Unable To Go Through Biopython'S Motif Tutorial - Ioerror
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1
Entering edit mode
11.9 years ago
Olivier ▴ 440

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'
biopython motif • 3.0k views
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2
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as it says: the file 'Arnt.sites' doesn't exist in your current working directory.

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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.

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5
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11.9 years ago

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.

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1
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11.9 years ago

add the Arnt.sites file to your work directory

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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

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You should definitely try those.

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