Unable To Go Through Biopython'S Motif Tutorial - Ioerror
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'
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Leonor Palmeira
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Olivier
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Olivier
2 answers
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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Leonor Palmeira
add the Arnt.sites file to your work directory
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Istvan Albert
You should definitely try those.
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Leonor Palmeira
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as it says: the file 'Arnt.sites' doesn't exist in your current working directory.
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.