Package manager
This module provides managing classes and methods for the tool.
Canvas
An Image object holds canvas;.
Attributes:
-
canvas
(Canvas
) –canvas object of the reportlab library.
Source code in lovis4u/Manager.py
__init__(filename, width, height, parameters)
Create a Canvas object.
Parameters:
-
filename
(str
) –path and name of the output pdf.
-
width
(float
) –width of the canvas.
-
height
(float
) –height of the pdf.
Source code in lovis4u/Manager.py
save()
Save canvas as a pdf file.
Returns:
-
None
–None
CanvasManager
Canvas manager object responsible for preprocessing data for visualisation and interaction between visualisation and raw data.
Attributes:
-
layout
(dict
) –Defines size and coordinate system of a canvas.
-
tracks
(list
) –List containing Track objects each of them represents visualisation unit (e.g. particular locus).
-
cross_tracks
(list
) –List containing CrossTrack objects each of them represents visualisation unit that interacts with multiple regular Track objects.
prms (Parameters): Parameters' class object that holds config and cmd arguments.
Source code in lovis4u/Manager.py
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__init__(parameters)
Create a CanvasManager object.
Parameters:
-
parameters
(Parameters
) –Parameters' class object that holds config and cmd arguments.
Source code in lovis4u/Manager.py
add_categories_colour_legend_track(loci)
Add categories colour legend tracks to your canvas.
Parameters:
-
loci
(Loci
) –Loci object with information about sequences and features.
Returns:
-
None
–None
Source code in lovis4u/Manager.py
add_homology_track()
Add homology track to your canvas.
You should add this track after you added loci tracks.
Returns:
-
None
–None
Source code in lovis4u/Manager.py
add_loci_tracks(loci)
Add loci tracks to your canvas.
Parameters:
-
loci
(Loci
) –Loci object with information about sequences and features.
Returns:
-
None
–None
Source code in lovis4u/Manager.py
add_scale_line_track()
Add scale line tracks to your canvas.
Returns:
-
None
–None
Source code in lovis4u/Manager.py
define_layout(loci)
Define canvas' layout based on input loci.
Parameters:
-
loci
(Loci
) –Loci object with information about sequences and features.
Returns:
-
None
–None
Source code in lovis4u/Manager.py
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plot(filename)
Plot all added tracks and save the plot as pdf.
Parameters:
-
filename
(str
) –filename for the output pdf.
Returns:
-
None
–None
Source code in lovis4u/Manager.py
CategoriesColorLegendLoader
Bases: Loader
A CategoriesColorLegendLoader object prepares data for a categories colour legend track Drawing object.
Attributes:
-
prms
(Parameters
) –Parameters' class object.
-
layout
(dict
) –Layout built by CanvasManager's define_layout() method.
-
track_data
(dict
) –Track specific data that will be sent to the Drawing module.
Source code in lovis4u/Manager.py
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__init__(parameters)
Create a CategoriesColorLegendLoader object.
Parameters:
-
parameters
(Parameters
) –Parameters' class object that holds config and cmd arguments.
calculate_track_height()
Calculate track height to define layout.
Returns:
-
float
–track height.
Source code in lovis4u/Manager.py
create_track()
Initialise a ColorLegendVis track object.
Returns:
-
–
lovis4u.Drawing.LocusVis | None: visualisation track.
Source code in lovis4u/Manager.py
prepare_track_specific_data(layout, loci)
Prepare ScaleLoader specific data.
Attributes:
-
layout
(dict
) –Layout built by CanvasManager's define_layout() method.
-
loci
(Loci
) –Loci object with information about sequences and features.
Returns:
-
None
–None
Source code in lovis4u/Manager.py
Loader
Parent class for tracks loaders.
Attributes:
-
prms
(Parameters
) –Parameters' class object.
-
layout
(dict
) –Layout built by CanvasManager's define_layout() method.
-
track_data
(dict
) –Track specific data that will be sent to the Drawing module.
Source code in lovis4u/Manager.py
__init__(parameters)
Parent's constructor for creating a Loader class object.
Parameters:
-
parameters
(Parameters
) –Parameters' class object that holds config and cmd arguments.
Source code in lovis4u/Manager.py
calculate_track_height()
create_track()
LocusLoader
Bases: Loader
A LocusLoader object prepares data for a Locus track Drawing object.
Attributes:
-
prms
(Parameters
) –Parameters' class object.
-
layout
(dict
) –Layout built by CanvasManager's define_layout() method.
-
track_data
(dict
) –Track specific data that will be sent to the Drawing module.
Source code in lovis4u/Manager.py
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__init__(parameters)
Create a LocusLoader object.
Parameters:
-
parameters
(Parameters
) –Parameters' class object that holds config and cmd arguments.
calculate_track_height()
Calculate track height to define layout.
Returns:
-
float
(float
) –track height.
Source code in lovis4u/Manager.py
create_track()
Initialise a LocusVis track object.
Returns:
-
–
lovis4u.Drawing.LocusVis: visualisation track.
Source code in lovis4u/Manager.py
prepare_track_specific_data(locus, layout)
Prepare LocusLoader specific data.
Attributes:
-
locus
(Locus
) –corresponding locus object.
-
layout
(dict
) –Layout built by CanvasManager's define_layout() method.
Returns:
-
None
–None
Source code in lovis4u/Manager.py
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Parameters
A Parameters object holds and parse command line's and config's arguments.
A Parameters object have to be created in each script since it's used almost by each class of the tool as a mandatory argument.
Attributes:
-
args
(dict
) –dictionary that holds all arguments.
Source code in lovis4u/Manager.py
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__init__()
load_config(path='standard')
Load configuration file.
Arguments path (str): path to a config file or name (only standard available at this moment).
Returns:
-
None
–None
Source code in lovis4u/Manager.py
load_fonts()
Load fonts.
Returns:
-
None
–None
Source code in lovis4u/Manager.py
load_palette()
Load palette file.
Returns:
-
None
–None
Source code in lovis4u/Manager.py
parse_cmd_arguments()
Parse command-line args
Returns:
-
None
–None
Source code in lovis4u/Manager.py
ScaleLoader
Bases: Loader
A LocusLoader object prepares data for a Scale track Drawing object.
Attributes:
-
prms
(Parameters
) –Parameters' class object.
-
layout
(dict
) –Layout built by CanvasManager's define_layout() method.
-
track_data
(dict
) –Track specific data that will be sent to the Drawing module.
Source code in lovis4u/Manager.py
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__init__(parameters)
Create a ScaleLoader object.
Parameters:
-
parameters
(Parameters
) –Parameters' class object that holds config and cmd arguments.
calculate_track_height()
Calculate track height to define layout.
Returns:
-
float
–track height.
Source code in lovis4u/Manager.py
create_track()
Initialise a ScaleVis track object.
Returns:
-
–
lovis4u.Drawing.LocusVis: visualisation track.
Source code in lovis4u/Manager.py
prepare_track_specific_data(layout)
Prepare ScaleLoader specific data.
Attributes:
-
layout
(dict
) –Layout built by CanvasManager's define_layout() method.
Returns:
-
None
–None