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Questions tagged [skbio]

scikit-bio is a general-purpose python 3 bioinformatics library.

scikit-bio is an open-source, BSD-licensed package providing data structures, algorithms and educational resources for bioinformatics.

scikit-bio is available for both and .

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Error using smith-waterman from skbio 0.5.4

I'm using the wrapped version of smith-waterman from skbio (0.5.4), but i have an unspected error: _, score, _ = local_pairwise_align_ssw(protein_list[idx1], protein_list[idx2], substitution_matrix = blosum62) File…
cw_cw
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cannot install scikit-bio in my window 7 with anaconda 3.x (64-bit)

I used the following code to install scikit-bio from Spyder 3, but it showed error. Therefore, could anyone please help? many thanks Code: import pip pip.main (['install', 'scikit-bio']) Error: Command…
Vanna
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Skbio python module to support python 2

I have python 2 installed on my machine. I want to use the skbio module for some part of my code. I tried installing skbio (pip install scikit-bio) but it says it does not support python 2 it is only available in python 3. I even tried importing…
shalini
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Cannot run pyLDAvis. Getting Error : ImportError: cannot import name PCoA

I have created LDA model using gensim. Now, I wanted to visualise it using pyLDAvis library but getting : ImportError: cannot import name PCoA Can anyone help me with this or suggest some alternatives. Thanks in advance.
newuser
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How to find dissimilarity matrix (Plant communities) in python?

I have a plant community matrix as numpy array where rows are species and columns are communities species 1,2,3 [[ 0 13 2 0 11 0 12 5 0 0] species 4,5,6 [ 0 97 1 5 117 0 64 24 58 3] species 7,8,9 [ 0 …
Bruce
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Output gene positions from GenBank file

Is it possible to output the gene location for a CDS feature or do I need to parse the 'location' or 'complement' field myself? For example, seq = Sequence.read(genbank_fp, format='genbank') for feature in seq.metadata['FEATURES']: if…
Jenya Kopylova
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scikit-bio not working after installation

I have installed scikit-bio on my mac and when I run python -m skbio.test, I get the following error: File "/macqiime/anaconda/lib/python2.7/site-packages/skbio/io/tests/test_util.py", line 17, in import httpretty ImportError: No module…
Jason
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Square a matrix in python

Hello let say I have a df such as : G1 G2 VALUE SP1 SP2 1 SP1 SP3 2 SP1 SP4 3 SP2 SP3 4 SP2 SP4 5 SP3 SP4 6 how can I get a the data as square ? (i.e., have the same number of rows and columns) with something like data = [[0, 1, 2, 3], [1, …
Grendel
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ImportError for skbio module

I am running Python 3 and have skbio v0.5.5 installed. Following the examples in this tutorial, I am trying to run the import statements for some skbio classes, but am getting errors. For example, from skbio.alignment import Alignment results…
Asad Tan
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