python/salus/cmplatform/h5ad.py

   1 #!/usr/bin/env python3
   2
   3 import squidpy as sq
   4 import os
   5
   6 prefix='/share/result/spatial/data/BoAo_sp/sub2/'
   7 outpath='/share/result/spatial/data/BoAo_sp/sub2/h5ad/'
   8 items=['srp_Illumina_mbrain', 'srp_Illumina_mkidney', 'srp_Salus_mbrain', 'srp_Salus_mkidney']
   9
  10 for ids in items:
  11     visiumPath = os.path.join( prefix,ids,'outs' )
  12     outfile = os.path.join( outpath,ids+'.rsp.h5ad' )
  13     print(f"{visiumPath}, {outfile}")
  14     adata=sq.read.visium(visiumPath, library_id=ids)
  15     adata.var_names_make_unique()
  16     adata.write_h5ad(outfile,compression='lzf')