coalispr.bedgraph_analyze.unselected

Module for dealing with unselected reads retrieved from unspecific data.

Attributes

logger

Functions

merge_unsel(tag, force[, tee])

Unselect bedgraphs are combined but kept separate from the data.

process_unselected([kind, tag, force])

Retrieve extra bamfiles, if any and prepare them for common analysis.

Module Contents

coalispr.bedgraph_analyze.unselected.logger
coalispr.bedgraph_analyze.unselected.merge_unsel(tag, force, tee=False)

Unselect bedgraphs are combined but kept separate from the data.

Parameters:

  • tag (str) – Flag TAG to indicate kind of aligned-reads, TAGUNCOLL or TAGCOLL.

  • tee (bool) – Flag defining to return dataframes for immediate use (storing them does not allow for this).

Returns:

  • None – When tee is False; print message upon completion of function.

  • dict, dict – When tee is True, dicts, one for each strand, with dataframes, one for each chromosome, with merged data for reference samples.

coalispr.bedgraph_analyze.unselected.process_unselected(kind=UNSPECIFIC, tag=None, force=False)

Retrieve extra bamfiles, if any and prepare them for common analysis.

Parameters:

  • kind (str (default: UNSPECIFIC)) – Flag to indicate kind of specified reads to analyze, either specific or unspecific (default) for retrieving reads adhering to characteristics, when known, of specific RNAs

  • tag (str) – Flag TAG to indicate kind of aligned-reads, TAGUNCOLL or TAGCOLL. Comes via TAGBAM from counted bam files, which -for efficiency reasons- is set to collapsed reads (TAGCOLL).