Documentation¶

Initialization¶

All functionality is accessed through the clibas facade after initialization:

import clibas as C
C.initialize('config.yaml')

initialize() reads the config file and sets up all tools. A no-config initialization is also possible:

import clibas as C
C.initialize()

After this call, the following attributes are available:

Attribute	Description
`C.fastq_parser`	Parsing, filtering, and manipulations with .fastq data
`C.analysis_tools`	Data analysis and statistics
`C.pipeline`	Pipeline construction and execution
`C.preprocessor`	Data preprocessing tools for ML applications
`C.data_loader`	Loading .fastq and .fastq.gz data from disk

Basic usage¶

import clibas as C
C.initialize('config.yaml')

C.pipeline.enque(
[
    C.fastq_parser.translate(stop_readthrough=False),
    C.analysis_tools.length_analysis(where='pep'),
    C.fastq_parser.len_filter(where='pep'),
	...
]
)

loader = C.data_loader.fetch_gz_from_dir(data_dir='./sequencing_data/')
C.pipeline.load_and_run(loader=loader, save_summary=True)

Refer to each module’s API reference below for full method documentation.

Module API reference¶