I'm running a loop for command and I want the output-name to be result of concatenation of variable and a character.
I have the variable d (that is the name of the folder) and want to add S to the end of the output name for file1: d=file1 and I want the name of the output like this: file1S.
When I did -outdir "$d"s the name of the output is just s and I get error msg running the second file
Tell me if more clarification is needed.
Not sure if that's what you are looking for, but if you want to add an "s" to all of your files inside the directory, you can simply run the following loop:
for file in *; do mv $file ${file}s; done
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 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
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 $objfil
Output:
abcd.o
P.S. It uses a different match/replace separator: default is / but it uses ,.
I am writing a bash script that will output a .tgz file to a specific directory, /tmp/ by default
I would like to provide an option to override this directory and I have chosen to do so using arguments provided at the command line
while getopts d: option
do
case "${option}" in
d) dir=${OPTARG};;
esac
done
As written, this works but I've run into a snag depending on user input
The name of my .tgz file is also a variable and my code that brings this all together is
output="$dir""$name"
The problem that I run into is if the user runs
./script -d /home/user
My resulting path and filename end up as
/home/userfilename.tgz
I need to either enforce a requirement for a trailing / or insert one if the user did not.
While it works, if I change my output variable to
output="$dir"/"$name"
If the user does provide a trailing / I end up with something like this and I am trying to keep my output aesthetic.
/home/user//filename.tgz
Any input would be greatly appreciated.
Add the line
output="${output//\/\///}"
after joining dir and name.
It looks complicated, but what it does is it replaces two slashes with one.
You may find more info in here.
I have a list of files that I need to copy. I want to recursively search a drive and copy those files to a set location if that filename exists in the list. The list is a text file/
the text file would look something like this:
A/ART-FHKFX1.jpg
B/BIG-085M.jpg
B/BIG-085XL.jpg
L/LL-CJFK.jpg
N/NRT-56808EA.jpg
P/PFE-25.10.jpg
P/PFE-7/60.jpg
P/PFE-7L.20.jpg
P/PFE-8.25.jpg
P/PFE-9.15.jpg
P/PFE-D11.1.tiff
P/PFE-D11.1.tiff
P/PFE-D12.2.tiff
P/PFE-D12.2.tiff
using find will take a lot of time, try to use locate if possible.
what will happen when there's several matches? like searching for foo.bar and having a/foo.bar and also b/foo.bar what would you do in that case?
your csv seems to include a path, given the previous I'll assume those paths are actually valid from where the script is run so in that case just do this:
#!/bin/bash
while read path; do
cp "$path" "$1"
done
then call it like this:
teh_script /path/to/destination < csv-file.csv