[Biopython-dev] [Biopython - Bug #3395] Biopython trie implementation can't load large data sets

[redmine at redmine.open-bio.org]

Issue #3395 has been updated by Michiel de Hoon.


Hi Michal,

Unfortunately I cannot load your minimal_data.pkl file. At
list = pickle.load(f)
I get
ImportError: No module named django.db.models.query

Can you check which item in list is actually causing the problem? Just reduce the list until you find the item that is causing the trie.load(f) to fail.
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Bug #3395: Biopython trie implementation can't load large data sets
https://redmine.open-bio.org/issues/3395

Author: Michał Nowotka
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


Imagine I have Biopython trie:

from Bio import trie
import gzip

f = gzip.open('/tmp/trie.dat.gz', 'w')
tr = trie.trie()
#fill in the trie
trie.save(f, trie)

Now /tmp/trie.dat.gz is about 50MB. Let's try to read it:

from Bio import trie
import gzip

f = gzip.open('/tmp/trie.dat.gz', 'r')
tr = trie.load(f)

Unfortunately I'm getting meaningless error saying:
"loading failed for some reason"

Any hints?



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