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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 .

39 questions
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can warn.filterwarnings be set to act locally when testing with nosetests

I'm running into some trouble with filtering warnings in python tests when using nosetests. I'd like my call to warn.filterwarnings to be local only to a single file, but instead if any of the files I test with nosetests calls warn.filterwarnings,…
gregcaporaso
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Unable to install scikit-bio in docker container

I was trying to install scikit-bio using pipenv install scikit-bio but I was facing some Cython issues, pasted the logs below. Can you please help me on how to resolve it. I was using python 3.7 version in a docker container and using pip file and…
harish reddy baireddy
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Scikit-bio installation error in windows 10 OS, "ERROR: Failed building wheel for scikit-bio"

I want to install scikit-bio in my windows 10 OS. But whenever I ran the command pip install scikit-bio, I got the error message related with "Failed to building wheel for hdmedians". I searched the similar questions, and upgraded pip(20.3),…
CheolHwan0122
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I get that there is no skbio module even though scikit-bio is successfully installed

I'm on mac, OS Catalina, and I run Python 3.8. I have installed scikit-bio successfully: But I try the test, I get that there is no module named skbio: And what I guess is expected is that when I call skbio on jupyter, I get the same message: Any…
Elsa
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scikit-bio v0.5.2 not working with python 3.5 in miniconda

I am trying to run a discrete False Discovery Rate correction on my next gen data. Per the owners code I need to set up the following environment: conda create -n dsfdr2 python=3.5 numpy scipy jupyter scikit-learn scikit-bio statsmodels (I am using…
pmaes
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scipy hierarchy.linkage and Bray-Curtis distances not consistent

I am working with a set of species counts (counts) from several different sample stations (stations). I have calculated the Bray-Curtis similarity between every possible pair of sample stations using the pw_distance function from scikit-bio. This…
user2619065
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Importing QIIME script as module, error importing from skbio

I'm trying to import a QIIME script as a module. The script works when I call it through linux cmd, but when I import the QIIME script as a module, I get the error ~/VirtualENV/lib/python2.7/site-packages/skbio/alignment/_ssw_wrapper.so:undefined…
Tichigan
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Reading from compressed FASTA bz2 file using skbio

Is it possible to read from a compressed file (e.g., FASTA bz2)? I usually use skbio.sequence.Sequence.read but don't see this option there. Thanks!
Jenya Kopylova
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Write multiple fasta entries using scikit-bio write

I am trying to read FASTA file entries using scikit-bio and then write certain entries back out to another file if it meets some requirement. The issue I am running into is that the .write methods seems to open and close a file so each entry…
johnchase
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TabularMSA replacement for Alignment (scikit-bio 0.4.1.dev0)

I would like to read a PHYLIP alignment (FASTA format), update the sequence labels and write results back to a file. How can I edit the following lines to use TabularMSA in scikit-bio 0.4.1.dev0 (instead of Alignment which was supported…
Jenya Kopylova
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scikit-bio python module not getting installed on windows 7

Scikit-bio package is not getting installed. I have numpy 1.9.1. I tried installing from command prompt C:\Python34\Scripts>pip install C:/Users/mgi14-9419/Downloads/scikit-bio-0.4.0.tar.gz I am getting the following error Error…
Bruce
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ModuleNotFoundError: No module named 'skbio.stats.diversity'

I am trying to import the beta_diversity function from the skbio.stats.diversity module in Python: from skbio.stats.diversity import beta_diversity but I am encountering a ModuleNotFoundError with the message No module named…
user17818805
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2-dimensional PCoA plot with skbio

I have a Jensen-Shannon distance (JSD) matrix and I would like to visualise it with Principal Coordinate Analysis (PCoA). I obtain the JSD with Scipy, and make the PCoA with Skbio. I can successfully obtain a 3D PCoA plot. Below, is my output and…
Maria
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Issues with scikit-bio on Mac M1

I tried installing scikit-bio by running conda install -c https://conda.anaconda.org/biocore scikit-bio per the documentation, but verifying the installation via python -m skbio.test yielded the following error: Error while finding module…
sharknado21
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verification of installation of skbio

I installed the Scikit-bio python module in Windows 10. After installation, I verified the installation by running python -m skbio.test I got the following result (end part of message) ERROR…
CheolHwan0122
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