ALLCools.plot.genome_track.GtfTrack

This GtfTrack class replaced the original pygenometracks class It supports read-in a gffutils database, rather than parse very time

Module Contents

DEFAULT_BED_COLOR = #1f78b4[source]
DISPLAY_BED_VALID = ['collapsed', 'triangles', 'interleaved', 'stacked'][source]
DISPLAY_BED_SYNONYMOUS[source]
DEFAULT_DISPLAY_BED = stacked[source]
AROUND_REGION = 100000[source]
_is_sqlite3(path)[source]
class ReadGtf(file_path, prefered_name='transcript_name', merge_transcripts=True)[source]

Bases: object

Reads a gtf file.

Example: gtf = ReadGtf(“file.gtf”) for interval in gtf:

print interval.start

__iter__(self)[source]
__next__(self)[source]
Returns

bedInterval object

get_bed_interval(self)[source]

Process a transcript from the database, retrieve all the values and return a namedtuple object

class GtfTrack(*args, **kwarg)[source]

Bases: pygenometracks.tracks.BedTrack.BedTrack

The GenomeTrack object is a holder for all tracks that are to be plotted. For example, to plot a bedgraph file a new class that extends GenomeTrack should be created.

It is expected that all GenomeTrack objects have a plot method.

SUPPORTED_ENDINGS = ['gtf', 'gtf.gz', 'gtf.db'][source]
TRACK_TYPE = gtf[source]
OPTIONS_TXT[source]
DEFAULTS_PROPERTIES[source]
NECESSARY_PROPERTIES = ['file'][source]
SYNONYMOUS_PROPERTIES[source]
POSSIBLE_PROPERTIES[source]
BOOLEAN_PROPERTIES = ['labels', 'merge_transcripts', 'global_max_row', 'arrowhead_included', 'all_labels_inside',...[source]
STRING_PROPERTIES = ['prefered_name', 'file', 'file_type', 'overlay_previous', 'orientation', 'title', 'style',...[source]
FLOAT_PROPERTIES[source]
INTEGER_PROPERTIES[source]
set_properties_defaults(self)[source]
get_bed_handler(self, plot_regions=None)[source]