gefpy.bgef_creater_cy

Provides an interface to create bgef format files from .

class bgef_creater_cy.BgefCreater(thcnt=8)

create_bgef(self, strin, bin, strmask, strout)

Create tisscuecut bgef by bgef/gem and mask.

Parameters

• strin – raw bgef or bgem

• bin – mask binsize

• strmask – mask path

• strout – out path

get_stereo_data(self, strin, bin, strmask)

Get tisscuecut stereo data by bgef/gem and mask.

Parameters

• strin – raw bgef or bgem

• bin – mask binsize

• strmask – mask path

• uniq_cell is list that save all cell, each cell val (exp.x<<32 | exp.y).

• gene_names is a list of gene names.

• count is a list that save the midcnt of each expression.

• cell_index is a list that save the cell idx of each expression.

• gene_index is a list that records the gene serial number corresponding to each exp.

Returns

(uniq_cell, gene_names, count, cell_index, gene_index)