Question: I keep getting this error when running this python script (that I know runs and works since I ran it in VI) within eclipse.

Traceback (most recent call last):
 File "/home/kt/Documents/workspace/Molly's Scripts/src/ProcessingPARFuMSData.py", line 181, in 
 annotations = open(sys.argv[1], 'r')
IOError: [Errno 2] No such file or directory: 'Tarr32\_Lane2\_Next34\_FinalAnnotations.txt'

I double checked to see that all of the txt files that I need to run the script with are included in the specific directory and yet it is still giving me a bit of trouble. I know it has to be something with eclipse or PyDev because like I mentioned previously it works in the other editor. Any help would be appreciated and I can try a screen shot if one is needed.

Thanks,

KT

Answer: 
I had the same issue, but it turned out that my text file was in fact in the wrong place, even though it was in the same directory as my python script. I had to move it into the same *package* as the script, not just the same directory (I did this by simply dragging the text file onto the package name in the sidebar in Eclipse).

So, for example, this is what my setup looked like:

* Hello World (project)
	+ helloworld (package)
		- \_\_init\_\_.py
		- hello\_world.py
	+ hello\_world.txt

Here's what it *should* have looked like (by moving hello\_world.txt into the helloworld package):

* Hello World (project)
	+ helloworld (package)
		- \_\_init\_\_.py
		- hello\_world.py
		- **hello\_world.txt**
Seems you're launching in the wrong dir. You can configure your launch in run > run configurations.