[Biopython-dev] [Bug 2883] New: Errors after unpickling of 1.49 seqrecords
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Wed Jul 22 15:14:46 UTC 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2883
Summary: Errors after unpickling of 1.49 seqrecords
Product: Biopython
Version: 1.51b
Platform: PC
OS/Version: Linux
Status: NEW
Severity: normal
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: andrea at biodec.com
I've the same error also with biopython 1.50b
I've the same errors either with python2.4 and python2.5
PROBLEM:
I've for testing purposes some cPickled seqrecords that i prepared with
biopython-1.49.
The unpickling doesn't produce any error at all, but if i try to:
1) print the unpickled seqrecord
2) use the unpickled seqrecord
i get errors.
1) =========================================================================
>>> print seqr
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/usr/lib/python2.5/site-packages/biopython-1.51b-py2.5-linux-x86_64.egg/Bio/SeqRecord.py",
line 501, in __str__
if self.letter_annotations :
File
"/usr/lib/python2.5/site-packages/biopython-1.51b-py2.5-linux-x86_64.egg/Bio/SeqRecord.py",
line 170, in <lambda>
fget=lambda self : self._per_letter_annotations,
AttributeError: 'SeqRecord' object has no attribute '_per_letter_annotations'
### This problem maybe is related to the one of the bug #2838
===============================================================================
2)=============================================================================
>>> seqr.seq
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/usr/lib/python2.5/site-packages/biopython-1.51b-py2.5-linux-x86_64.egg/Bio/SeqRecord.py",
line 538, in __repr__
% tuple(map(repr, (self.seq, self.id, self.name,
File
"/usr/lib/python2.5/site-packages/biopython-1.51b-py2.5-linux-x86_64.egg/Bio/SeqRecord.py",
line 233, in <lambda>
seq = property(fget=lambda self : self._seq,
AttributeError: 'SeqRecord' object has no attribute '_seq'
===============================================================================
According to me old seqrecords didn't have any "_per_letter_annotations"
or any "_seq" in SeqRecord class/instances.
Maybe i've to split the two errors in two different bugs but i prefer
to keep together because are related to the same main problem of
"unpickling an old seqrecord" (or maybe is not a problem and i haven't
to try to unpickle old seqrecord instance with new biopython versions)
I didn't try the CVS code because i didn't find any related error in
bugzilla.open-bio.org.
I've added a dump of a seqrecord generated with biopython-1.49
Thanks
Andrea
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