ERANGE - getsplicefa.py

[sylee]

Hi, All..
I have a question related to "ERANGE" for RNA-seq analysis.

I got an empty file after running the "getsplicefa.py" script..

the following messege :

psyco not running
/B/sylee/ERANGE/commoncode/getsplicefa.py: version 3.2
60922
545588
10000enes
20000enes
30000enes
40000enes
50000enes
60000enes
3310 splices too short to be seen
634 splices will be under-reported


Any help is appreciable!
Thank you.
- sunyoung

[David]

What was your exact command?

[sylee]

I typed ..
$python getsplicefa.py human ~/genome_data/hg18/knownGene.txt hg18splice36.fa 32

Thank you!

[David]

That looks correct. I would check your variables to make sure that they are pointing to the proper directories. PYTHONPATH and CISTEMATIC_ROOT should both be pointing to one directory above your Cistematic directory.

[yh253]

Hi sylee,

Just wondering have you solved your problem?

I got the same problem as you that getsplicefa.py generated an empty file even I did check according to David's point.

Appreciate any commons.

[sylee]

sorry for late reply,..

yh253, I also haven't solved the problem yet..
David, PYTHON PATH and CISTEMATIC_ROOT were pointed to one directory above the Cistematic directory. but, I got empty file ...

regards,

[yh253]

Sylee,

The problem is you should change the genome from 'human' to 'hsapiens' if you use Cistematic-3.0

Try:

$python getsplicefa.py hsapiens ~/genome_data/hg18/knownGene.txt hg18splice36.fa 32

Make sure: $PATHONPATH indicates where you keep all the ERANGE python script; and $CISTEMATIC_ROOT points to where you keep the 'H_sapiens' genome (downloaded from Cistematic website).