[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 Peter Cock.


Kevin Wu reported a related issue, which we discussed with Jeff Chang (off list), where a key in the trie exceeded 1000 bytes (the original value of MAX_KEY_LENGTH). See:
http://lists.open-bio.org/pipermail/biopython-dev/2013-February/010284.html
https://github.com/biopython/biopython/commit/31909c8725d5cfbfba2096b7c15ef7afeaf20a5b

(Ideally we could give a specific ValueError exception here, but nevertheless the current print message is an improvement)
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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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