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MAJ terminée. Nous sommes passés en version 14.6.2 . Pour consulter les "releases notes" associées c'est ici :

https://about.gitlab.com/releases/2022/01/11/security-release-gitlab-14-6-2-released/
https://about.gitlab.com/releases/2022/01/04/gitlab-14-6-1-released/

Commit 893cbcc6 authored by htyao's avatar htyao
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Documentation

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__pycache__
*.pyc
*.png
*.svg
site
build
docs/varna.md 0 → 100644
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::: varnaapi.VARNA
docs/varnaapi.md
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::: varnaapi.VARNA
::: varnaapi
selection:
filters: ["!^VARNA", "!^_", "__init__"]
mkdocs.yml
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......@@ -8,11 +8,17 @@ theme:
nav:
- Overview: index.md
- API: varnaapi.md
- VARNA: varna.md
plugins:
- search
- mkdocstrings:
default_handler: python
handlers:
python:
selection:
filters:
- "!^_"
- "^__init__$"
watch:
- varnaapi.py
......
varnaapi.py
View file @ 893cbcc6
import re
import os
from string import ascii_lowercase, ascii_uppercase
from typing import Union
VARNA_PATH="VARNAv3-93.jar"
HEX = re.compile('^#(?:[0-9a-fA-F]{3}){1,2}$')
BORDER = re.compile('^\d+x\d+$')
DEFAULT_COLOR_LIST = ['backbone', 'background', 'baseInner', 'baseName', 'baseNum',
'baseOutline', 'bp', 'gapsColor', 'nsBasesColor']
OPTIONS = ['autoHelices', 'autoInteriorLoops', 'autoTerminalLoops', 'drawBackbone', 'drawBases', 'drawNC', 'drawTertiary', 'fillBases', 'flat']
"""Allowed options for color setting
| 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`) |
"""
NUMERIC_OPTIONS = ['bpIncrement', 'periodNum', 'resolution', 'rotation', 'spaceBetweenBases', 'zoom']
OPTIONS = ['autoHelices', 'autoInteriorLoops', 'autoTerminalLoops', 'drawBackbone', 'drawBases', 'drawNC', 'drawTertiary', 'fillBases', 'flat']
"""Boolean option list
| 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 |
__See Also:__ [VARNA.toggle_options][varnaapi.VARNA.toggle_options]
[^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.
"""
NUMERIC_PARAMS = ['bpIncrement', 'periodNum', 'resolution', 'rotation', 'spaceBetweenBases', 'zoom']
"""Allowed numeric parameters
| Label | Type | Description |
|-------------------|-------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| bpIncrement | float | In linear drawing mode, defines the vertical increment used to separate two successive, nested base-pairs |
| periodNum | int | Sets the interval between two successive base numbers. More specifically, if `k` is the period, then the first and last bases of the RNA are numbered, along with each base whose number is a multiple of `k` |
| resolution | float | Chooses the resolution of a bitmap export, _i.e._ the multiplier in the number of pixels in each dimension of the exported picture. |
| rotation | float | Rotates the whole RNA of a certain angular increment |
| spaceBetweenBases | float | Sets the distance between consecutive bases |
| zoom | float | Defines the level of zoom and zoom increment used to display the RNA within this panel |
"""
BP_STYLES = ['none', 'simple', 'rnaviz', 'lw']
"""Allowed options for base-pair style
| Label | Description |
|--------|--------------------------------------------------------------------------------------------------------|
| none | Base-pairs are not drawn, but can be implicitly seen from "ladders", _i.e_ helix structures |
| simple | 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 |
__See Also:__ [VARNA.set_bp_style][varnaapi.VARNA.set_bp_style]
"""
PARENTHESES_SYSTEMS = [
("(", ")"),
......@@ -24,11 +83,32 @@ PARENTHESES_CLOSING = {c2: c1 for c1, c2 in PARENTHESES_SYSTEMS}
class BasesStyle:
"""Defines a custom base-style, to be applied later to a set of bases.
A BasesStyle style contains colors used for different components of a base.
See [\_\_init\_\_][varnaapi.BasesStyle.\_\_init\_\_] for more details.
__See Also:__ [VARNA.add_bases_style][varnaapi.VARNA.add_bases_style]
"""
def __init__(self, fill=None, outline=None, label=None, number=None):
"""Basesstyle constructor from given colors for different components.
At least one argument should be given.
Args:
fill (Hex): color of inner part of base
outline (Hex): color of outline of base
label (Hex): base text color
number (Hex): base number color
Examples:
>>> style = BasesStyle(fill='#FF0000', outline='#00FF00')
"""
self.color = {}
self.update(fill, outline, label, number)
def update(self, fill=None, outline=None, label=None, number=None):
"""Update component colors.
Same rule as [\_\_init\_\_][varnaapi.BasesStyle.\_\_init\_\_]
"""
if fill is None and outline is None and label is None and number is None:
raise Exception("At least one should not be None")
if fill is not None:
......@@ -99,13 +179,25 @@ def _parse_vienna(ss):
class VARNA:
"""VARNA object
"""
def __init__(self, seq=None, structure=None):
"""Test
def __init__(self, seq:str=None, structure=None):
"""Constructor from given RNA sequence or/and secondary structure.
If sequence and structure have different size, the larger one is used
and ` `s or `.`s will be added to sequence or structure to complement.
Args:
seq: Raw nucleotide sequence for the displayed RNA.
Each base must be encoded in a single character.
Letters others than `A`, `C`, `G`, `U` and space are tolerated.
structure (str or list): RNA (pseudoknotted) secondary structure in one of three formats
- Dot-Bracket Notation (DBN)
- List of pair of int representing a list of base-pairs
- List of int, in which i-th value is `j` if `(i,j)` is a base pair or `-1` if i-th base is unpaired
"""
self.length = -1
self.structure = []
self.sequence = ""
self.dbn = None
self.aux_BPs = []
self.highlight_regions = []
self.params = {'algorithm': "naview"}
......@@ -202,22 +294,8 @@ class VARNA:
"""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`) |
**kwargs (dict): See [DEFAULT_COLOR_LIST][varnaapi.DEFAULT_COLOR_LIST] for the list of allowed keywords.
Value of a keyword is the default color, in Hex color codes, used for the related object.
Examples:
>>> set_default_color({'backbone': '#000000', 'bp':'#FFFF00'})
......@@ -233,26 +311,9 @@ class VARNA:
"""Enable or disable options of drawing
Args:
**kwargs: See below for detailed option lists.
**kwargs (dict): See [OPTIONS][varnaapi.OPTIONS] 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():
......@@ -263,8 +324,16 @@ class VARNA:
self.options = kwargs
def set_numeric_params(self, **kwargs):
"""Change value of numeric parameters in one function.
This is equivalent to use setting function of each parameter,
such as [set_bp_increment][varnaapi.VARNA.set_bp_increment].
Args:
**kwargs (dict): See [NUMERIC_PARAMS][varnaapi.NUMERIC_PARAMS] for allowed keywords.
"""
for key, value in kwargs.items():
if key not in NUMERIC_OPTIONS:
if key not in NUMERIC_PARAMS:
raise Exception("{} is not a valid keyword".format(key))
assert_is_number(value)
if key == "periodNum":
......@@ -273,6 +342,8 @@ class VARNA:
self.params[key] = float(value)
def format_structure(self):
"""Return secondary structure in dot-brackaet notation
"""
def greedy_fill(c1, c2, res, ss, i, j):
if i <= j:
k = ss[i]
......@@ -312,27 +383,45 @@ class VARNA:
self.params['border'] = "\"{}\"".format(border)
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 |
"""Set default style for base-pairs rendering, chosen among [BP_STYLES][varnaapi.BP_STYLES]
__Note:__ `lw` is set by default
Example:
>>> varna.set_bp_style("simple")
"""
if style not in ['none', 'line', 'rnaviz', 'lw']:
raise Exception('Should be one of none, line, rnaviz or lw')
if style not in BP_STYLES:
raise Exception('Should be one of {}'.format(BP_STYLES))
self.params['bpStyle'] = style
def set_bp_increment(self, value):
def set_bp_increment(self, value:float):
"""In linear drawing mode, defines the vertical increment used to
separate two successive, nested base-pairs.
Example:
>>> varna.set_bp_increment(1.2)
"""
assert_is_number('value', value)
self.params['bpIncrement'] = float(value)
def add_bases_style(self, style, bases):
def add_bases_style(self, style:BasesStyle, bases:list):
"""Apply a [BasesStyle][varnaapi.BasesStyle] to a list of positions.
If a position is assigned to more than one styles,
one of them will be randomly used.
Args:
style: Style to apply
bases: List of 0-indexed positions
Examples:
>>> style1 = BasesStyle(fill="#FF0000")
>>> style2 = BasesStyle(fill="#FFFF00" outline="#00FF00")
>>> varna.add_bases_style(style1, [0,2,4])
>>> varna.add_bases_style(setye1, [10,11,12])
>>> varna.aff_bases_style(style2, [4,5,6,7])
"""
if not isinstance(style, BasesStyle):
raise Exception("style should be BasesStyle object")
if len(bases) > 0:
......@@ -390,6 +479,5 @@ class VARNA:
print(cmd)
os.popen(cmd).close()
def __repr__(self):
return repr((self.format_structure(),self.sequence))
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