Unable To Go Through Biopython'S Motif Tutorial - Ioerror

Question

[Olivier]

Hello

I'm trying the Sequence motif analysis tutorial in the Biopython cookbook and it's not working. Can someone help? Here's how it is:

from Bio import Motif
arnt = Motif.read(open("Arnt.sites"), "jaspar-sites")
Traceback (most recent call last):
  File "<pyshell#1>", line 1, in <module>
    arnt = Motif.read(open("Arnt.sites"), "jaspar-sites")
IOError: [Errno 2] No such file or directory: 'Arnt.sites'

[Pierre Lindenbaum]

as it says: the file 'Arnt.sites' doesn't exist in your current working directory.

[Olivier]

You're right Pierre. But its location is not mentioned in the tutorial. Do you have an idea what "Arnt.sites" and "jaspar-sites" refer to? It's about JASPAR-formatted motifs but I don't know how to carry on.

Answer 1

[Leonor Palmeira]

These Arnt.sites and SRF.pfm from the BioPython manual are from the JASPAR database. Somewhere in here: http://jaspar.genereg.net/html/DOWNLOAD/

These are just example files to fill the manual, you should make your own in case you're doing your own analysis.

Answer 2

[Istvan Albert]

add the Arnt.sites file to your work directory

[Olivier]

Could you please tell me where I can get this file? I can't really find it on the JASPAR database... unless it's something like this 'MA0001.1.sites'? Thanks

[Leonor Palmeira]

You should definitely try those.