example-1kg-pca.py

   1 #!/usr/bin/env python
   2
   3 """
   4 lightning gvcf2numpy -tag-library ~/keep/by_id/su92l-4zz18-92bx4zjg5hgs3yc/tagset.fa.gz -ref ./hg38.fa.gz ~/keep/by_id/su92l-4zz18-s3e6as6uzsoocsb > example.npy
   5 example-1k-pca.py example.npy
   6 example-1k-plot.py example.npy.pca.npy sample_info.csv ~/keep/by_id/su92l-4zz18-s3e6as6uzsoocsb
   7 ls -l example.npy.pca.npy.png
   8 """
   9
  10 import sys
  11 infile = sys.argv[1]
  12
  13 import scipy
  14 X = scipy.load(infile)
  15
  16 from sklearn.decomposition import PCA
  17 pca = PCA(n_components=4)
  18 X = pca.fit_transform(X)
  19 scipy.save(infile+".pca.npy", X)