For me line 259 returns a list which causes an error down the line. I replaced it with model = binding_models.get_from_tfname(self.factor)[0] and that seems to work Hi Nathan,
Sure. Another thing is in line 33 of shape.py:
```
prefix = os.path.join(os.path.dirname(__file__), './shape_data/')
```
In my system, the variable 'prefix' will return a path that has '/./' in it. Although it can be fixed by users manually, it would be better to change it in the original script. These are all minor issues and it may only happen in my system. The overall script looks neat :)
Best Hi Lin,
mitra is our internal DB server. I stripped out that dependency so it should work now.
Thanks for reporting this bug - please let me know if you are having additional problems.
Best, Nathan Hi Nathan,
Thanks for sharing the scripts. I encountered an issue when using one of the required dependencies, 'pyDNAbinding'. I noticed that this package is also written by you. So I hope to get some help from you to debug the error below:
```
$ python baseline.py
Traceback (most recent call last):
File "baseline.py", line 23, in
from pyDNAbinding.DB import (
File "/usr/local/lib/python2.7/dist-packages/pyDNAbinding-0.1.1-py2.7-linux-x86_64.egg/pyDNAbinding/DB.py", line 6, in
conn = psycopg2.connect("host=mitra dbname=cisbp")
File "/usr/lib/python2.7/dist-packages/psycopg2/__init__.py", line 164, in connect
conn = _connect(dsn, connection_factory=connection_factory, async=async)
psycopg2.OperationalError: could not translate host name "mitra" to address: Name or service not known
```
What is 'mitra'? I checked DB.py and found it is not defined. The installation process of this package didn't return any errors. So I am thinking maybe I need to provide the detailed path for 'mitra'?
Thanks Hi Amumu,
I've shared the baseline estimation code here:
https://github.com/nboley/DREAM_invivo_tf_binding_prediction_challenge_baseline
There are several dependencies and you'll need to specify the directory structure at the top of one of the files, but it should all work.
Hope this helps!
Best, Nathan Sure. We'll share the baseline code and the scoring code early this week.