diff dna_features_viewer/GraphicFeature.py @ 1:e923c686ead9 draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dna_features_viewer/GraphicFeature.py	Mon Jun 05 02:45:31 2023 +0000
@@ -0,0 +1,160 @@
+from copy import deepcopy
+
+
+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
+
+    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
+
+    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
+
+    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)
+
+    @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
+        )