I am currently working on a little script for the "nslookup"-command and in my testing I encountered a problem I don't understand. In my script a .txt file is automatically created and the user can input some text to it if he wishes to. He can also delete specific lines in the document. I tried writing it with "sed" but it doesn't seem to be working correctly.
Here the menu from the terminal output:
Domains:
1) new_domain
2) domain
3) Create new Domain
4) Delete a Domain
5) Quit
Input>
The first two numbers also representing the line of each text.
The code for deleting a domain is the following:
filename=domains.txt
old_filename=domains_backup.txt
read -p "Which domain-number shall be deleted?: " num_input
mv $filename $old_filename
sed "/$num_input/d" < $old_filename > $filename
rm $old_filename
But when executing that script and the user wants to delete line 2 (domain) the text-file remains the same and is not updated.
When I try the same only using the terminal everything works fine.
Is there something I'm missing?
To delete a line by its line number you will want to use $num_input d rather than /$num_input/d : the second one matches lines that contain $num_input.
As a side note, if you use GNU sed you could let it handle the backup :
sed -i.backup "$num_input d" domains.txt
This would create a copy of the untouched domains.txt as domains.txt.backup (or whatever suffix you specify after -i) and update the domains.txt file.
Related
I made a shell script the purpose of which is to find files that don't contain a particular string, then display the first line that isn't empty or otherwise useless. My script works well in the console, but for some reason when I try to direct the output to a .txt file, it comes out empty.
Here's my script:
#!/bin/bash
# takes user input.
echo "Input substance:"
read substance
echo "Listing media without $substance:"
cd media
# finds names of files that don't feature the substance given, then puts them inside an array.
searchresult=($(grep -L "$substance" *))
# iterates the array and prints the first line of each - contains both the number and the medium name.
# however, some files start with "Microorganisms" and the actual number and name feature after several empty lines
# the script checks for that occurence - and prints the first line that doesnt match these criteria.
for i in "${searchresult[#]}"
do
grep -m 1 -v "Microorganisms\|^$" $i
done >> output.txt
I've tried moving the >>output.txt to right after the grep line inside the loop, tried switching >> to > and 2>&1, tried using tee. No go.
I'm honestly feeling utterly stuck as to what the issue could be. I'm sure there's something I'm missing, but I'm nowhere near good enough with this to notice. I would very much appreciate any help.
EDIT: Added files to better illustrate what I'm working with. Sample inputs I tried: Glucose, Yeast extract, Agar. Link to files [140kB] - the folder was unzipped beforehand.
The script was given full permissions to execute. I don't think the output is being rewritten because even if I don't iterate and just run a single line of the loop, the file is empty.
I am new to Shellscripting.I am working on a poc in which a script should read a log file and then append to a existing file for the purpose of alert.It should work as per below
There will be some predefined format according to which it will decide whether to append in file or not.For example:
WWXXX9999XS message
**XXX** - is a 3 letter acronym (application code) like for **tom** for tomcat application
9999 - is a 4 numeric digit in the range 1001-1999
**E or X** - For notification X ,If open/active alerts already existing for same error code and same message,new alerts will not be raised for existing one.Once you have closed existing alerts,it will raise alarm for new error.There is any change in message for same error code from existing one, it will raise a alarm even though open/active alerts present.
X option is only for drop duplicates on code and message otherwise all alert mechanisms are same.
**S** - is the severity level, I.e 2,3
**message** - is any text that will be displayed
The script will examine the log file, and look for error like cloud server is down,then it would append 'wwclo1002X2 cloud server is down'if its a new alert.
2.If the same alert is coming again,then it should append 'wwclo1002E2 cloud server is down
There are some very handy commands you can use to do this type of File manipulation. I've updated this in response to your comment to allow functionality that will check if the error has already been appended to the new file.
My suggestion would be that there is enough functionality here to warrant saving it in a bash script.
My approach would be to use a combination of less, grep and > to read and parse the file and then append to the new file. First save the following into a bash script (e.g. a file named script.sh)
#!/bin/bash
result=$(less $1 | grep $2)
exists=$(less $3 | grep $2)
if [[ "$exists" == "$result" ]]; then
echo "error, already present in file"
exit 1
else
echo $result >> $3
exit 0
fi
Then use this file in the command passing in the log file as the first argument, the string to search for as the second argument and the target results file as the third argument like this:
./script.sh <logFileName> "errorToSearchFor" <resultsTargetFileName>
Don't forget to run the file you will need to change the permissions - you can do this using:
chmod u+x script.sh
Just to clarify as you have mentioned you are new to scripting - the less command will output the entire file, the | command (an unnamed pipe) will pass this output to the grep command which will then search the file for the expression in quotes and return all lines from the file containing that expression. The output of the grep command is then appended to the new file with >>.
You may need to tailor the expression in quotes after grep to get exactly the output you want from the log file.
The filenames are just placeholders, be sure to update these with the correct file names. Hope this helps!
Note updated > to >> (single angle bracket overwrites, double angle bracket appends
I am trying to iterate through every file in a specific directory (called sequences), and perform two functions on each file. I know that the functions (the 'blastp' and 'cat' lines) work, since I can run them on individual files. Ordinarily I would have a specific file name as the query, output, etc., but I'm trying to use a variable so the loop can work through many files.
(Disclaimer: I am new to coding.) I believe that I am running into serious problems with trying to use my file names within my functions. As it is, my code will execute, but it creates a bunch of extra unintended files. This is what I intend for my script to do:
Line 1: Iterate through every file in my "sequences" directory. (All of which end with ".fa", if that is helpful.)
Line 3: Recognize the filename as a variable. (I know, I know, I think I've done this horribly wrong.)
Line 4: Run the blastp function using the file name as the argument for the "query" flag, always use "database.faa" as the argument for the "db" flag, and output the result in a new file that is has the same name as the initial file, but with ".txt" at the end.
Line 5: Output parts of the output file from line 4 into a new file that has the same name as the initial file, but with "_top_hits.txt" at the end.
for sequence in ./sequences/{.,}*;
do
echo "$sequence";
blastp -query $sequence -db database.faa -out ${sequence}.txt -evalue 1e-10 -outfmt 7
cat ${sequence}.txt | awk '/hits found/{getline;print}' | grep -v "#">${sequence}_top_hits.txt
done
When I ran this code, it gave me six new files derived from each file in the directory (and they were all in the same directory - I'd prefer to have them all in their own folders. How can I do that?). They were all empty. Their suffixes were, ".txt", ".txt.txt", ".txt_top_hits.txt", "_top_hits.txt", "_top_hits.txt.txt", and "_top_hits.txt_top_hits.txt".
If I can provide any further information to clarify anything, please let me know.
If you're only interested in *.fa files I would limit your input to only those matching files like this:
for sequence in sequences/*.fa;
do
I can propose you the following improvements:
for fasta_file in ./sequences/*.fa # ";" is not necessary if you already have a new line for your "do"
do
# ${variable%something} is the part of $variable
# before the string "something"
# basename path/to/file is the name of the file
# without the full path
# $(some command) allows you to use the result of the command as a string
# Combining the above, we can form a string based on our fasta file
# This string can be useful to name stuff in a clean manner later
sequence_name=$(basename ${fasta_file%.fa})
echo ${sequence_name}
# Create a directory for the results for this sequence
# -p option avoids a failure in case the directory already exists
mkdir -p ${sequence_name}
# Define the name of the file for the results
# (including our previously created directory in its path)
blast_results=${sequence_name}/${sequence_name}_blast.txt
blastp -query ${fasta_file} -db database.faa \
-out ${blast_results} \
-evalue 1e-10 -outfmt 7
# Define a file name for the top hits
top_hits=${sequence_name}/${sequence_name}_top_hits.txt
# alternatively, using "%"
#top_hits=${blast_results%_blast.txt}_top_hits.txt
# No need to cat: awk can take a file as argument
awk '/hits found/{getline;print}' ${blast_results} \
| grep -v "#" > ${sequence_name}_top_hits.txt
done
I made more intermediate variables, with (hopefully) meaningful names.
I used \ to escape line ends and allow putting commands in several lines.
I hope this improves code readability.
I haven't tested. There may be typos.
You should be using *.fa if you only want files with a .fa ending. Additionally, if you want to redirect your output to new folders you need to create those directories somewhere using
mkdir 'folder_name'
then you need to redirect your -o outputs to those files, something like this
'command' -o /path/to/output/folder
To help you test this script out, you can run each line one by one to test them. You need to make sure each line works by itself before combining.
One last thing, be careful with your use of colons, it should look something like this:
for filename in *.fa; do 'command'; done
What I'm basically trying to do is automatically detect if there is text in a line, and if so create a new variable containing the text in said line , within a script. If there is no text in a line then the variable doesn't get created. I can do this manually by opening the file -
$ cat file.txt
sometxt
somemoretext
evenmoretext
...
then adding to my script the appropriate lines -
TXT=file.txt
VAR1=$(sed -n 1p $TXT)
VAR2=$(sed -n 2p $TXT)
...
but this is a pain since I have to count how many lines there are total, then copy and paste each line assigning the variables and changing 'VAR!' to 'VAR2' and '1p' to '2p'. There has to be an easier way. Thanks
#JNevil thanks for pointing me in the right direction.
Heres what ended up working for me -
for var_name in (cat links.txt); do
wget <servername.com>$var_name
done
Still dont know how to use curl but this worked fine!
I'm totally new to bash scripting but i want to solve this problem..
the command is:
objfil=`echo ${srcfil} | sed -e "s,c$,o,"`
the idea about the bash script program is to check for the source files, and check if there is an adjacent object file in the OBJ directory, if so, the rest of the program runs smoothly, if not, the iteration terminates and skips the current source file, and moves on to the next one.. it works with .c files but not on the headers, since the object filenames depend on .c files.. i want to write this command so it checks the object files not just the .c but the .h files too.. but without skipping them. i know i have to do something else too, but i need to understand what this line of command does exactly to move on. Thanks. (Sorry for my english)
UPDATE:
if test -r ${curOBJdir}/${objfil}
then
cp -v ${srcfil} ./SAVEDSRC/${srcfil}
fdone="NO"
linenums=ALL
else
fdone="YES"
err="${curOBJdir}/${objfil} is missing - ${srcfil} skipped)"
echo ${err}
echo ${err} >>${log}
fi
while test ${fdone} == "NO"
do
#rest of code ...
here is the rest of the program.. i tried to comment out the "test" part to ignore the comparison just because i only want my script to work on .h files, but without checking the e.g abc.h files has an abc.o file.. (the object file generation is needed because the end of the script there's a comparison between the hexdump of the original and modified object files). The whole script is for changing the basic types with typedefs like int to sint32_t for example.
This concrete command will substitute all c's right before line-end to o:
srcfill=abcd.c
objfil=`echo ${srcfil} | sed -e "s,c$,o,"`
echo $objfil
Output:
abcd.o
P.S. It uses a different match/replace separator: default is / but it uses ,.