lostruct-py 0.0.1

Re-implementation of lostruct in Python

lostruct-py

This is a reimplementation of lostruct from the original code: Lostruct. Please cite the original paper

Demonstration / How to use

Please see the Example Notebook

Citing

Original Lostruct Paper

Please cite the original lostruct paper:

Li, Han, and Peter Ralph. "Local PCA shows how the effect of population structure differs along the genome." Genetics 211.1 (2019): 289-304.

CyVCF2

This paper also uses cyvcf2 for fast VCF processing and should be cited:

Brent S Pedersen, Aaron R Quinlan, cyvcf2: fast, flexible variant analysis with Python, Bioinformatics, Volume 33, Issue 12, 15 June 2017, Pages 1867–1869, https://doi.org/10.1093/bioinformatics/btx057

Requirements

Python >= 3.6 (may work with older versions)

• numba
• numpy
• pandas
• scipy
• skbio
• sklearn
• cyvcf2

CyVCF2 requires zlib-dev, libbz2-dev, libcurl-dev, liblzma-dev, and probably others

Easiest to install all of these through conda

Correlation Data

Used Medicago HapMap sister taxa chromsoome 1, processed, and run with LoStruct

Data

bcftools annotate chr1-filtered-set-2014Apr15.bcf -x INFO,FORMAT | bcftools view -a -i 'F_MISSING<=0.2' | bcftools view -q 0.05 -q 0.95 -m2 -M2 -a -Oz -o chr1-filtered.vcf.gz

Lostruct Processing

Rscript run_lostruct.R -t SNP -s 95 -k 10 -m 10 -i data/

This generates the mds_coords.tsv that is used in the correlation comparison.

FAQ / Notes

PCA, MDS, PCoA

PCoA returns the same results as lostruct's MDS implementation (cmdscale). In the example Jupyter notebook you can see the correlation is R =~ 0.998. Some examples of other methods of clustering / looking at differences are included in the notebook.

Casting complex values to real discards the imaginary part

This is fine.