Contents

ALLCools.__main__

ALLCools.__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[source]
DESCRIPTION = Multiline-String[source]
Show Value
 1The ALLCools command line toolkit contains multiple functions to manipulate the ALLC format,
 2a core file format that stores single base level methylation information.
 3Throughout this toolkit, we use bgzip/tabix to compress and index the ALLC file to allow
 4flexible data query from the ALLC file.
 5
 6Current Tool List in ALLCools:
 7
 8[Generate ALLC]
 9bam-to-allc          - Generate 1 ALLC file from 1 position sorted BAM file via
10                       samtools mpileup.
11
12[Manipulate ALLC]
13standardize-allc     - Validate 1 ALLC file format, standardize the chromosome names,
14                       compression format (bgzip) and index (tabix).
15tabix-allc           - A simple wrapper of tabix command to index 1 ALLC file.
16profile-allc         - Generate some summary statistics of 1 ALLC
17merge-allc           - Merge N ALLC files into 1 ALLC file
18extract-allc         - Extract information (strand, context) from 1 ALLC file
19
20[Get Region Level]
21allc-to-bigwig       - Generate coverage (cov) and ratio (mc/cov) bigwig track files
22                       from 1 ALLC file
23allc-to-region-count - Count region level mc, cov by genome bins or provided BED files.
24generate-mcds        - Generate methylation dataset (MCDS) for a group of ALLC file and
25                       different region sets. This is a convenient wrapper function for
26                       a bunch of allc-to-region-count and xarray integration codes.
27                       MCDS is inherit from xarray.DataSet
28generate-mcad        - Generate mCG hypo-methylation score AnnData dataset (MCAD) for
29                       a group of ALLC file and one region set.
EPILOG = Multiline-String[source]
Show Value
1Author: Hanqing Liu
2
3See ALLCools documentation here: https://lhqing.github.io/ALLCools/intro.html
class NiceFormatter(fmt=None, datefmt=None, style='%', validate=True)[source]

Bases: logging.Formatter

From Cutadapt https://github.com/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(self, record)[source]

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()[source]
setup_logging(stdout=False, quiet=False, debug=False)[source]

From Cutadapt https://github.com/marcelm/cutadapt Attach handler to the global logger object

_str_to_bool(v: str) → bool[source]
bam_to_allc_register_subparser(subparser)[source]
standardize_allc_register_subparser(subparser)[source]
tabix_allc_register_subparser(subparser)[source]
profile_allc_register_subparser(subparser)[source]
merge_allc_register_subparser(subparser)[source]
extract_context_allc_register_subparser(subparser)[source]
allc_to_region_count_register_subparser(subparser)[source]
allc_to_bigwig_register_subparser(subparser)[source]
generate_mcds_register_subparser(subparser)[source]
generate_mcad_register_subparser(subparser)[source]
convert_mcds_to_zarr_register_subparser(subparser)[source]
generate_dataset_register_subparser(subparser)[source]
table_to_allc_register_subparser(subparser)[source]
main()[source]

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