Stack Overflow
Stack Overflow

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
7
votes
1 answer

scikit-bio extract genomic features from gff3 file

Is it possible in scikit-bio to extract genomic features stored in a gff3 formatted file from a genome fasta…
holmrenser
  • 425
  • 3
  • 11
6
votes
2 answers

Why is `sklearn.manifold.MDS` random when `skbio's pcoa` is not?

I'm trying to figure out how to implement Principal Coordinate Analysis with various distance metrics. I stumbled across both skbio and sklearn with implementations. I don't understand why sklearn's implementation is different everytime while…
O.rka
  • 29,847
  • 68
  • 194
  • 309
6
votes
2 answers

Trouble installing scikit-bio on Windows

When attempting to install the scikit-bio toolkit via pip on Windows XP using Python 2.78 and Visual C++ 2008 Express Edition, the process is interrupted with the following message issued by VC: cl : Command line error D8021 : invalid numeric…
maurobio
  • 1,480
  • 4
  • 27
  • 38
5
votes
1 answer

How to get `skbio` PCoA (Principal Coordinate Analysis) results?

I'm looking at the attributes of skbio's PCoA method (listed below). I am new to this API and I want to be able to get the eigenvectors and the original points projected onto the new axis similar to .fit_transform in sklearn.decomposition.PCA so I…
O.rka
  • 29,847
  • 68
  • 194
  • 309
5
votes
1 answer

future.utils.six not found when trying to import skbio modules

I just installed numpy and scikit-bio using pip3. If I import DNASequence in an interactive session I get an error message: >>> from skbio.sequence import DNASequence Traceback (most recent call last): File "", line 1, in File…
John Conery
  • 51
  • 5
4
votes
0 answers

How can I make a cca triplot using scikit-bio (python)?

How can I make a triplot for CCA using scikit-bio (python)? I'm trying to make a triplot from canonical correspondence analysis; for example: This should have points for both samples and species and should have vectors for environmental variables.…
John
  • 1,335
  • 12
  • 17
3
votes
2 answers

Fastest way to read a fastq with scikit-bio

I am trying to read a fastq formatted text file using scikit-bio. Given that it is a fairly large file, performing operations is quite slow. Ultimately, I am attempting to dereplicate the fastq file into a dictionary: f =…
johnchase
  • 13,155
  • 6
  • 38
  • 64
3
votes
0 answers

Error when running skbio.stats.ordination.CA: 'LinAlgErr: SVD did not converge'

I would like to use Emperor to create an interactive PCoA plot outside the context of QIIME. To do this I need to generate an ordination file from my data matrix, like the results provided by skbio.stats.ordination.CA. My data is a pandas DataFrame…
Nastassia Patin
  • 31
  • 1
3
votes
1 answer

#error “SSE2 instruction set not enabled” when installing scikit-bio via pip

I want to install the python library scikit-bio via pip using following command: sudo pip install scikit-bio on my system: uname -a Linux grassgis 3.2.0-69-generic-pae #103-Ubuntu SMP Tue Sep 2 05:15:53 UTC 2014 i686 i686 i386 GNU/Linux However…
Johannes
  • 1,024
  • 13
  • 32
2
votes
2 answers

Error: cannot import name 'SpearmanRConstantInputWarning' from 'scipy.stats'

I'm getting an error when importing the skbio package on Google Colab. The error message is related to SpearmanRConstantInputWarning of the scipy.stats package. What should I do to solve this problem? I've tried to uninstall and install skbio and…
kvratto
  • 89
  • 7
2
votes
0 answers

I'm trying to run skbio and keep getting 'ModuleNotFoundError: No module named 'skbio.core'

I'm trying to run skbio in my python script and keep getting the error: ModuleNotFoundError: No module named 'skbio.core.' I am on a Mac running Mojave version 10.14.3 I have tried the following: 1) Updating the bash script like so does not help (as…
user2533160
  • 21
  • 3
2
votes
1 answer

Opening filehandles for use with TabularMSA in skbio

Hey there skbio team. So I need to allow either DNA or RNA MSAs. When I do the following, if I leave out the alignment_fh.close() skbio reads the 'non header' line in the except block making me think I need to close the file first so it will start…
JTFouquier
  • 389
  • 1
  • 4
  • 17
2
votes
0 answers

scikit-bio installation test failure, FAIL: _plot_box_data() should return a dictionary for Line2D's

Installed scikit-bio on Mac, with dependencies for scikit-bio installed. Received error below. Traceback included. Followed instruction on https://pypi.python.org/pypi/scikit-bio for skbio test and used "conda install scikit-bio" which installed…
Ronald Miller
  • 21
  • 1
2
votes
1 answer

Needleman-Wunsch implementation gives different alignments in cogent and in skbio

The implementation in skbio gives an odd result compared to the result that you would get from the implementation in pycogent. from cogent.align.algorithm import nw_align as nw_align_cogent from skbio.alignment import…
El Developer
  • 3,345
  • 1
  • 21
  • 40
2
votes
2 answers

determine length of polypurine tract

how to determine/ find the longest poly-purine tract in any genome (consecutive As and Gs with no interspersed C or T, or vice versa) and this needs to be on the E. coli genome . is it to figure out the polypurine tract and then figure out the…
user3923728
  • 21
  • 1
  • 3
1
2 3