I'm trying to perform quality control of rna seq data in rna seq analysis. I am using miniconda on a mac.
I have set up fastqc however I don't know the command to run a fastqc file.
I have tried fastqc SRR8668774.fastq-009.gz but it doesn't seem to work.
Thankyou.
Related
First of all, I'm using Ubuntu 20.04 and Python 3.8.
I would like to run a program that takes command line inputs. I managed to start the program from python with the os.system() command, but after starting the program it is impossible to send the inputs. The program in question is a product interface application that uses the CubeSat Space Protocol (CSP) as a language. However, the inputs used are encoded in a .c file with their corresponding .h header.
In the shell, it looks like this:
starting the program
In python, it looks like this:
import os
os.chdir('/home/augustin/workspaceGS/gs-sw-nanosoft-product-interface-application-2.5.1')
os.system('./waf')
os.system('./build/csp-client -k/dev/ttyUSB1')
os.system('cmp ident') #cmp ident is typically the kind of command that does not work on python
The output is the same as in the shell but without the "cmp ident output", that is to say it's impossible for me to use the csp-client#
As you can probably see, I'm a real beginner trying to be as clear and precise as possible. I can of course try to give more information if needed. Thanks for your help !
It sounds like the pexpect module might be what you're looking for rather than using os.system it's designed for controlling other applications and interacting with them like a human is using them. The documentation for it is available here. But what you want will probably look something like this:
import pexpect
p = pexpect.spawnu("/home/augustin/workspaceGS/gs-sw-nanosoft-product-interface-application-2.5.1/build/csp-client -k/dev/ttyUSB1")
p.expect("csp-client")
p.sendline("cmp indent")
print(p.read())
p.close()
I'll try and give you some hints to get you started - though bear in mind I do not know any of your tools, i.e. waf or csp-client, but hopefully that will not matter.
I'll number my points so you can refer to the steps easily.
Point 1
If waf is a build system, I wouldn't keep running that every time you want to run your csp-client. Just use waf to rebuild when you have changed your code - that should save time.
Point 2
When you change directory to /home/augustin/workspaceGS/gs-sw-nanosoft-product-interface-application-2.5.1 and then run ./build/csp-client you are effectively running:
/home/augustin/workspaceGS/gs-sw-nanosoft-product-interface-application-2.5.1/build/csp-client -k/dev/ttyUSB1
But that is rather annoying, so I would make a symbolic link to that that from /usr/local/bin so that you can run it just with:
csp-client -k/dev/ttyUSB1
So, I would make that symlink with:
ln -s /home/augustin/workspaceGS/gs-sw-nanosoft-product-interface-application-2.5.1/build/csp-client /usr/local/bin/csp-client
You MAY need to put sudo at the start of that command. Once you have that, you should be able to just run:
csp-client -k/dev/ttyUSB1
Point 3
Your Python code doesn't work because every os.system() starts a completely new shell, unrelated to the previous line or shell. And the shell that it starts then exits before your next os.system() command.
As a result, the cmp ident command never goes to the csp-client. You really need to send the cmp ident command on the stdin or "standard input" of csp-client. You can do that in Python, it is described here, but it's not all that easy for a beginner.
Instead of that, if you just have aa few limited commands you need to send, such as "take a picture", I would make and test complete bash scripts in the Terminal, till I got them right and then just call those from Python. So, I would make a bash script in your HOME directory called, say csp-snap and put something like this in it:
#/bin/bash
# Extend PATH so we can find "/usr/local/bin/csp-client"
PATH=$PATH:/usr/local/bin
{
# Tell client to take picture
echo "nanoncam snap"
# Exit csp-client
echo exit
} | csp-client -k/dev/ttyUSB1
Now make that executable (only necessary once) with:
chmod +x $HOME/csp-snap
And then you can test it with:
$HOME/csp-snap
If that works, you can copy the script to /usr/local/bin with:
cp $HOME/csp-snap /usr/local/bin
You may need sudo at the start again.
Then you should be able to take photos from anywhere just with:
csp-snap
Then your Python code becomes easy:
os.system('/usr/local/bin/csp-snap')
I’ve searched and read many posts but none actually describe what I would like to do. Using Debian Stretch, I’ve been trying to create a Python 3 program that runs what would otherwise be a typed command with switches at the gnome terminal. This is how it should run:
Double click the created *.py file that contains the code for the program.
The gnome terminal appears and the command/switches appear after the $ and then the program runs. Some of the switches have zeros (0) which seems to present an issue. Example command:
$ ./binary.bin -j 0 -n 1300
Anyone have any ideas on how I should start to write this program? Any suggestions would be helpful. Thank you.
export_graphviz(treeclf, out_file='tree_titanic.dot', feature_names=feature_cols)
At the command line, run this to convert to PNG:
dot -Tpng tree_titanic.dot -o tree_titanic.png
I am using the above code, but when I try to run the (dot command) in the terminal, it doesn't work. How can I run this command in jupyter to visualize the tree? Thanks.
You can run terminal commands in jupyter by putting a ! before the command. For example:
! dot -Tpng tree_titanic.dot -o tree_titanic.png
You'll probably need to have Graphviz installed on your system in order to have the dot program.
You can then use the display sub-module in jupyter/ipython to display the image off the local file system.
I would like to view the source code for a Linux command to see what is actually going on inside each command. When I attempt to open the commands in /bin in a text/hex editor, I get a bunch of garbage. What is the proper way to view the source on these commands?
Thanks in advance,
Geoff
EDIT:
I should have been more specific. Basically I have a command set that was written by someone who I can no longer reach. I would like to see what his command was actually doing, but without a way to 'disassemble' the command, I am dead in the water. I was hoping for a way to do this within the OS.
Many of the core Linux commands are part of the GNU core utils. The source can be found online here
The file you are opening is the binary executables which are the stuff the kernel passes to the CPU. These files are made using a compiler that takes in the source code you and I understand and turns it via a number of stages into this CPU friendly format.
You can find out the system calls that are being made using strace
strace your_command
Most likely you can download the source code with your distribution's package manager. For example, on Debian and related distros (Ubuntu included), first find which package the command belongs to:
$ dpkg -S /bin/cat
coreutils: /bin/cat
The output tells you that /bin/cat is in the coreutils package. Now you can download the source code:
apt-get source coreutils
This question is related to reverse engineering.
Some keyword is static analysis and dynamic analysis
use gdb to check that the binary file have symbol table inside or not. (if binary compile with debugging flag, you can get the source code and skip below step)
observe program behavior by strace/ltrace.
write seudo-code by use objdump/ida-pro or other disassembler.
run it by gdb to dynamic analysis and correct the seudo-code.
A normal binary file can be reverted back to source code if you want and have time. Conversely, an abnormal program is not easy to do this, but it only appear on specific ctf competition. (Some special skill like strip/objcopy/packer ... etc)
You can see assembly code of /bin/cat with:
objdump -d /bin/cat
Then analyze it and see what command can be launch.
Another way of approaching is strings /bin/cat, it is usefull make a initial idea and then reverse it.
You can get the source code of every linux command online anyway :D
everyone, I am a fresh here as well as to linux
i want to use the intel pin tool to help me count the instructions executed in a quick sort program, just a homework, but when i did this as the readme document told me, like
cd source/tools/SimpleExamples
make obj-ia32/opcodemix.so
the system told me
make: * No rule to make target `obi-ia32/opcodemix.so'. Stop.
and i also tried obj-intel64,nothing changed.
can anybody tell me what is going on here, i am really confused with this pin stuff.
cd pintool/source/tools/ManualExamples
type command as
make inscount0.test
this commnad compile and show you the out put file then use following command on same directory
../../../pin -t obj-ia32/inscount0.so -- /bin/ls
this will make .so file after that see the ouput by using following command
cat inscount.out
I can't tell exactly what your question is. Format your commands with the code and separate them line by line, so I can know what you executed.
Anyway, if I'm right, you should just type:
make
(without targets) in under source/tools/ManualExamples, and it should build them all.