gefpy 1.3.0

A thin, pythonic wrapper around geftool.

gefpy使用文档(gefpy is a thin, pythonic wrapper around geftools, which runs on Python 3 (3.7+).)

bgef_creater_cy模块

• 对geftools中creat bgef的python接口
• 相关接口

  .. py:module:: bgef_creater_cy
  
    .. py:class:: BgefCreater(thcnt=8)
  
    .. py:method:: create_bgef(self, strin, bin, strmask, strout)
  
        Create tisscuecut bgef by bgef/gem and mask.
  
        :param strin: raw bgef or bgem
        :param bin: mask binsize
        :param strmask: mask path
        :param strout: out path
  
    .. py:method:: get_stereo_data(self, strin, bin, strmask)
  
        Get tisscuecut stereo data by bgef/gem and mask. 
  
        :param strin: raw bgef or bgem
        :param bin: mask binsize
        :param 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.
  
  
        :return: (uniq_cell, gene_names, count, cell_index, gene_index)
  

---

bgef_reader_cy模块

• 提供了对gef文件的读取接口
• 相关接口

    .. py:module:: bgef_reader_cy
  
    .. py:class:: BgefR(filepath, bin_size, n_thread)
  
    .. py:method:: get_expression_num(self)
  
    Get the number of expression.
  
    .. py:method:: get_cell_num(self)
  
    Get the number of cell.
  
    .. py:method:: get_gene_num(self)
  
    Get the number of gene.
  
    .. py:method:: get_gene_names(self)
  
    Get a list of gene names.
  
    .. py:method:: get_cell_names(self)
  
    Get a list of cell ids, each item is (exp.x<<32 | exp.y)
  
    .. py:method:: get_gene_data(self)
  
    Get gene data.
  
    + gene_index is a list that records the gene serial number corresponding to each exp.
    + gene_names is a list of gene names.
  
    :return: (gene_index, gene_names)
  
    .. py:method:: get_expression(self)
  
    Get the all expression from bgef. 
  
    + explist is a list, each item is (x, y, count, exon).
  
    :return: explist
  
    .. py:method:: get_exp_data(self)
  
    Get sparse matrix indexes of expression data.
  
    + uniq_cell is list that save all cell, each cell val (exp.x<<32 | exp.y).
    + cell_index is a list that save the cell idx of each expression.
    + count is a list that save the midcnt of each expression.
  
    :return: (uniq_cell, cell_index, count)
  
    .. py:method:: get_genedata_in_region(self, min_x, max_x, min_y, max_y, key)
  
    Get the explist by the specified gene name in the region.
  
    :param min_x: region minx
    :param max_x: region maxx
    :param min_y: region miny
    :param max_y: region maxy
    :param key: gene name
    :return: explist
  
    .. py:method:: get_offset(self)
  
    Get the offset in bgef.
  
    :return: (minx, miny)
  
    .. py:method:: get_exp_attr(self)
  
    Get the bgef attr.
  
    :return: (minx, miny, maxx, maxy, maxexp, resolution)
  
    .. py:method:: get_filtered_data(self, region, genelist)
  
    Get the filtered data from bgef by region or gene.
  
    :param region: rect region(minx,maxx,miny,maxy)
    :param genelist: gene name list
  
    + 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.
  
    :return: (uniq_cell, gene_names, count, cell_index, gene_index)
  

---

bgef_writer_cy模块

• bgef文件的写入功能的python接口
• 相关接口

    .. py:module:: bgef_writer_cy
  
    .. py:function:: generate_bgef(input_file, bgef_file, stromics="Transcriptomics", n_thread = 8, bin_sizes = None, region = None)
  
    Function to generate common bin GEF file(.bgef).
  
    :param input_file:  The input file path of gem file or bin1 bgef.
    :param bgef_file:   Output BGEF filepath.
    :param stromics:    input the omics.
    :param n_thread:    Number of thread, default 8
    :param bin_sizes:   A list of bin sizes, default: 1,10,20,50,100,200,500
    :param region:      A list of region (minX, maxX, minY, maxY)
  
    .. py:function:: gem2tif(gempath, tif_path)
  
    Function to generate tif file by GEM file(.gem & .gem.gz).
  
    :param gempath:  The input file path of gem file.
    :param tif_path:   Output tiff filepath.
  

---

cgef_adjust_cy模块

• 该模块提供了一些函数，包含lasso、mid count filter、渲染热图采样等功能，主要是stereo map使用
• 相关接口

    .. py:module:: cgef_adjust_cy
  
    .. py:class:: CgefAdjust()
  
    .. py:method:: get_cell_data(self, bgef, cgef)
  
        Get raw cell data from cgef and bgef file.
  
        :param bgef: the bgef file path
        :param cgef: the cgef file path
        :returns: (genelist, vec_cell)
  
    .. py:method:: write_cgef_adjustdata(self, path, celldata, dnbdata)
  
        write the adjust cell data to cgef
  
        :param path: set the Output path
        :param celldata: input the cell data
        :param dandata: input the dandata
        
    .. py:method:: create_Region_Bgef(self, inpath, outpath, pos)
  
        generate spatial bin gef file by lasso region datas
  
        :param inpath: the bgef file path
        :param outpath: set the Output path
        :param pos: lasso region datas
  
    .. py:method:: create_Region_Cgef(self, inpath, outpath, pos)
  
        generate cell bin gef file by lasso region datas
  
        :param inpath: the cgef file path
        :param outpath: set the Output path
        :param pos: lasso region datas
  
    .. py:method:: get_regiondata_frombgef(self, inpath, bin, thcnt, pos)
  
        Get gene info from spatial bin gef file by lasso region datas
  
        :param inpath: the bgef file path
        :param bin: set bin size
        :param thcnt: thread counts
        :param pos: lasso region datas
        :returns vecdata: gene info{genecnt,midcnt,x,y} in region
  
    .. py:method:: get_regiondata_fromcgef(self, input_path, pos)
  
        Get cell statistical info from cell bin gef file by lasso region datas
  
        :param input_path: the cgef file path
        :param pos: lasso region datas
        :returns vecdata: statistical info{cell_count,total_area,average_gene_count,average_exp_count,average_dnb_count,average_area,median_gene_count,median_exp_count,median_dnb_count,median_area} in region
  
    .. py:method:: get_multilabel_regiondata_bgef(self, inpath, pos, bin=1, thcnt=4)
  
        The gene name and MIDcount of multiple labels are returned after the lasso
  
        :param inpath: the input bgef file path
        :param pos: lasso region datas(contain multi labels)
        :param bin: binsize
        :param thcnt: thread count
        :returns region_data, total_mid: region_data(gene_name, MIDcount), total midcount in region
  
    .. py:method:: get_multilabel_regiondata_cgef(self, inpath, pos)
  
        The gene name and MIDcount of multiple labels are returned after the lasso
  
        :param inpath: the input cgef file path
        :param pos: lasso region datas(contain multi labels)
        :returns vecdata, total_data: vecdata(cluster_id, mid_cnt, area, cell_id, x, y), total_data(cluster_id, mid_cnt, area, cell_id)
  
    .. py:method:: get_position_by_clusterid(self, inpath, clusterid)
  
        Get position value(x, y) by cluster id from h5ad file
  
        :param inpath: the input h5ad file
        :param clusterid: input cluster id need to get position
        :returns region_data: position value(x, y)
  
    .. py:method:: generate_filter_bgef_by_midcnt(self, inpath, outpath, binsize, filter_data, only_filter=False)
  
        generate complete bgef file by gene&protein mid count value
  
        :param inpath: input bgef file
        :param outpath: output bgef file
        :param binsize: current binsize
        :param only_filter: generate bgef only have filter gene&protein
        :param filter_data: filter gene&protein name and mid count
        :returns ret: generate result
  
    .. py:method:: get_filter_bgef_process_rate(self)
  
        Get generate process rate, Must be used in conjunction with the generate_filter_bgef_by_midcnt
  
        :returns ret: current process rate
        
    .. py:method:: generate_bgef_by_lasso(self, inpath, outpath, pos)
  
        generate complete bgef file by lasso region datas
  
        :param inpath: the input bgef file path
        :param outpath: the generate bgef file path
        :param pos: lasso region datas
        :returns ret: generate result
  
    .. py:method:: get_lasso_bgef_process_rate(self)
  
        Get generate process rate, Must be used in conjunction with the generate_bgef_by_lasso
  
        :returns ret: current process rate
  
    .. py:method:: generate_bgef_by_coordinate(self, inpath, outpath, cord, bin_size)
  
        generate bgef file by input coordinate in lasso region
  
        :param inpath: the bgef file path
        :param inpath: the bgef file path
        :param cord: lasso region datas
        :param bin_size: input binsize
        :returns ret: generate result
  
    .. py:method:: generate_cgef_by_coordinate(self, inpath, outpath, cord)
  
        generate cell bin gef file by coordinate in lasso region
  
        :param inpath: the input cgef file path
        :param outpath: the output cgef file path
        :param cord: lasso region datas
        :returns ret: generate result
  

---

cgef_reader模块

• 提供了对cgef文件的读取功能
• 相关接口

    .. py:module:: cgef_reader_cy
  
    .. py:class:: CgefR(filepath)
  
    .. py:method:: get_expression_num(self)
  
        Get the number of expression.
  
    .. py:method:: get_cell_num(self)
  
        Get the number of cell.
  
    .. py:method:: get_gene_num(self)
  
        Get the number of gene.
  
    .. py:method:: get_gene_names(self)
  
        Get a list of gene names. The type of gene name is 32 chars.
  
    .. py:method:: get_cell_names(self)
  
        Get an array of cell ids. Each cell id is (cell.x <<32 | cell.y)
  
    .. py:method:: get_cells(self)
  
        Get cells, each cell include (id, x, y, offset, geneCount, expCount, dnbCount, area, cellTypeID, clusterID)
  
    .. py:method:: get_genes(self)
  
        Get genes, each gene include(geneName, offset, cellCount, expCount, maxMIDcount)
  
    .. py:method:: get_cellid_and_count(self)
  
        Get the count of each cell in each gene.
  
        :return:  (cell_id, count)
  
    .. py:method:: get_geneid_and_count(self)
  
        Get the count of each gene in each cell.
        
        :return:  (gene_id, count)
  
    .. py:method:: get_cellborders(self)
  
        Gets cell borders.
        
        :return: borders_list
  
    .. py:method:: get_filtered_data(self, region, genelist)
  
        Get the filtered data from cgef by region or gene.
  
        :param region: rect region(minx,maxx,miny,maxy)
        :param genelist: gene name list
  
        + 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.
  
        :return: (uniq_cell, gene_names, count, cell_index, gene_index)
  

---

cgef_writer_cy模块

• 提供对cgef文件的写入
• 相关接口

    .. py:module:: cgef_writer_cy
  
    .. py:function:: generate_cgef(cgef_file, bgef_file, mask_file, block_size: list)
  
    Generate cell bin GEF file from bgef + mask.
  
    :param cgef_file: Output CGEF filepath.
    :param bgef_file: Input BGEF filepath.
    :param mask_file: Input make filepath.
    :param block_size: Block size list, usually set to [256,256].
  
    .. py:function:: cgem_to_cgef(cgem_file, outpath, block_size: list)
  
    Generate cell bin GEF file from cgem.
  
    :param cgem_file: Input cgem path.
    :param outpath: Output cgef path.
    :param block_size: Block size list,  usually set to [256,256].
  

---

gef_to_gem_cy模块

• 提供gem文件转gef文件的功能
• 相关接口

    .. py:module:: gef_to_gem_cy
  
    .. py:class:: GefToGem(strout, strsn, boutexon)
  
    .. py:method:: bgef2gem(self, strbgef, binsize)
  
        Create bgem file by bgef.
  
        :param strbgef: the bgef file path
        :param binsize: set the binsize
  
    .. py:method:: cgef2gem(self, strbgef, binsize)
  
        Create cgem file by cgef and bgef.
  
        :param strcgef: the cgef file path
        :param strbgef: the bgef file path
  
    .. py:method:: bgef2cgem(self, strmask, strbgef)
  
        Create cgem file by mask and bgef.
  
        :param strcgef: the mask file path
        :param strbgef: the bgef file path
  

API(also can see here)

See here.

Reporting bugs

Open a bug at https://github.com/STOmics/gefpy/issues.