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

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Issue #3395 has been updated by Michiel de Hoon.


The problem was indeed that one of the chunks had a size of 2000.
I've uploaded a fix to github; could you please give it a try? See

https://github.com/biopython/biopython/commit/6e09a4a67b7dec1910b13e3d730e3a1f5c2261c9

In particular, please make sure that new_trie is identical to trie.
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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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