I want to make a loop to run over multiple input files and produce one output file per input file.
I can use this command to make 1 output bam files, from 1 input sam file:
samtools view -S -b -h $input_file > $output_file
where:
input_file="/scratch/RNAseq/hisat2_alignment/456.sam"
output_file="/scratch/RNAseq/BAM_files/raw_BAM/456.bam"
When making this command into a loop I am unsure of what to do with the $output_file equivalent. Because I don't know how to make the file path and file extension change required for the $many_output_file variable:
many_input_files="/scratch/RNAseq/hisat2_alignment/*.sam"
for i in $many_input_files
do
samtools view -S -b -h $i > $many_output_file
done
Can anyone help please? I am new to Bash, I usually use R. I have tried using sed and tr but they seem to come up with errors when I try to make the file list of many_output_file from many_input_files
This is how I made the loop work, thanks to the help in the comments:
for i in $input_files
do
tmp=${i/hisat2_alignment/BAM_files/raw_BAM}
samtools view -S -b -h $i > ${tmp/.sam/.bam}
done
Related
I need to creat a bash file in order to run a certain command on a server.
Here is one of the lines
Programm/programm.pl -k 1 -q --acc_number
where --acc_number needs a Comma-separated list of accession numbers, e.g. --acc_number Number13JJ2,Number0090D93,Number088DF.
but I actually have a file calle file_acc_number where I have each of the accession number in line such as :
Number13JJ2
Number0090D93
Number088DF
does someone have an idea how to parse this tab file and to directly put the accessio number in a comma-separated way and get :
Programm/programm.pl -k 1 -q --acc_number Number13JJ2,Number0090D93,Number088DF
Thank you for your help
Try using paste:
Programm/programm.pl -k 1 -q --acc_number `paste -s -d, file_acc_number`
Try running paste -s -d, file_acc_number first to understand whether you get what you require.
with an inline expansion maybe? Like this
Programm/programm.pl -k 1 -q --acc_number $(sed -z 's/\n/,/g' file_acc_number)
Make sure your file "file_acc_number" has no "new line" at the end of it.
With this, you will replace the "new line" character with a comma on the fly without affecting the original file.
I need to create a file that lists all the files in a folder into a text file, along with a comma and the number 15 after. For example
My folder has video.mp4, video2.mp4, picture1.jpg, picture2.jpg, picture3.png
I need the text file to read as follows:
video.mp4,15
video2.mp4,15
picture1.jpg,15
picture2.jpg,15
picture3.png,15
No spaces, just filename.ext,15 on each line. I am using a raspberry pi. I am aware that the command ls > filename.txt would put all the file names into a folder, but how would I get a ,15 after every line?
Thanks
bash one-liner:
for f in *; do echo "$f,15" >> filename.txt; done
To avoid opening the output file on each iteration you may redirect the entire output with > filename.txt:
for f in *; do echo "$f,15"; done > filename.txt
$ printf '%s,15\n' *
picture1.jpg,15
picture2.jpg,15
picture3.png,15
video.mp4,15
video2.mp4,15
This will work if those are the only files in the directory. The format specifier %s,15\n will be applied to each of printf's arguments (the names in the current directory) and they will be outputted with ,15 appended (and a newline).
If there are other files, then the following would work too, regardless of whether there are files called like this or not:
$ printf '%s,15\n' video.mp4 video2.mp4 picture1.jpg picture2.jpg "whatever this is"
video.mp4,15
video2.mp4,15
picture1.jpg,15
picture2.jpg,15
whatever this is,15
Or, on all MP4, PNG and JPEG files:
$ printf '%s,15\n' *.mp4 *.jpg *.png
video.mp4,15
video2.mp4,15
picture1.jpg,15
picture2.jpg,15
picture3.png,15
Then redirect this to a file with printf ...as above... >output.txt.
If you're using Bash, then this will not make use of any external utility, as printf is built into the shell.
You need to do something like this:
#!/bin/bash
for i in $(ls folder_name); do
echo $i",15" >> filename.txt;
done
It's possible to do this in one line, however, if you want to create a script, consider code readability in the long run.
Edit 1: better solution
As #CristianRamon-Cortes suggested in the comments below, you should not rely on the output of ls because of the problems explained in this discussion: why not parse ls. As such, here's how you should write the script instead:
#!/bin/bash
cd folder_name
for i in *; do
echo $i",15" >> filename.txt;
done
You can skip the part cd folder_name if you are already in the folder.
Edit 2: Enhanced solution:
As suggested by #kusalananda, you'd better do the redirection after done to avoid opening the file in each iteration of the for loop, so the script will look like this:
#!/bin/bash
cd folder_name
for i in *; do
echo $i",15";
done > filename.txt
Just 1 command line using 2 msr commands recusively (-r) search specific files:
msr -rp your-dir1,dir2,dirN -l -f "\.(mp4|jpg|png)$" -PAC | msr -t .+ -o '$0,15' -PIC > save-file.txt
If you want to sort by time, add --wt to first command like: msr --wt -l -rp your-dirs
Sort by size? Add --sz but only the prior one is effective if use both --sz and --wt.
If you want to exclude some directory, add like: --nd "^(test|garbage)$"
remove tail \r\n in save-file.txt : msr -p save-file.txt -S -t "\s+$" -o "" -R
See msr.exe / msr.gcc48 etc in my open project https://github.com/qualiu/msr tools directory.
A solution without a loop:
ls | xargs -i echo {},15 > filename.txt
I am trying to to provide a file for my shell as an input which in return should test if the file contains a specific word and decide what command to execute. I am not figuring out yet where the mistake might lie. Please find the shell script that i wrote:
#!/bin/(shell)
input_file="$1"
output_file="$2"
grep "val1" | awk -f ./path/to/script.awk $input_file > $output_file
grep "val2" | sh ./path/to/script.sh $input_file > $output_file
when I input the the file that uses awk everything get executed as expected, but for the second command I don't even get an output file. Any help is much appreciated
Cheers,
You haven't specified this in your question, but I'm guessing you have a file with the keyword, e.g. file cmdfile that contains x-g301. And then you run your script like:
./script "input_file" "output_file" < cmdfile
If so, the first grep command will consume the whole cmdfile on stdin while searching for the first pattern, and nothing will be left for the second grep. That's why the second grep, and then your second script, produces no output.
There are many ways to fix this, but choosing the right one depends on what exactly you are trying to do, and how does that cmdfile look like. Assuming that's a larger file with other things than just the command pattern, you could pass that file as a third argument to your script, like this:
./script "input_file" "output_file" "cmdfile"
And have your script handle it like this:
#!/bin/bash
input_file="$1"
output_file="$2"
cmdfile="$3"
if grep -q "X-G303" "$cmdfile"; then
awk -f ./mno/script.awk "$input_file" > t1.json
fi
if grep -q "x-g301" "$cmdfile"; then
sh ./mno/tm.sh "$input_file" > t2.json
fi
Here I'm also assuming that your awk and sh scripts don't really need the output from grep, since you're giving them the name of the input file.
Note the proper way to use grep for existence search is via its exit code (and the muted output with -q). Instead of the if we could have used shortcircuiting (grep ... && awk ...), but this way is probably more readable.
I know this question has been asked before. However, none of the examples seems to work for me. Hence:
I've got files all of the type
XXXX1.txt
XXXX2.txt
XXXX3.txt
...
XXXX9.txt in the same directory.
Now I want to grep a certain value from each file using bash:
for file in *$i.txt
do
for ((i = 1; i < 10; i++))
do
grep "energy" *.txt >> energies.txt
done
done
The code and grep works fine without any errors, but I always get the grep from the first iteration, the first energy printed 9 times. It never looks at the others. I know these kind of loops are complicated in bash. However, please don't suggest to move all files into separate directories and loop through them.
You don't need such complicated (and wrong) nested loops.
Try this only command:
grep -h "energy" *{1..9}.txt >> energies.txt
if you just need content of file(s):
grep -h "energy" *[1-9].txt >> energies.txt
if you need file name with content:
grep -H "energy" *[1-9].txt >> energies.txt
Specifically, I'm using a combination of >> and tee in a custom alias to store new Homebrew updates in a text file, as well as output on screen:
alias bu="echo `date "+%Y-%m-%d at %H:%M"` \
>> ~/Documents/Homebrew\ Updates.txt && \
brew update | tee -a ~/Documents/Homebrew\ Updates.txt"
Question: What if I wish to prepend this output in my textfile, i.e. placed at the beginning of the file as opposed to appending it to the end?
Edit1: As someone reported in the answers below, the use of temp files might be a good approach, which at least helped me partially:
targetLog="~/Documents/Homebrew\ Updates.txt"
alias bu="(brew update | cat - $targetLog \
> /tmp/out1 && mv /tmp/out1 $targetLog \
&& echo `date "+%Y-%m-%d at %H:%M":%S` | \
cat - $targetLog > /tmp/out2 \
&& mv /tmp/out2 $targetLog)"
But the problem is the output to STDOUT (previously made possible by tee), which I'm not sure can be incorporated in this tempfile approach …?
sed will happily do that for you, using -i to edit in place, eg.
sed -i -e "1i `date "+%Y-%m-%d at %H:%M"`" some_file
This works by creating an output file:
Let's say we have the initial contents on file.txt
echo "first line" > file.txt
echo "second line" >> file.txt
So, file.txt is our 'bottom' text file. Now prepend into a new 'output' file
echo "add new first line" | cat - file.txt > output.txt # <--- Just this command
Now, output has the contents the way we want. If you need your old name:
mv output.txt file.txt
cat file.txt
The only simple and safe way to modify an input file using bash tools, is to use a temp file, eg. sed -i uses a temp file behind the scenes (but to be robust sed needs more).
Some of the methods used have a subtle "can break things" trap, when, rather than running your command on the real data file, you run it on a symbolic link (to the file you intend to modify). Unless catered for correctly, this can break the link and convert it into a real file which receives the mods and leaves the original real file without the intended mods and without the symlink (no error exit-code results)
To avoid this with sed, you need to use the --follow-symlinks option.
For other methods, just be aware that it needs to follow symlinks (when you act on such a link)
Using a temp file, then rm temp file works only if "file" is not a symlink.
One safe way is to use sponge from package moreutils
Unlike a shell redirect, sponge soaks up all its input before
opening
the output file. This allows for constructing pipelines that read from
and write to the same file.
sponge is a good general way to handle this type of situation.
Here is an example, using sponge
hbu=~/'Documents/Homebrew Updates.txt'
{ date "+%Y-%m-%d at %H:%M"; cat "$hbu"; } | sponge "$hbu"
Simplest way IMO would be to use echo and cat:
echo "Prepend" | cat - inputfile > outputfile
Or for your example basically replace the tee -a ~/Documents/Homebrew\ Updates.txt with cat - ~/Documents/Homebrew\ Updates.txt > ~/Documents/Homebrew\ Updates.txt
Edit: As stated by hasturkun this won't work, try:
echo "Prepend" | cat - file | tee file
But this isn't the most efficient way of doing it any more...
Similar to the accepted answer, however if you are coming here because you want to prepend to the first line - rather than prepend an entirely new line - then use this command.
sed -i "1 s/^/string_replacement/" some_file
The -i flag will do a replacement within the file (rather than creating a new file).
Then the 1 will only do the replacement on line 1.
Finally, the s command is used which has the following syntax s/find/replacement/flags.
In our case we don't need any flags. The ^ is called a caret and it is used to represent the very start of a string.
Try this http://www.unix.com/shell-programming-scripting/42200-add-text-beginning-file.html
There is no direct operator or command AFAIK.You use echo, cat, and mv to get the effect.
{ date; brew update |tee /dev/tty; cat updates.txt; } >updates.txt.new
mv updates.txt.new updates.txt
I've no idea why you want to do this. It's pretty standard that logs like this have later entries appearing, well, later in the file.