labtools.adtools.sort

Module Contents

Classes

Sort	A sort object.

class labtools.adtools.sort.Sort(data_files: list, bin_counts: list, bin_values: list, design_file: str = None, bc_dict: str = False)

A sort object.

data_files

List of str paths to fastq files in order of bins.

Type:

list

bin_counts

List of number of cells per bin in order of data files.

Type:

list

bin_values

List of mean or median fluorescence values per bin in order of data files.

Type:

list

design_file

Path to design csv file containing “ArrayDNA” header with DNA sequences to search

Type:

str or None

bc_dict

Path to bc_dict csv file (see seqlib.write_bc_dict)

Type:

str or False, default False

process(csv=False, **kwargs)

Calculate the activity for each tile.

Parameters:

• csv (bool, default False) – Use a csv input for predetermined AD counts (for example, bowtie output).

• **kwargs (dict, optional) – Extra arguments to pull_AD (for example changing the anchor sequences).

Returns:

• processed_sort (pandas.DataFrame)

• numreads

• reads

Examples

>>>Sort.process()

downsample(subset_size: int) → pandas.DataFrame

Perform downsampling on raw reads, then error compared to using all reads.

Parameters:

subset_size (int) – Size in # of reads to subset each file by.

Returns:

errors

Return type:

pandas.DataFrame

Examples

>>>Sort.downsample(100000)