I have some directory called mydirectory with a bunch of text files containing the words 'SAVE' 'ME!' multiple times so I want it to print all the times for this specific pattern 'SAVE'|ANYTHING HERE, FOR ANY AMOUNT OF CHARACTERS|'ME'|Any non-zero amount of !s|'
To do this, I came up with sed -n '/SAVE/,/ME!\{1\}/p' mydirectory/* but this did not work, does anybody know how to do this? I can only use sed and grep for this.
File:
SAVE US OR JUST ME!!
BRAINSSSSSSSSSSSSS
SAVE US OR JUST ME
BRAINSSSSSSSSSSSSS
SAVE ME!
BRAINNNNNNNNNNNNS
SAVE ME
Desired Output
SAVE US OR JUST ME!!
SAVE ME!
$ grep -E '^SAVE.*ME!+$' file
output:
SAVE US OR JUST ME!!
SAVE ME!
anchors the pattern to the beginning and end, which I guess what you want.
Related
I am really new to regex and I was following other StackOverflow answers to make sed command to remove invalid XML characters.
sed -ie 's/[^\u0009\r\n\u0020-\uD7FF\uE000-\uFFFD\ud800\udc00-\udbff\udfff]//g' myfile.xml
When I run this, it looks like it deletes a bunch of alphabets,,, For example, if it is company, it deletes o,m,p,a,y,etc. Especially lower cases.
There is something wrong with my regex OR maybe it doesn't think it as regex. Would you please help me? Thank you.
Apologies for a seemingly inane question. But I have spent the whole day trying to figure it out and it drives me up the walls. I'm trying to write a seemingly simple bash script that would take a list of files in the directory from ls, replace part of the file names using sed, get unique names from the list and pass them onto some command. Like so:
inputs=`ls *.ext`
echo $inputs
test1_R1.ext test1_R2.ext test2_R1.ext test2_R2.ext
Now I would like to put it through sed to replace 1.ext and 2.ext with * to get test1_R* etc. Then I'd like to remove resulting duplicates by running sort -u to arrive to the following $outputs variable:
echo $outputs
test1_R* test2_R*
And pass this onto a command, like so
cat $outputs
I can do something like this in a command line:
ls *.ext | sed s/..ext/\*/g | sort -u
But if I try to assign the above to a variable in the script it just returns the output from the ls. I have tried several ways to do it: including the whole pipe in the script. Running each command separately and assigning it to a variable, then passing that variable to the next command and writing the outputs to files then passing the file to the next command. But so far none of this managed to achieve what I aimed to. I think my problem lies in (except general cluelessness aroung bash scripting) inability to run seq on a variable within script. There seems to be a lot of advice around in how to pass variables to pattern or replacement string in sed, but they all seem to take files as input. But I understand that it might not be the proper way of doing it anyway. Therefore I would really appreciate if someone could suggest an elegant way to achieve, what I'm trying to.
Many thanks!
Update 2/06/2014
Hi Barmar, thanks for your answer. Can't say it solved the problem, but it helped pin-pointing it. Seems like the problem is in me using the asterisk. I have to say, I'm very puzzled. The actual file names I've got are:
test1_R1.fastq.gz test1_R2.fastq.gz test2_R1.fastq.gz test2_R2.fastq.gz
If I'm using the code you suggested, which seems to me the right way do to it:
ins=$(ls *.fastq.gz | sed 's/..fastq.gz/\*/g' | sort -u)
Sed doesn't seem to do anything and I'm getting the output of ls:
test1_R1.fastq.gz test1_R2.fastq.gz test2_R1.fastq.gz test2_R2.fastq.gz
Now if I replace that backslash with anything else, the sed works, but it also returns whatever character I'm putting in front (or after) the asteriks:
ins=$(ls *.fastq.gz | sed 's/..fastq.gz/"*/g' | sort -u)
test1_R"* test2_R"*
That's odd enough, but surely I can just put an "R" in front of the asteriks and then replace R in the search pattern string, right? Wrong! If I do that whichever way: 's/R..fastq.gz/R*/g' 's/...fastq.gz/R*/g' 's/[A-Z]..fastq.gz/R*/g' I'm back to the original names! And even if I end up with something like test1_RR* test2_RR* and try to run it through sed again and replace "_R" for "_" or "RR" for "R", I'm having no luck and I'm back to the original names. And yet I can replace the rest of the file name no problem, just not to get me test1_R* I need.
I have a feeling I should be escaping that * in some very clever way, but nothing I've tried seems to work. Thanks again for your help!
This is how you capture the result of the whole pipeline in a variable:
var=$(ls *.ext | sed s/..ext/\*/g | sort -u)
I am essentially trying to use sed to remove a few lines within a text document. To clean it up. But I'm not getting it right at all. Missing something and I have no idea what...
#!/bin/bash
items[0]='X-Received:'
items[1]='Path:'
items[2]='NNTP-Posting-Date:'
items[3]='Organization:'
items[4]='MIME-Version:'
items[5]='References:'
items[6]='In-Reply-To:'
items[7]='Message-ID:'
items[8]='Lines:'
items[9]='X-Trace:'
items[10]='X-Complaints-To:'
items[11]='X-DMCA-Complaints-To:'
items[12]='X-Abuse-and-DMCA-Info:'
items[13]='X-Postfilter:'
items[14]='Bytes:'
items[15]='X-Original-Bytes:'
items[16]='Content-Type:'
items[17]='Content-Transfer-Encoding:'
items[18]='Xref:'
for f in "${items[#]}"; do
sed '/${f}/d' "$1"
done
What I am thinking, incorrectly it seems, is that I can setup a for loop to check each item in the array that I want removed from the text file. But it's simply not working. Any idea. Sure this is basic and simple and yet I can't figure it out.
Thanks,
Marek
Much better to create a single sed script, rather than generate 19 small scripts in sequence.
Fortunately, generating a script by joining the array elements is moderately easy in Bash:
regex=$(printf '\|%s' "${items[#]}")
regex=${regex#'\|'}
sed "/^$regex/d" "$1"
(Notice also the addition of ^ to the final regex -- I assume you only want to match at beginning of line.)
Properly, you should not delete any lines from the message body, so the script should leave anything after the first empty line alone:
sed "1,/^\$/!b;/$regex/d" "$1"
Add -i if you want in-place editing of the target file.
I have a tsv file with thousands of tab delimmited lines and I need to search for someones name and then copy the entire line to a seperate file over and over. Can anyone help? Thanks!!
Question is vague but this should generally work:
grep "some-name" *.tsv > ouput
It sounds very simple:
grep "someone's name" tsv-file > separate-file
What's the catch? Is the name in one or two fields? Middle initials?
I'm trying to make a script that will go into a directory and run my own application with each file matching a regular expression, specifically Test[0-9]*.txt.
My input filenames look like this TestXX.txt. Now, I could just use cut and chop off the Test and .txt, but how would I do this if XX wasn't predefined to be two digits? What would I do if I had Test1.txt, ..., Test10.txt? In other words, How would I get the [0-9]* part?
Just so you know, I want to be able to make a OutputXX.txt :)
EDIT:
I have files with filename Test[0-9]*.txt and I want to manipulate the string into Output[0-9]*.txt
Would something like this help?
#!/bin/bash
for f in Test*.txt ;
do
process < $f > ${f/Test/Output}
done
Bash Shell Parameter Expansion
A good tutorial on regexes in bash is here. Summarizing, you need something like:
if [[$filenamein =~ "^Test([0-9]*).txt$"]]; then
filenameout = "Output${BASH_REMATCH[1]}.txt"
and so on. The key is that, when you perform the =~" regex-match, the "sub-matches" to parentheses-enclosed groups in the RE are set in the entries of arrayBASH_REMATCH(the[0]entry is the whole match,1` the first parentheses-enclosed group, etc).
You need to use rounded brackets around the part you want to keep.
i.e. "Test([0-9]*).txt"
The syntax for replacing these bracketed groups varies between programs, but you'll probably find you can use \1 , something like this:
s/Test(0-9*).txt/Output\1.txt/
If you're using a unix shell, then 'sed' might be your best bet for performing the transformation.
http://www.grymoire.com/Unix/Sed.html#uh-4
Hope that helps
for file in Test[0-9]*.txt;
do
num=${file//[^0-9]/}
process $file > "Output${num}.txt"
done