I'm trying to remove a long text of various lines contained in a file from another file.
I've tried with
egrep -v $(cat text) original
with no success....
You can use -f pattern-file option in grep:
grep -vxFf test original
x is for exact pattern match (remove this if you want partial match also)
F is for fixed string search instead of regex
Related
I have a file with partial matches to lines in another file. In order to do this I was looking to generate a while loop with read and substituting a variable for each line of partial matches into a grep command to search a database files with a partial match but for some reason, I am not getting an output (an empty outputfile.txt).
Here is my current script
while read -r line; do
grep $line /path/to/databasefile >> /path/to/folder/outputfile.txt
done < "/partial_matches.txt"
the database has multiple lines with a sequence name then DNA sequence after:
>transcript_ab
AGTCAGTCATGTC
>transcript_ac
AGTCAGTCATGTC
>transctipt_ad
AGTCAGTCATGTC
and the partial matching search file has lines of text:
ab
ac
and I'm looking for a return of:
>transcript_ab
>transcript_ac
any help would be appreciated. Thanks.
If you are using GNU grep, then its -f option is what you are looking for:
grep -f /partial_matches.txt /path/to/databasefile
(if you don't have any pattern in partial_matches.txt but only strings, then use grep -F instead of grep)
you can use a for loop instead:
for i in $(cat partial_matches.txt); do
grep $i /path/to/databasefile >> /path/to/folder/outputfile.txt
done
Also, check if you have a typo:
"/partial_matches.txt" -> "./partial_matches.txt"
I would like to know how to search from the command line for a string in various files of type .rb.
And replace:
.delay([ANY OPTIONAL TEXT FOR DELETION]).
with
.delay.
Besides sed an awk are there any other command line tools included in the OS that are better for the task?
Status
So far I have the following regular expression:
.delay\(*.*\)\.
I would like to know how to match only the expression ending on the first closing parenthesis? And avoid replacing:
.delay([ANY OPTIONAL TEXT FOR DELETION]).sometext(param)
Thanks in advance!
If you need to find and replace text in files - sed seems to be the best command line solution.
Search for a string in the text file and replace:
sed -i 's/PATTERN/REPLACEMENT/' file.name
Or, if you need to process multiple occurencies of PATTERN in file, add g key
sed -i 's/PATTERN/REPLACEMENT/g' file.name
For multiple files processing - redirect list of files to sed:
echo "${filesList}" | xargs sed -i ...
You can use find to generate your list of files, and xargs to run sed over the result:
find . -type f -print | xargs sed -i 's/\.delay.*/.delay./'
find will generate a list of files contained in your current directory (., although you can of course pass a different directory), xargs will read that list and then run sed with the list of files as an argument.
Instead of find, which here generates a list of all files, you could use something like grep to generate a list of files that contain a specific term. E.g.:
grep -rl '\.delay' | xargs sed -i ...
For the part of the question where you want to only match and replace until the first ) and not include a second pair of (), here is how to change your regex:
.delay\(*.*\)\.
->
\.delay\([^\)]*\)
I.e. match "actual dot, delay, brace open, everything but brace close and brace close".
E.g. using sed:
>echo .delay([ANY OPTIONAL TEXT FOR DELETION]).sometext(param) | sed -E "s/\.delay\([^\)]*\)/.delay/"
.delay.sometext(param)
I recommend to use grep for finding the right files:
grep -rl --include "*.rb" '\.delay' .
Then feed the list into xargs, as recommended by other answers.
Credits to the other answers for providing a solution for feeding multiple files into sed.
I am following the example in this post finding contents of one file into another file in unix shell script but want to print out differently.
Basically file "a.txt", with the following lines:
alpha
0891234
beta
Now, the file "b.txt", with the lines:
Alpha
0808080
0891234
gamma
I would like the output of the command is:
alpha
beta
The first one is "incorrect case" and second one is "missing from b.txt". The 0808080 doesn't matter and it can be there.
This is different from using grep -f "a.txt" "b.txt" and print out 0891234 only.
Is there an elegant way to do this?
Thanks.
Use grep with following options:
grep -Fvf b.txt a.txt
The key is to use -v:
-v, --invert-match
Invert the sense of matching, to select non-matching lines.
When reading patterns from a file I recommend to use the -F option as long as you not explicitly want that patterns are treated as regular expressions.
-F, --fixed-strings
Interpret PATTERN as a list of fixed strings (instead of regular expressions), separated by newlines, any of which
is to be matched.
I am using grep on an entire directory and sed to replace the string. There are some conflicts in replacing the as there are two strings that are very similar and have the same pattern. Only big difference is the file extension at the end.
String1
xargs sed -i
's,//website.net/resources/special.js,//newsite.net/location/newspecial.js,g'
String2
xargs sed -i
's,//website.net/resources/file.swf,//newsite.net/location/player.swf,g'
How do I specify that .js receives the correct replacement and .swf receives the correct replacement?
For the first, you can restrict the match easily, for the second you need a mapping to provide the old file name to new file name otherwise how the script is going to know that "file.swf" to be replaced with "player.swf".
$ echo '//website.net/resources/special.js' |
sed -r 's,(.*/)(.*.js)$,\1new\2,'
//website.net/resources/newspecial.js
first match group will include every char until the last /., second match things ending with .js, you may need another anchor if there are multiple elements on the same line. Note that in one element case g is unnecessary.
I would like to find a particular string in two text files - I know how to do it in a single file, but how do I select more than one file, the example below does it for a single text file, I want to search file myfile.txt and otherfile.txt
grep "redeem" /home/tom/myfile.txt
You can do like this,
grep 'redeem' file1 file2 file3..
Syntax:
grep [OPTIONS] PATTERN [FILE...]
Normally, grep can do the pattern matching in more than one files.