ERANGE - getsplicefa.py

sylee · 04-08-2010, 10:02 PM

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 · 06-29-2010, 09:31 AM

What was your exact command?

sylee · 06-29-2010, 04:22 PM

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

Thank you!

David · 06-30-2010, 04:25 AM

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 · 07-20-2010, 03:03 PM

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 · 07-20-2010, 04:42 PM

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 · 07-22-2010, 07:50 AM

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).

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04-08-2010, 10:02 PM	#1
sylee Junior Member Location: south korea Join Date: Apr 2010 Posts: 3	ERANGE - getsplicefa.py 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

06-29-2010, 09:31 AM	#2
David Junior Member Location: Baltimore Maryland Join Date: Jul 2009 Posts: 5	What was your exact command?

06-29-2010, 04:22 PM	#3
sylee Junior Member Location: south korea Join Date: Apr 2010 Posts: 3	I typed .. $python getsplicefa.py human ~/genome_data/hg18/knownGene.txt hg18splice36.fa 32 Thank you!

06-30-2010, 04:25 AM	#4
David Junior Member Location: Baltimore Maryland Join Date: Jul 2009 Posts: 5	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.

07-20-2010, 03:03 PM	#5
yh253 Member Location: Ireland Join Date: Jul 2009 Posts: 16	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.

07-20-2010, 04:42 PM	#6
sylee Junior Member Location: south korea Join Date: Apr 2010 Posts: 3	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,

07-22-2010, 07:50 AM	#7
yh253 Member Location: Ireland Join Date: Jul 2009 Posts: 16	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).