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Commit 8c76aa88 authored by htyao's avatar htyao
Browse files

Some documentation

parent 0845c5b7
......@@ -81,6 +81,9 @@ def bp_to_struct(bps):
return ss
def parse_vienna(ss):
"""
Parse secondary structure in dot-bracket notation
"""
stacks = {c:[] for c in PARENTHESES_OPENING}
res = [-1 for i in range(len(ss))]
for i,c in enumerate(ss):
......@@ -92,7 +95,11 @@ def parse_vienna(ss):
return res
class VARNA:
"""VARNA object
"""
def __init__(self, seq=None, structure=None):
"""Test
"""
self.length = -1
self.structure = []
self.sequence = ""
......@@ -126,11 +133,20 @@ class VARNA:
# Now we know the length, let's extend the sequence and structure if necessary
self.sequence += " "*(self.length-len(self.sequence))
self.structure += [-1]*(self.length-len(self.structure))
if self.dbn is not None:
self.dbn += "."*(self.length-len(self.structure))
def add_aux_BP(self, i, j, edge5='wc', edge3='wc', stericity='cis', color='#0000FF', thickness=1.0):
def add_aux_BP(self, i:int, j:int, edge5:str='wc', edge3:str='wc', stericity:str='cis', color:str='#0000FF', thickness:float=1.0):
"""Add an additional base pair `(i,j)`, possibly defining and using custom style
Args:
i: 5' position of base pair
j: 3' position of base pair
edge5: Edge 5' used for interaction in non-canonical base-pairs, as defined by the Leontis/Westhof classification of base-pairs. Admissible values are __wc__ (Watson/Crick edge), __h__ (Hoogsteen edge) and __s__ (Sugar edge).
edge3: Edge 3' used for interaction in non-canonical base-pairs. Admissible values are __wc__, __h__ and __s__.
stericity: Orientation of the strands. Admissible values are __cis__ and __trans__
color: Base-pair color in Hex color codes
thickness: Base-pair thickness
"""
assert_valid_interval(self.length, i, j)
if edge5 not in ['wc', 's', 'h']:
raise Exception("edge5 should be one of wc, s, and h")
......@@ -143,7 +159,18 @@ class VARNA:
self.aux_BPs.append((i+1, j+1, color, thickness, edge5, edge3, stericity))
def add_highlight_region(self, i, j, fill="#9999FF", radius=15.0, outline="#3333FF"):
def add_highlight_region(self, i:int, j:int, radius:float=15.0, fill:str="#9999FF", outline:str="#3333FF"):
"""Highlights a region by drawing a polygon of predefined radius,
fill color and outline color around it.
A region consists in an interval from base `i` to base `j`.
Args:
i: 5'-end of the highlight
j: 3'-end of the highlight
radius: Thickness of the highlight
fill: The color used to fill the highlight
outline: The color used to draw the line around the highlight
"""
assert_valid_interval(self.length, i, j)
fill = assert_hex_color(fill)
outline = assert_hex_color(outline)
......@@ -152,18 +179,48 @@ class VARNA:
self.highlight_regions.append((i+1, j+1, radius, fill, outline))
def set_algorithm(self, algo):
if algo not in ['line', 'circular', 'radiate', 'naview']:
"""Set algorithm other than __naview__ to draw secondary structure.
Supported options are __line__, __circular__, __radiate__ and __naview__.
"""
if algo not in ['line', ' circular', 'radiate', 'naview']:
raise Exception("Sould be one of line, circular, radiate or naview")
self.params['algorithm'] = algo
def set_title(self, title, color='#808080', size=10):
def set_title(self, title:str, color:str='#808080', size:int=10):
"""Set title displayed at the bottom of the panel with color and font size
"""
self.title = (title, color, size)
def set_zoom_level(self, level):
def set_zoom_level(self, level:float):
"""Defines the level of zoom and zoom increment used to display the RNA within this panel"""
self.param['zoom'] = level
def set_default_color(self, **kwargs):
"""Set default color used for different objects in the panel.
Args:
**kwargs: See below for the list of allowed keywords.
Value of a keyword is the default color, in Hex color codes, used for the related object.
__Keywords:__
| Name | Object in panel |
|--------------|---------------------------------------------------------|
| backbone | phosphate-sugar backbone (aka skeleton) of the RNA |
| background | background color used within the panel |
| baseInner | inner base color |
| baseName | nucleotide name |
| baseNum | base numbers |
| baseOutline | outer base color |
| bp | base-pair |
| nsBasesColor | non-standard bases (Anything but `A`, `C`, `G` or `U`) |
Examples:
>>> set_default_color({'backbone': '#000000', 'bp':'#FFFF00'})
"""
for key, value in kwargs.items():
if key not in DEFAULT_COLOR_LIST:
raise Exception("{} is not a valid keyword".format(key))
......@@ -171,6 +228,31 @@ class VARNA:
self.default_color = kwargs
def toggle_options(self, **kwargs):
"""Enable or disable options of drawing
Args:
**kwargs: See below for detailed option lists.
Value of keyword is either `True` or `False`
__Keywords:__
Default value is set while [VARNA] object is created.
| Name | Option | Default |
|-------------------|-----------------------------------------------------------------------------------------------------------------------------------------------|---------|
| autoHelices | Annotates each and every helix in the RNA with a unique `Hn` label | False |
| autoInteriorLoops | Annotates each and every interior loop of the RNA with a unique `In` label | False |
| autoTerminalLoops | Annotates each and every terminal loop of the RNA with a unique `Tn` label | False |
| drawBackbone | Backbone drawing | True |
| drawBases | Displays the outline of a nucleotide base | True |
| drawNC | Displays non-canonical base-pairs | True |
| drawTertiary | Display of `non-planar` base-pairs, _i.e._ pseudoknots [^1] | False |
| fillBases | Fill bases | True |
| flat | In `radiate` drawing mode, redraws the whole structure, aligning to a baseline the base featured on the exterior loops (aka "dangling ends") | False |
[^1]: Since there is no canonical definition of pseudoknotted portions, a maximal planar subset is extracted from the input structure, defined to be the planar portion, and used as a scaffold for the drawing algorithms.
"""
for key, value in kwargs.items():
if key not in OPTIONS:
raise Exception("{} is not a valid keyword".format(key))
......@@ -214,13 +296,31 @@ class VARNA:
return "".join(res)
def set_border(self, border):
def set_border(self, border:str):
"""Sets the width and height of the panel border, _i.e._ the gap
between the panel boundaries and those of the surface used to draw the RNA.
Parameter `border` is in format `"wxh"` where `w` and `h` are width and height separated by `x`.
Example:
>>> set_border("20x30")
"""
match = BORDER.search(border)
if not match:
raise Exception("border should be the format nxm where n and m are numbers")
self.params['border'] = "\"{}\"".format(border)
def set_bp_style(self, style):
def set_bp_style(self, style:str):
"""Set default style for base-pairs rendering, chosen among:
| Label | Description |
|--------|--------------------------------------------------------------------------------------------------------|
| none | Base-pairs are not drawn, but can be implicitly seen from "ladders", _i.e_ helix structures |
| line | A simple line is used to draw any base-pair, regardless of its type |
| rnaviz | A small square is drawn at equal distance of the two partners |
| lw | Both canonical and non-canonical base-pairs are rendered according to the Leontis/Westhof nomenclature |
__Note:__ `lw` is set by default
"""
if style not in ['none', 'line', 'rnaviz', 'lw']:
raise Exception('Should be one of none, line, rnaviz or lw')
self.params['bpStyle'] = style
......@@ -237,6 +337,9 @@ class VARNA:
self.bases_styles[style] = self.bases_styles.get(style, set()).union({i+1 for i in bases})
def _gen_command(self):
"""
Return command to run VARNA
"""
cmd = "java -cp {} fr.orsay.lri.varna.applications.VARNAcmd".format(VARNA_PATH)
cmd += " -sequenceDBN \"{}\" -structureDBN \"{}\" -o {}".format(self.sequence, self.format_structure(), self.output)
......@@ -277,6 +380,9 @@ class VARNA:
return cmd
def savefig(self, output):
"""
Call VARNA to draw and store the paint in output
"""
self.output = output
cmd = self._gen_command()
print(cmd)
......
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