Classify_nucleotide_sequences

[eallen4040]

Hello!

I am relatively new to the world of neural networks! I've been in contact with this group before and you all have been a tremendous help! I am currently attempting to run the examples available in jupyter notebook. I specifically want to ask about Classify_nucleotide_sequences. I have a couple errors return when I run the first cell:

ImportError Traceback (most recent call last)
in
9 from keras.layers import Maximum
10
---> 11 from janggu import Janggu
12 from janggu import Scorer
13 from janggu import inputlayer

~/anaconda3/envs/janggu/lib/python3.6/site-packages/janggu/init.py in
4 from janggu.decorators import outputconv # noqa
5 from janggu.decorators import outputdense # noqa
----> 6 from janggu.evaluation import Scorer # noqa
7 from janggu.layers import Complement # noqa
8 from janggu.layers import DnaConv2D # noqa

~/anaconda3/envs/janggu/lib/python3.6/site-packages/janggu/evaluation.py in
18 from sklearn.metrics import roc_curve
19
---> 20 from janggu.utils import ExportJson
21 from janggu.utils import ExportScorePlot
22 from janggu.utils import ExportTsv

~/anaconda3/envs/janggu/lib/python3.6/site-packages/janggu/utils.py in
10 import pandas as pd
11 from Bio import SeqIO
---> 12 from Bio.Alphabet import IUPAC
13 from Bio.Seq import Seq
14 from Bio.SeqRecord import SeqRecord

~/anaconda3/envs/janggu/lib/python3.6/site-packages/Bio/Alphabet/init.py in
19
20 raise ImportError(
---> 21 "Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information."
22 )

ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

Can I get a little insight on these errors and how to fix them? I would really appreciate it!

[wkopp]

Hi @eallen4040,

The issue use caused by an update in the package Biopython==1.78.
Install Biopython==1.77 with pip install biopython==1.77. This should resolve the issue.

I've adjusted setup.py such that it requires Biopython==1.77. This is available in the github master branch and will be part of the new version soon.

Best,
Wolfgang