How to run HTSeq in batch operation

Question

[yangzituo]

Hi everyone, I am new in RNA-seq and Python. Recently, I meet a problem. When I use HTSeq to count my SAM file, I have to do it one by one. So I check in the website and someone say it can be done in batch operation. There is following commands:

for i in *.sam
do
echo $i
./local/bin/htseq-count  $i ./hg19.gtf > $i.count
done

But I cannot use it in my python. Does anyone may help me?? Thanks a lot!!!

[WouterDeCoster]

But I cannot use it in my python.

What does that mean?
If you get an error message, it's very helpful to share that message too.

I have also added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[yangzituo]

sorry, i am new in this fiels, here is the code that guy post:

for i in *.sam:
do
echo $i
.local/bin/ht-seq-count  $i ./hg19.gtf > $i.count

But when I follow him, it stop in line 1:

the system tells me "invalid syntax"

[Devon Ryan]

That's shell scripting code, not python.

[yangzituo]

oh, so it cannot use in the Python?

[WouterDeCoster]

I again added code formatting to your post. See my previous comment on how you can do this yourself next time.

There are a couple of things wrong with that you command.

• There shouldn't be a : after sam
• You didn't add done (while you did include that in the previous command)
• It's also not sure that you htseq-count (which you spelt differently the second time) is in that location. Try which htseq-count
• Same for your hg19.gtf. Is the path specified correctly?

You have to be quite exact when executing commands.

[yangzituo]

thank you. But when I wirte the first code

for i in *.sam

the python tells me that "invalid syntax"

[WouterDeCoster]

That's because, as Devon said, it's not Python code. You execute it just in your terminal (assuming you are using Linux/Mac).

Answer 1

[WouterDeCoster]

You execute it just in your terminal (assuming you are using Linux/Mac).