coalispr.bedgraph_analyze.references

Module for dealing with reference data.

Attributes

logger

Functions

has_reference_loaded(chrnam, tag)
retrieve_merged_reference()	Return merged reference data, organized per binned chromosome.
referencetrack(chrnam)	Return references separately to allow transposition.
filtered_referencetrack(chrnam, tag[, kind])	Return transposed references linked to specified reads.

Module Contents

coalispr.bedgraph_analyze.references.logger

coalispr.bedgraph_analyze.references.has_reference_loaded(chrnam, tag)

coalispr.bedgraph_analyze.references.retrieve_merged_reference()

Return merged reference data, organized per binned chromosome.

coalispr.bedgraph_analyze.references.referencetrack(chrnam)

Return references separately to allow transposition.

Parameters:

chrnam (str) – Name of chromosome for which RNA-seq data to return.

Returns:

Tuple of dataframes, for PLUS and MINUS strand of chromosome chrnam, with transposed RNA-seq signals.

Return type:

pandas.DataFrame, pandas.DataFrame

coalispr.bedgraph_analyze.references.filtered_referencetrack(chrnam, tag, kind=SPECIFIC)

Return transposed references linked to specified reads.

Parameters:

• chrnam (str) – Name of chromosome for which filtered, transposed RNA-seq data to return.

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

• kind (str) – Flag to indicate what kind of reads to return data for; SPECIFIC or UNSPECIFIC reads.

Returns:

Tuple of dataframes, for PLUS and MINUS strand of chromosome chrnam, with filtered and transposed RNA-seq signals.

Return type:

pandas.DataFrame, pandas.DataFrame