I have a problem with writing the output of a program to a different directory when I loop different files as variables as inputs. I run this in the command line. The problem is that I do not know how to "tell" the program to put the output with a changed filename into another directory than the input directory.
Here is the command, although it is a bioinformatic tool which requires specific input file formats. I am sorry that I could not give a better example. Nonetheless, the program is called computeMatrix in a software-tool box called deeptools2.
command:
for f in ~/my/path/*spc_files*; do computeMatrix reference-point--referencePoint center --regionsFileName /target/region.bed --binSize 500 --scoreFileName "$f" **--outFileName "$f.matrix"** ; done \
So far, I tried to use the command basename to just get the filename and then change the directory before that. However I could not figure out:
if this is combinable
what is the correct order of the commands (e.g.:
outputFile='basename"$f"', "~/new/targetDir/'basename$f'")
Probably there are other options to solve the problem which I could not think of/ find.
Related
I'm trying to run a command that takes one location input (intended for a single directory of files), but I need to run it on files in several locations. While I'd normally run it on */*.type, I'm looking for some way to run the command over (*/dirA/*.type AND dirB/*.type).
I basically need all files of *.type within a directory structure, but they're not all at the same directory level (or I'd just do */*/*.type or something to grab them all). Unfortunately they're in a particular layout for a reason, which I can't just reorganize to make this command run.
Is there any bash shortcut/command/whatever-it's-called that I could use to get both sets of files at once?
you can say
dir{A,B}/*.type
For example running this with ls command
root#do:/tmp# ls dir{A,B}/*.type
dirA/test.type dirB/test.type
If the command works when you pass one wildcard in, that means it is expecting a list of file names. In that case you can pass it two wildcards just as easily.
command */dirA/*.type dirb/*.type
I'm trying to get this code to process all files in a directory : https://github.com/kieranjol/ifi-ffv1/blob/master/ifi-ffv1.sh
I run it in the terminal and add path to file ./ifi-ffv1.sh /path/to/file.mov. How can I get it to move on to the next? I'll also need to make sure that it only processes AV files, such as .avi/.mkv/*.mov etc.
I've tried using while loops with shift but I can't get that to work either.
I've tried adding a specific path like here but I'm failing http://www.cyberciti.biz/faq/unix-loop-through-files-in-a-directory/
I've tried this https://askubuntu.com/a/315338 and it keeps looping the same file rather than moving on to the next one. http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO-7.html this didn't help me either.
I know this is going to be a horribly simple solution but I'm very new to this.
You don't actually have any kind of loop in your code. You need to do something like
for file in path/to/*.avi path/to/*.avg
do
./ifi-ffv1.sh "$file"
done
which will loop through all the specified files and substitute each one for $1
You can put whatever file names you want instead of the path/to/*.avi path/to/*.avg. If you cd to the directory first, you can leave out the paths, and just use *.avi *.avg
To do it all in one script, do something like this:
cd <your directory>
for file in *.avi *.avg
do
<your existing script here>
done
replacing all the $1's in your script with "$file" (not duplicating any quotes you already have, of course)
Can the shell override where output files are placed? (Not the console/screen output, but files created by a program.) I have a script that currently runs a sequence of input files through a program and for each one produces a lot of different output files.
for i in `seq 1 24`
do
../Bin/myprog inputfile.$i.in
done
Is there a way to create new directories for each run of the program and place the corresponding output files in each directory? So I would get dir1: <output files from run 1>; dir2 <output files from run 2> etc. I suppose one way would be to just write another script to create directories and sort all the files after the program(s) had run, but is there a more elegant way to do it?
As suggested in the comments, this might be what you need, assuming that your program just dumps output into the current working directory.
for i in `seq 1 24`
do
mkdir $i
pushd $i
../../Bin/myprog ../inputfile.$i.in
popd
done
If you are trying to change where an existing program (e.g., myprog) writes its files, this is only possible if the program writes its files relative to the current directory. In this case, the outer script that invokes myprog, can create a "destination" directory and chdir to it before invoking myprog.
If the myprog program writes to an absolute path, e.g., /var/tmp/myprog.tmp, the only way to override where this write actually goes is to place a symbolic link at the absolute path linking to the desired destination. This will only work if the program (myprog) doesn't first delete an existing file before writing to it.
The third and most extreme possibility for directing absolute file path writes is to create a chroot'ed file system, in which the myprog output files will be contained, after which the outer script can copy or move them to where they are desired.
To summarize: other than changing the source, setting the working directory for relative-path output files, or chrooting a filesystem for absolute-path files, there really is no "elegant" way to replace the actual output files used in a program.
I installed Strawberry Perl to run the rouge program in Windows. But when I want to run my program, I receive an error message that you can see on the image:
The system can't find the path specified.
My code is attempting to run "ROUGE-1.5.5.pl" but i think the system can't find this file. So I think maybe I don't initialize the path correctly?
I change my code to :
#!/usr/bin/perl
use Cwd;
$curdir=getcwd;
$ROUGE="..\ROUGE-1.5.5.pl";
chdir("sample-test");
$cmd="$ROUGE -e ..\data -c 95 -2 -1 -U -r 1000 -n 4 -w 1.2 -a DUC2002-ROUGE.in.26.spl.xml > ..\sample-output\output.out";
print $cmd,"\n";
system($cmd);
chdir($curdir);
and i receive this error:
Missing braces on \o{} at C:\runROUGE-test.pl line 7, near "$ROUGE" Execution of C:\runROUGE-test.pl aborted due to compilation errors.
As per the screen shot, you are attempting to run \ROUGE-1.5.5.pl where you probably want it without the spurious backslash (or with ..\ROUGE-1.5.5.pl if the parent directory is not on your PATH).
Similarly, you probably want the output in sample-output\output.out, or even just output.out, not \sample-output\output.out unless you specifically have a folder C:\sample-output for this purpose.
The backslash is significant; it is the absolute path to the root (of the current drive, on Windows). ..\ is the relative path to the parent folder.
Why are you writing a Perl script to run a Perl script, though? Either a simple batch file, or copy/pasting the command directly at the DOS prompt would seem like a less roundabout solution.
The problem is that when you are outputting the contents of the program to the file output.out in folder sample-output, the sample-output folder does not exist.
Command Prompt will not create the folders for you, only the files. Try creating a directory first called "sample-output" (In your drive root) such that the path resolves to something like C:\sample-output and run it again.
If the same problem results, try using an absolute path such as C:\sample-output\output.out instead.
I am using PVRTexTool to convert png files to pvr files but the tool seems to only be able to run on one file at a time(wont accept *.png as file name).
does anyone know how to run it on a group of files at once?
Its really a hassle to run it on all of my textures.
In a shell, run
for file in *.png ; do
PVRTexToll $file
done
(I don't know how to call PVRTeXTool from a command line, so please substitute the second line with a correct version)
This is a general way to feed each file to a command which only accepts one file at a time. See any introduction on shell scripting, e.g. this discussion of the for loop.