[Biopython-dev] [Biopython (old issues only) - Bug #3395] (Closed) Biopython trie implementation can't load large data sets

[redmine at redmine.open-bio.org]

Issue #3395 has been updated by Travis Wrightsman.

Status changed from New to Closed
% Done changed from 0 to 100
URL set to https://github.com/biopython/biopython/issues/892

Migrated to GitHub, see URL.

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Bug #3395: Biopython trie implementation can't load large data sets
https://redmine.open-bio.org/issues/3395#change-15311

* Author: Michał Nowotka
* Status: Closed
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 
* URL: https://github.com/biopython/biopython/issues/892
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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?


---Files--------------------------------
trie_debug.patch (1.63 KB)
minimal_data.pkl (1.23 MB)
minimal_data.pkl (1.24 MB)


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