`epiout.annotation_config`

Module Contents

Config file for annotation files.

`download_ccres`(output_dir)	Download cCREs from https://wenglab.org/registry/
`_read`(path)
`read_hic`()	Read config file for Hi-C
`read_histone`()	Read config file for histone chipseq experiments.
`read_tf`()	Read config file for TF chipseq experiments.
`create_config`(tissue, output_dir, tf=False, hic=False, ccres=False)	Create config file for annotation for given list of cell types

epiout.annotation_config._encode_bed_url = https://www.encodeproject.org/files/{encode_id}/@@download/{encode_id}.bed.gz

epiout.annotation_config._encode_hic_url = https://www.encodeproject.org/files/{encode_id}/@@download/{encode_id}.hic

epiout.annotation_config.download_ccres(output_dir): Download cCREs from https://wenglab.org/registry/

epiout.annotation_config.read_histone(): Read config file for histone chipseq experiments.

epiout.annotation_config.read_tf(): Read config file for TF chipseq experiments.

epiout.annotation_config.create_config(tissue, output_dir, tf=False, hic=False, ccres=False)

Create config file for annotation for given list of cell types

Parameters

tissue – list of cell types or tissues to include in the config file.
output_dir – output directory where the config file will be saved and the annotation files will be downloaded.
hic – whether include hic files (takes a very long time to download)
ccres – whether include ccres files contains pre-defiend promoter, proximal enhancer, distal enhancers.

class epiout.annotation_config.AnnotationConfig(config_path)

Config file for annotation files.