gefpy.bgef_writer_cy

Provides access to the bgef_writer interface.

bgef_writer_cy.generate_bgef(input_file, bgef_file, stromics='Transcriptomics', n_thread=8, bin_sizes=None, region=None)

Function to generate common bin GEF file(.bgef).

Parameters

  • input_file – The input file path of gem file or bin1 bgef.

  • bgef_file – Output BGEF filepath.

  • stromics – input the omics.

  • n_thread – Number of thread, default 8

  • bin_sizes – A list of bin sizes, default: 1,10,20,50,100,200,500

  • region – A list of region (minX, maxX, minY, maxY)

bgef_writer_cy.gem2tif(gempath, tif_path)

Function to generate tif file by GEM file(.gem & .gem.gz).

Parameters

  • gempath – The input file path of gem file.

  • tif_path – Output tiff filepath.