line is in both files then it is not unique in cat file1 file2.
Furthermore in cat file1 file2| sort, all doubles are in sequence. Using uniq -u we get unique lines and have this pipe:
cat file1 file2 | sort | uniq -u
Using sed to remove leading whitespace, empty and comment lines, we get this final pipe:
cat file1 file2 | sed -r 's/^[ \t]+//; /^#/ d; /^$/ d;' | sort | uniq -u > file3
Say we have file1.csv like this
"agvsad",314
"gregerg",413
"dfwer",53214
"fewf",344
and file2.csv like this
"dfwer"
"fewf"
how to use awk to delete those lines whose column 1 values exist in file2 and get a file3 looks like:
"agvsad",314
"gregerg",413
By the way I am dealing with millions of lines
awk 'NR==FNR{seen[$0]++; next} !seen[$1]' file2.csv FS=, file1.csv should do what you want but it will require enough memory to store an entry for each line in file2.csv.
As an alternative, using grep:
$ grep -vf file2.csv file1.csv
"agvsad",314
"gregerg",413
I have two files like below:
file1
"Connect" CONNECT_ID="12"
"Connect" CONNECT_ID="11"
"Connect" CONNECT_ID="122"
"Connect" CONNECT_ID="109"
file2
"Quit" CONNECT_ID="12"
"Quit" CONNECT_ID="11"
The file contents are not exactly same but similar to above and the number of records are minimum 100,000.
Now i want to get the result as show below into file1 (means the final result should be there in file1)
"Connect" CONNECT_ID="122"
"Connect" CONNECT_ID="109"
I have used a while loop something like below:
awk {'print $2'} file2 | sed "s/CONNECTION_ID=//g" > sample.txt
while read actual; do
grep -w -v $actual file1 > file1_tmp
mv -f file1_tmp file1
done < sample.txt
Here I have adjusted my code according to example. So it may or may not work.
My problem is the loop is repeating for more than 1 hour to complete the process.
So can any one suggest me how to achieve the same with any other ways like using diff or comm or sed or awk or any other linux command which will run faster?
Here mainly I want to eliminate this big typical while loop.
Most UNIX tools are line based and as you don't have whole line matches that means grep, comm and diff are out the window. To extract field based information like you want awk is perfect:
$ awk 'NR==FNR{a[$2];next}!($2 in a)' file2 file1
"Connect" CONNECT_ID="122"
"Connect" CONNECT_ID="109"
To store the results back to file1 you'll need to redict the output to a temporary file and then move the file into file1 like so:
$ awk 'NR==FNR{a[$2];next}!($2 in a)' file2 file1 > tmp && mv tmp file1
Explanation:
The awk variable NR increments for every record read, that is each line in every file. The FNR variable increments for every record but gets reset for every file.
NR==FNR # This condition is only true when reading file1
a[$2] # Add the second field in file1 into array as a lookup table
next # Get the next line in file1 (skips any following blocks)
!($2 in a) # We are now looking at file2 if the second field not in the look up
# array execute the default block i.e print the line
To modify this command you just need to change the fields that matched. In your real case if you want to match field 1 from file1 with field 4 from file2 then you would do:
$ awk 'NR==FNR{a[$1];next}!($4 in a)' file2 file1
This might work for you (GNU sed):
sed -r 's|\S+\s+(\S+)|/\1/d|' file2 | sed -f - -i file1
The tool best suited to this job is join(1). It joins two files based on values in a given column of each file. Normally it just outputs the lines that match across the two files, but it also has a mode to output the lines from one of the files that do not match the other file.
join requires that the files be sorted on the field(s) you are joining on, so either pre-sort the files, or use process substitution (a bash feature - as in the example below) to do it on the one command line:
$ join -j 2 -v 1 -o "1.1 1.2" <(sort -k2,2 file1) <(sort -k2,2 file2)
"Connect" CONNECT_ID="122"
"Connect" CONNECT_ID="109"
-j 2 says to join the files on the second field for both files.
-v 1 says to only output fields from file 1 that do not match any in file 2
-o "1.1 1.2" says to order the output with the first field of file 1 (1.1) followed by the second field of file 1 (1.2). Without this, join will output the join column first followed by the remaining columns.
You may need to analyze file2 at fist, and append all ID which have appered to a cache(eg. memory)
Than scan file1 line by line to adjust whether the ID in the cache.
python code like this:
#!/usr/bin/python
# -*- coding: utf-8 -*-
import re
p = re.compile(r'CONNECT_ID="(.*)"')
quit_ids = set([])
for line in open('file2'):
m = p.search(line)
if m:
quit_ids.add(m.group(1))
output = open('output_file', 'w')
for line in open('file1'):
m = p.search(line)
if m and m.group(1) not in quit_ids:
output.write(line)
output.close()
The main bottleneck is not really the while loop, but the fact that you rewrite the output file thousands of times.
In your particular case, you might be able to get away with just this:
cut -f2 file2 | grep -Fwvf - file1 >tmp
mv tmp file1
(I don't think the -w option to grep is useful here, but since you had it in your example, I retained it.)
This presupposes that file2 is tab-delimited; if not, the awk '{ print $2 }' file2 you had there is fine.