schicluster.__main__

CLI defined here

When adding new function: 1. add a func_register_subparser function to register the subparser 2. add a condition in main func about this new func name, import the real func as func in main

Module Contents

log

DESCRIPTION = Multiline-String

Show Value

"""
scHiCluster is a toolkit for single-cell HiC data preprocessing, imputation, and clustering analysis.

Current Tool List in scHiCluster:

"""

EPILOG = ''

class NiceFormatter(fmt=None, datefmt=None, style='%', validate=True)

Bases: logging.Formatter

From Cutadapt marcelm/cutadapt Do not prefix “INFO:” to info-level log messages (but do it for all other levels). Based on http://stackoverflow.com/a/9218261/715090 .

format(record)

Format the specified record as text.

The record’s attribute dictionary is used as the operand to a string formatting operation which yields the returned string. Before formatting the dictionary, a couple of preparatory steps are carried out. The message attribute of the record is computed using LogRecord.getMessage(). If the formatting string uses the time (as determined by a call to usesTime(), formatTime() is called to format the event time. If there is exception information, it is formatted using formatException() and appended to the message.

validate_environment()

setup_logging(stdout=False, quiet=False, debug=False)

From Cutadapt marcelm/cutadapt Attach handler to the global logger object

_str_to_bool(v: str) → bool

comp_cpg_cell_register_subparser(subparser)

comp_concatcell_chr_register_subparser(subparser)

domain_insulation_cell_register_subparser(subparser)

domain_concatcell_chr_register_subparser(subparser)

embed_concatcell_chr_register_subparser(subparser)

embed_mergechr_register_subparser(subparser)

generatematrix_cell_register_subparser(subparser)

impute_cell_register_subparser(subparser)

loop_bkg_cell_register_subparser(subparser)

loop_sumcell_chr_register_subparser(subparser)

loop_mergechr_register_subparser(subparser)

generate_scool_register_subparser(subparser)

prepare_imputation_register_subparser(subparser)

call_domain_register_subparser(subparser)

call_compartment_register_subparser(subparser)

cpg_ratio_register_subparser(subparser)

embedding_register_subparser(subparser)

gene_score_register_subparser(subparser)

merge_cell_raw_register_subparser(subparser)

merge_cool_register_subparser(subparser)

filter_contacts_register_subparser(subparser)

contact_distance_register_subparser(subparser)

main()