episcanpy.ct.bld_atac_mtx

episcanpy.ct.bld_atac_mtx(list_bam_files, loaded_feat, output_file_name=None, path=None, writing_option='a', header=None, mode='rb', check_sq=True, chromosomes=['1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', '2', '3', '4', '5', '6', '7', '8', '9', 'X', 'Y'])

Build a count matrix one set of features at a time. It is specific of ATAC-seq data. It curently do not write down a sparse matrix. It writes down a regular count matrix as a text file.

Parameters

list_bam_files : input must be a list of bam file names. One for each cell to

build the count matrix for

loaded_feat : the features for which you want to build the count matrix

output_file_name : name of the output file. The count matrix that will be written

down in the current directory. If this parameter is not specified, the output count amtrix will be named ‘std_output_ct_mtx.txt’

path : path where to find the input file. The output file will be written down

your current directory, it is not affected by this parameter. : in

writing_option : standard writing options for the output file. 'a' or 'w'

‘a’ to append to an already existing matrix. ‘w’ to overwrite any previously exisiting matrix. default: ‘a’

header : if you want to write down the feature name specify this argument.

Input must be a list.

mode : bamnostic argument 'r' or 'w' for read and write 'b' and 's' for bam or sam

if only ‘r’ is specified, bamnostic will try to determine if the input is either a bam or sam file.

check_sq : bamnostic argument. when reading, check if SQ entries are present in header

chromosomes : chromosomes of the species you are considering. default value

is the human genome (not including mitochondrial genome). HUMAN = [‘1’, ‘10’, ‘11’, ‘12’, ‘13’, ‘14’, ‘15’, ‘16’, ‘17’, ‘18’, ‘19’, ‘20’, ‘21’, ‘22’,

‘2’, ‘3’, ‘4’, ‘5’, ‘6’, ‘7’, ‘8’, ‘9’,’X’, ‘Y’]

MOUSE = ‘1’, ‘10’, ‘11’, ‘12’, ‘13’, ‘14’, ‘15’, ‘16’, ‘17’, ‘18’, ‘19’,

‘2’, ‘3’, ‘4’, ‘5’, ‘6’, ‘7’, ‘8’, ‘9’,’X’, ‘Y’]

Returns

It does not return any object. The function write down the desired count matrix in a txt file