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fhcrc / taxtastic

Create and maintain phylogenetic "reference packages" of biological sequences.
GNU General Public License v3.0
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ImportError related to biopython #16

Closed nhoffman closed 13 years ago

nhoffman commented 13 years ago

After installing the most recent version of biopython (1.56+), alignment.py generates an ImportError on installation:

% cd taxtastic/taxonomy
% python setup.py install
... 
Traceback (most recent call last):
  File "setup.py", line 10, in <module>
    from __init__ import __version__
  File "/shared/silo_researcher/Fredricks_D/bvdiversity/src/taxtastic/taxonomy/__init__.py", line 11, in <module>
    from alignment import Alignment
  File "/shared/silo_researcher/Fredricks_D/bvdiversity/src/taxtastic/taxonomy/alignment.py", line 5, in <module>
    from Bio.Seq import Seq, SeqRecord
ImportError: cannot import name SeqRecord

Until this is fixed, I eliminated the reference to SeqRecord, but this will generate runtime errors!

bhodges commented 13 years ago

Import statement is fixed, but let me know if you are still having problems.

https://github.com/fhcrc/taxtastic/commit/b36df2b018106d16ccb5a990367d04ba9585f243