I have a c program. I compiled it using gcc. After running the executable file. I saved the output to a separate file.
$ ./a.out > outputs
Then I compiled another program and ran it. I directed to output to the same output file where it erased the old content and wrote the new content. How do i direct all the outputs to the same file with out erasing the previous content.
output redirection > in the ./a.out > outputs will create a new file(outputs) every time. Instead of that use
./a.out >> outputs
>> will append new data to old one every time.
Related
I am using a third-party C++ program to generate intermediate results for the python program that I am working on. The terminal command that I use looks like follows, and it works fine.
./ukb/src/ukb_wsd --ppr_w2w -K ukb/scripts/wn30g.bin -D ukb/scripts/wn30_dict.txt ../data/glass_ukb_input2.txt > ../data/glass_ukb_output2w2.txt
If I break it down into smaller pieces:
./ukb/src/ukb_wsd - executable program
--ppr_w2w - one of the options/switches
-K ukb/scripts/wn30g.bin - parameter K indicates that the next item is a file (network file)
-D ukb/scripts/wn30_dict.txt - parameter D indicate that the next item is a file (dictionary file)
../data/glass_ukb_input2.txt - input file
> - shell command to write the output to a file
../data/glass_ukb_output2w2.txt - output file
The above works fine for one instance. I am trying to do this for around 70000 items (input files). So found a way by using the subprocess module in Python. The body of the python function that I created looks like this.
with open('../data/glass_ukb_input2.txt', 'r') as input, open('../data/glass_ukb_output2w2w_subproc.txt', 'w') as output:
subprocess.run(['./ukb/src/ukb_wsd', '--ppr_w2w', '-K', 'ukb/scripts/wn30g.bin', '-D', 'ukb/scripts/wn30_dict.txt'],
stdin=input,
stdout=output)
This error is no longer there
When I execute the function, it gives an error as follows:
...
STDOUT = subprocess.STDOUT
AttributeError: module 'subprocess' has no attribute 'STDOUT'
Can anyone shed some light about solving this problem.
EDIT
The error was due to a file named subprocess.py in the source dir which masked Python's subprocess file. Once it was removed no error.
But the program could not identify the input file given in stdin. I am thinking it has to do with having 3 input files. Is there a way to provide more than one input file?
EDIT 2
This problem is now solved with the current approach:
subprocess.run('./ukb/src/ukb_wsd --ppr_w2w -K ukb/scripts/wn30g.bin -D ukb/scripts/wn30_dict.txt ../data/glass_ukb_input2.txt > ../data/glass_ukb_output2w2w_subproc.txt',shell=True)
I'm trying to follow this tutorial in abinit: https://docs.abinit.org/tutorial/paral_images/
When trying to run abinit for any of the tstring files, no output file is produced. For instance, I copy the files tstring_01.in and tstring.files into the subdirectory work_paral_string, edit the tstring.files with the appropriate file names, and run the command mpirun -n 20 abinit < tstring.files > log 2> err. No error message is shown but also no output is produced. (The expected output file would be tstring_01.out.)
Any suggestions?
How do I rewrite the following to properly replace the variable with my genomeID? (I have it working with this method in Spades and Masurca assemblers, so it's something about Abyss that doesnt like this approach and I need a work-around)
I am trying to run abyss on a cluster server but am running into trouble with how abyss-pe is reading my variable input:
my submit file loads a script for each genome listed in a .txt file
my script writes in the genome name throughout the script
the abyss assembly fumbles the variable replacement
Input.sub:
queue genomeID from genomelisttest.txt
Input.sh:
#!/bin/bash
genomeID=$1
cp /mnt/gluster/harrow2/trim_output/${genomeID}_trim.tar.gz ./
tar -xzf ${genomeID}_trim.tar.gz
rm ${genomeID}_trim.tar.gz
for k in `seq 86 10 126`; do
mkdir k$k
abyss-pe -C k$k name=${genomeID} k=$k lib='pe1 pe2' pe1='../${genomeID}_trim/${genomeID}_L1_1.fq.gz ../${genomeID}_trim/${genomeID}_L1_2.fq.gz' pe2='../${genomeID}_trim/${genomeID}_L2_1.fq.gz ../${genomeID}_trim/${genomeID}_L2_2.fq.gz'
done
Error that I get:
`../enome_trim/enome_L1_1.fq.gz': No such file or directory
This is where "enome" is supposed to replace with a five digit genomeID, which happens properly in the earlier part of the script up to this point, where abyss comes in.
pe1='../'"$genomeID"'_trim/'"$genomeID"'_L1_1.fq.gz ...'
I added a single quote before and after the variable
I execute a program which print some texts. I redirect the texts to file by using > but I cannot see any texts on the file. For example, if the program prints "Hello" I can see the result on the shell:
$ ./a.out arg
Hello
But after I redirect I cannot get any message hello on shell as well as the redirected file.
$ ./a.out arg > log.txt
(print nothing)
$ cat log.txt
(print nothing)
I have no idea what's going on. Is there someone who knows what's happening here? Or is there someone who suffered similar situation?
OS: Ubuntu 14.10, x86_64 arch, and the program is really chromium-browser rather than ./a.out. I edited its JavaScript engine (v8, which is included in chromium-browser) and I tried to print some logs with lots of texts. I tried to save it by redirection but it doesn't work.
Surely I checked whether > symbol work or not. It works as expected on other programs like echo, ls, and so on.
$ echo hello > hello.txt
$ cat hello.txt
hello
How can the messages just go away? I think it should be printed on stdout (or stderr) or file. But it just goes away when I use > symbol.
It is somewhat common for programs to check isatty(stdout) and display different output based on whether stdout is connected to a terminal or not. For example, ls will display file names in a tabular format if output is to a terminal, but display them strictly one per line otherwise. It does this to make it easy to parse its output when it's part of a pipeline.
Not having looked at Chrome's source code myself, this is speculation, but it's possible Chrome is performing this sort of check and changing its output based on where stdout is redirected to.
Try to use "2>" which should redirect stderr to file
Or you can also try to use "&>" which should redirect everything (stderr and stdout)
See more at http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO-3.html
i want input from a file for my user process and store the result in another file . i have done like:
$ ./a.out < inputFile.txt > outputFile.txt
this is working for me . but i m worried about redirection , for example what if inputFile.txt contents got redirected to outputFile.txt and then it is made availble to a.out.
i wanted to know is there any order for evaluation or atleast how the shell interprets the above lines.
You can only redirect live entity to dead entity. You cannot redirect dead entity to live entity.
In your case file is dead entity. and ./a.out is live entity (which is a running process).
You can redirect ./a.out to file, but the reverse is not possible.
$ ./a.out > file #should work
$ ./a.out < file #will execute a.out and will not redirect file to ./a.out