coalispr.bedgraph_analyze.tracks¶

This module produces annotation tracks to display with bedgraph plots.

Attributes¶

logger

Classes¶

`Track`	A class to represent a track of segments.
`SegmentTrack`	A class to represent a track of countable segments.
`GTFtrack`	A Track class to represent a track with annotation info from a GTF file.

Functions¶

`ref_at_clickpoint`(chrnam, clickp, kind)	Get reference label for segment with clickpoint.
`ref_in_segment`(chrnam, segm, kind, ref)	Get reference labels for segment.

Module Contents¶

coalispr.bedgraph_analyze.tracks.logger¶

class coalispr.bedgraph_analyze.tracks.Track(chrnam)¶

A class to represent a track of segments.

A track provides input for a matplotlib.collections.PolyCollection (formerly matplotlib.collections.BrokenBarHCollection) used in coalispr.bedgraph_analyze.bedgraph_plotting.

chrnam¶

The name of the chromosome for which the track is made

Type:: str

df1, df2

Tuple of pandas dataframes, for strand 1 (PLUS) and strand 2 (MINUS).

Type:: pandas.DataFrame, pandas.DataFrame

df¶

Pandas dataframe, used for obtaining segment information.

Type:: pandas.DataFrame

chrnam¶

df = None¶

textlist(clickp)¶

Show list of information for regions under the cursor.

Parameters:: clickp (int) – X-coordinate of point under cursor; registered after mouse-click.
Returns:: List of information associated with segments under the cursor.
Return type:: list

get_segments(df)¶

Return list of segments with information that form the track.

Parameters:: df (pandas.DataFrame) – A pandas dataframe with segment information
Returns:: List of lower boundaries and length of segments, parseable by matplotlib.collections.BrokenBarHCollection.
Return type:: list

get_ctext(clickp)¶

Decribe (first) region under the cursor after clicking (if any).

Parameters:: clickp (int) – X-coordinate of point under cursor; registered after mouse-click.
Returns:: Text associated with first entry of listed regions under cursor.
Return type:: str

class coalispr.bedgraph_analyze.tracks.SegmentTrack(chrnam, tag)¶

Bases: Track

A class to represent a track of countable segments.

chrnam¶

The name of the chromosome for which the track is made

Type:: str

tag¶

Kind of data (TAGCOLL or TAGUNCOLL) to annotate.

Type:: str

dfs, dfa

Tuple of pandas dataframes, for strand 1 (plus) and strand 2 (minus).

Type:: pandas.DataFrame, pandas.DataFrame

df¶

Pandas dataframe, used for obtaining segment information.

Type:: pandas.DataFrame

tag¶

df¶

textlist(clickp)¶

Show list of information for regions under the cursor.

Parameters:: clickp (int) – X-coordinate of point under cursor; registered after mouse-click.
Returns:: List of information associated with segments under the cursor.
Return type:: list

class coalispr.bedgraph_analyze.tracks.GTFtrack(chrnam, kind, strand)¶

Bases: Track

A Track class to represent a track with annotation info from a GTF file.

kind¶

The kind of GTF information, for reference, or regions with SPECIFIC or UNSPECIFIC reads.

Type:: str

strand¶

The strand with the segment the annotation refers to.

Type:: str

kind¶

strand¶

textlist(clickp)¶

Get list of information for regions under the cursor.

Method overwrites that of parent, using another function.

Parameters:: clickp (int) – X-coordinate of point under cursor; registered after mouse-click.
Returns:: List of information associated with segments under the cursor.
Return type:: list

coalispr.bedgraph_analyze.tracks.ref_at_clickpoint(chrnam, clickp, kind)¶

Get reference label for segment with clickpoint.

Parameters:

chrnam (str) – The name of the chromosome for which GTF info is retrieved.
clickp (int) – The click point of the segment under the cursor.
kind (str) – The kind of specified reads for which a GTF could be prepared: (SPECIFIC, UNSPECIFIC, REFERENCE)

Returns:

Lists with gene_id’s from the GTF described by kind; one list for each strand of chromosome chrnam,

Return type:

tuple of lists

coalispr.bedgraph_analyze.tracks.ref_in_segment(chrnam, segm, kind, ref)¶

Get reference labels for segment.

Parameters:

chrnam (str) – The name of the chromosome for which GTF info is retrieved.
segm ((int,int)) – The segment to check.
kind (str) – The kind of specified reads for which a GTF could be prepared: (SPECIFIC, UNSPECIFIC)
ref (bool) – Include general REFERENCE GTF for annotations (slow). 0: No; 1: Yes.

Returns:

Lists with gene_id’s from the GTF described by kind; one list for each strand of chromosome chrnam.

Return type:

tuple of lists