Source code for dna_features_viewer.GraphicFeature

from copy import deepcopy

[docs]class GraphicFeature: """Genetic Feature to be plotted. Parameters ---------- start, end Coordinates of the feature in the final sequence. strand Directionality of the feature. can be +1/-1/0 for direct sense, anti-sense, or no directionality. label Short descriptive text associated and plotted with the feature color Color of the feature, any Matplotlib-compatible format is accepted, such as "white", "w", "#ffffff", (1,1,1), etc. linecolor Color of the feature's border, any Matplotlib-compatible format is accepted, such as "white", "w", "#ffffff", (1,1,1), etc. linewidth Width of the line (=edge) surrounding the graphic feature, in pixels. thickness Vertical span of the feature box_color Color of the label box. Set to None for no box around the label. Leave to "auto" for a box color that is a lightened version of the feature's color. data Any other keyword is kept into the feature.data[] dictionary. fontdict A Matplotlib fontdict for the font to be used in the label, e.g. ``size=11``, ``weight='bold'``, ``family='Helvetica'``, etc. open_left, open_right Set to True if this feature does not end on the right or left because it is a cropped version of a bigger feature. box_linewidth Width of the line delimiting the text box when the annotation is outside the graphic feature. Set to 0 for no box borders box_color Background color of the annotation's text box. If left to "auto" the color will be a lighter version of the feature's color. label_link_color Color of the line linking the text annotation to its respective graphic feature. Set to auto for the line to automatically be a darker version of the feature's color. """ feature_type = "feature" def __init__( self, start=None, end=None, strand=None, label=None, color="#000080", thickness=14, linewidth=1.0, linecolor="#000000", fontdict=None, html=None, open_left=False, open_right=False, box_linewidth=1, box_color="auto", legend_text=None, label_link_color="black", **data ): self.start = start self.end = end self.strand = strand self.label = label self.color = color self.linecolor = linecolor self.data = data self.thickness = thickness self.linewidth = linewidth self.box_linewidth = box_linewidth self.box_color = box_color self.label_link_color = label_link_color self.fontdict = dict( [("fontsize", 11)] + list((fontdict or {}).items()) ) self.html = html self.open_left = open_left self.open_right = open_right self.legend_text = legend_text
[docs] def split_in_two(self, x_coord=0): """Return two features by cutting this feature at x_coord.""" copy1 = deepcopy(self) copy2 = deepcopy(self) copy1.end = x_coord copy2.start = x_coord + 1 return copy1, copy2
[docs] def crop(self, window): """Return a the fragment of the feature that is in the window. If there is no overlap between the feature location and the window, None is returned. """ s, e = window if (s > self.end) or (e < self.start): return None copy = deepcopy(self) if s > self.start: copy.start = s copy.open_left = True if e < self.end: copy.end = e copy.open_right = True return copy
[docs] def overlaps_with(self, other): """Return whether the feature's location overlaps with feature `other` """ loc1, loc2 = (self.start, self.end), (other.start, other.end) loc1, loc2 = sorted(loc1), sorted(loc2) loc1, loc2 = sorted([loc1, loc2], key=lambda loc: loc[0]) return loc1[1] > loc2[0]
@property def length(self): """Return the length of the feature (end-start)""" return abs(self.end - self.start) @property def x_center(self): """Return the x-center of the feature, (start+end)/2""" return 0.5 * (self.start + self.end - 1)
[docs] @staticmethod def from_biopython_feature(feature, **props): """Create a GraphicalFeature from a Biopython.Feature object.""" return GraphicFeature( start=feature.location.start, end=feature.location.end, strand=feature.location.strand, **props )
def __repr__(self): return ("GF(%(label)s, %(start)d-%(end)d " % self.__dict__) + ( ")" if self.strand is None else "(%d))" % self.strand )