Issue #3395 has been updated by Michał Nowotka.
File minimal_data.pkl added
Minimal test case with stripped django dependencies, loading code below:
from Bio import trie
import pickle
f = open('minimal_data.pkl', 'r')
list = pickle.load(f)
f.close()
index = trie.trie()
for item in list:
for chunk in item[0].split('/')[1:]:
if len(chunk) > 2:
if index.get(str(chunk)):
index[str(chunk)].append(item[1])
else:
index[str(chunk)] = [item[1]]
f = open('trie.dat', 'w')
trie.save(f, index)
f.close()
f = open('trie.dat', 'r')
new_trie = trie.load(f)
f.close()
----------------------------------------
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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