coalispr.bedgraph_analyze.collect_bedgraphs¶

Module for collecting data and configured experiment information.

Attributes¶

logger

Functions¶

`checkset`(listofexps[, omit])	In order to prevent duplication make sure that all input will be unique.
`label_frame`()	Dataframe linking files by a filename-derived key to a short name.
`get_categories_dict`()	Returns dict for categories with SHORT names as keys.
`checkSRCDIR`(src_dir, tag)	Returns path to main folder with folders containing data files.
`get_experiments`([category, method, fraction, plusdiscards])	Returns list of short names based on properties of experiments.
`collect_bedgraphs`(tag[, src_dir, ndirlevels, category])	Find file paths to bedgraphs and return as list.
`collect_references`()	Find file paths to bedgraphs for reference data and return as list.

Module Contents¶

coalispr.bedgraph_analyze.collect_bedgraphs.logger¶

coalispr.bedgraph_analyze.collect_bedgraphs.checkset(listofexps, omit=None)¶

In order to prevent duplication make sure that all input will be unique.

Parameters:: listofexperiments (list) – A list of experimental samples.
Returns:: A non-redundant list of experimental samples.
Return type:: list

coalispr.bedgraph_analyze.collect_bedgraphs.label_frame()¶

Dataframe linking files by a filename-derived key to a short name.

This is the start-dataframe. It defines abbreviated names for display (SHORT), their CATEGORY, etc.. and is built from a tabbed text file EXPFILE containing all details. Try to correct for errors in EXPFILE that easily occur, like spaces by themselves as a value in a group column.

Returns:: Dataframe of EXPFILE with SHORT as index.
Return type:: pandas.DataFrame

coalispr.bedgraph_analyze.collect_bedgraphs.get_categories_dict()¶: Returns dict for categories with SHORT names as keys.

coalispr.bedgraph_analyze.collect_bedgraphs.checkSRCDIR(src_dir, tag)¶: Returns path to main folder with folders containing data files.

coalispr.bedgraph_analyze.collect_bedgraphs.get_experiments(category=None, method=None, fraction=None, plusdiscards=True)¶

Returns list of short names based on properties of experiments.

Parameters:

category (str or list) – Name or list of category item(s) as present in EXPFILE
method (str or list) – Name or list of method(s) as given in EXPFILE
fraction (str or list) – Name or list of fraction(s) as given in EXPFILE
plusdiscards (bool) – Flag to indicate whether to include samples marked as a discard.

Returns:

A list of SHORT names representing the samples/experiments requested.

Return type:

list

coalispr.bedgraph_analyze.collect_bedgraphs.collect_bedgraphs(tag, src_dir=SRCDIR, ndirlevels=SRCNDIRLEVEL, category=None)¶

Find file paths to bedgraphs and return as list.

Parameters:

tag (str (default: TAG))
src_dir (str (default: SRCDIR)) – File path as string to main folder with folders containing data files.
ndirlevels (int (default: SRCNDIRLEVEL)) – Number of folders in between SRCDIR and data files.
category (str or list) – Name or list of category item(s) as present in EXPFILE.

Returns:

A tuple of dictionaries with FILEKEY items and paths to separate bedgraph files for PLUS - and MINUS strand data.

Return type:

dict, dict

coalispr.bedgraph_analyze.collect_bedgraphs.collect_references()¶

Find file paths to bedgraphs for reference data and return as list.

Parameters:

tag (str (default: TAG))
refsdir (str (default: REFDIR)) – File path as string to main folder with folders containing reference data files.
ndirlevels (int (default: REFNDIRLEVEL)) – Number of folders in between SRCDIR and data files.

Returns:

A tuple of dictionaries with FILEKEY items and paths to separate bedgraph files for the reference with PLUS - and MINUS strand data.

Return type:

dict, dict