biotite 0.41.1__cp311-cp311-macosx_10_16_x86_64.whl

biotite/sequence/graphics/plasmid.py

@@ -0,0 +1,661 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+__name__ = "biotite.sequence.graphics"
+__author__ = "Patrick Kunzmann"
+__all__ = ["plot_plasmid_map"]
+
+import copy
+import warnings
+import abc
+import numpy as np
+import re
+from ...visualize import colors
+from ..annotation import Annotation, Feature, Location
+
+
+def plot_plasmid_map(axes, annotation, plasmid_size, tick_length=0.02,
+                     tick_step=200, ring_width=0.01, feature_width=0.06,
+                     spacing=0.01, arrow_head_length=0.04, label=None,
+                     face_properties=None, label_properties=None,
+                     omit_oversized_labels=True, feature_formatter=None):
+    """
+    Plot a plasmid map using the sequence features in the given
+    :class:`Annotation`.
+
+    Each feature location is depicted either by a curved arrow,
+    indicating on which strand the feature resides, or an arc.
+    The ticks indicate the sequence position.
+
+    **EXPERIMENTAL**: The API and the resulting plots will probably
+    change in future versions.
+
+    Parameters
+    ----------
+    axes : PolarAxes
+        A *Matplotlib* axes, that is used as plotting area.
+        A polar projection is required.
+    annotation : Annotation
+        The annotation to be visualized.
+    plasmid_size : int
+        The size of the plasmid, i.e. the length of its sequence.
+    tick_length : float, optional
+        The length of the axis ticks as percentage of the plot radius.
+    tick_step : int, optional
+        The interval between the displayed sequence positions.
+        For example ``tick_step=200`` means that ticks will be displayed
+        at ``1``, ``200``, ``400``, ``600``, etc.
+    ring_width : float, optional
+        The width of the outer ring as percentage of the plot radius.
+    feature_width : float, optional
+        The width of each feature arrow/arc as percentage of the
+        plot radius.
+    spacing : float, optional
+        The spacing between the rows of feature arrows/arcs as
+        percentage of the plot radius.
+    arrow_head_length : float, optional
+        The length of the arrow heads as percentage of the radius
+        at which the respective arrow is plotted.
+    label : str, optional
+        The central label of the plot. Ususally the plasmid name.
+    face_properties : dict, optional
+        A dictionary of properties given to the patches that make up the
+        feature arrows/arcs.
+        Internally the arrow tail is a *Matplotlib* :class:`Rectangle`,
+        and the arrow head is a :class:`Polygon`.
+        For example this parameter could be used to add edge lines to
+        the arrows/arcs.
+    label_properties : dict, optional
+        A dictionary of properties given to the feature labels.
+        Internally each feature label is one or multiple *Matplotlib*
+        :class:`Text` instances.
+        For example this parameter could be used to set the font weight
+        or size.
+    omit_oversized_labels : bool, optional
+        If true, a feature label will not be displayed, if the label is
+        larger than its containing arc/arrow.
+        This ensures, that labels from different features will not
+        overlap each other.
+        If false, the feature labels will always be displayed.
+    feature_formatter : function, optional
+        A function that determines *how* each feature is displayed.
+        The given function must take a :class:`Feature` and must return
+        the following tuple:
+
+        - *directional* : bool
+           
+            True, if the direction of the feature should be indicated by
+            an arrow.
+            Otherwise, the feature is plotted is arc.
+        
+        - *face_color* : tuple or str, optional
+            
+            A *Matplotlib* compatible color for the feature arrow/arc.
+        
+        - *label_color* : tuple or str, optional
+            
+            A *Matplotlib* compatible color for the feature label.
+        
+        - *label* : str or None
+            
+            The label to be displayed for this feature.
+            None, if no label should be displayed.
+    """
+    from matplotlib.projections.polar import PolarAxes
+    
+    if not isinstance(axes, PolarAxes):
+        raise TypeError("The given axes must be a 'PolarAxes'")
+
+    ### Setup parameters ###
+    if plasmid_size is None:
+        # 'stop' of 'get_location_range()' is exclusive -> -1
+        plasmid_size = annotation.get_location_range()[1] - 1
+    if face_properties is None:
+        face_properties = {}
+    if label_properties is None:
+        label_properties = {}
+    if feature_formatter is None:
+        feature_formatter = _default_feature_formatter
+
+
+    ### Setup matplotlib ###
+    # The x-coordinate is given as angle (rad)
+    # Full circle -> 2*pi
+    axes.set_xlim(0, 2*np.pi)
+    axes.set_ylim(0, 1)
+    axes.yaxis.set_visible(False)
+    axes.xaxis.set_tick_params(
+        bottom=False, labelbottom=True
+    )
+    axes.set_theta_zero_location("N")
+    axes.set_theta_direction("clockwise")
+    axes.spines["polar"].set_visible(False)
+    axes.grid(False)
+    # Setup ticks
+    ticks = [1]
+    tick_labels = [str(1)]
+    for tick in range(tick_step, plasmid_size, tick_step):
+        ticks.append(tick)
+        tick_labels.append(str(tick))
+    # Sequence location is replaced by angle
+    axes.xaxis.set_ticks([_loc_to_rad(tick, plasmid_size) for tick in ticks])
+    axes.xaxis.set_ticklabels(tick_labels)
+    ### Draw plasmid ring with ticks and central label ###
+    
+    # Plasmid ring
+    # Use 'barh()' instead of a Rectangle patch to ensure that the axes
+    # is properly initialized
+    # Otherwise the feature rectangles are not curved, but straight
+    axes.barh(
+        1-ring_width-tick_length, 2*np.pi, ring_width,
+        align="edge", color="black"
+    )
+    
+    # Ticks (ticks itself, not the tick labels)
+    for tick in ticks:
+        angle = _loc_to_rad(tick, plasmid_size)
+        axes.plot(
+            (angle, angle), (1-tick_length, 1),
+            color="black", linewidth=1, linestyle="-"
+        )
+    
+    # Central plasmid label
+    if label is not None:
+        axes.text(
+            0, 0, label, ha="center", va="center",
+            color="black", size=32, fontweight="bold"
+        )
+
+
+    ### Draw plasmid interior ###
+    inner_radius = 1 - ring_width - tick_length
+    features = sorted(
+        [
+            _merge_over_periodic_boundary(feature, plasmid_size)
+            for feature in annotation
+        ],
+        # Features are sorted by the length of their location range
+        # The shortest come first
+        key = lambda feature: np.diff(feature.get_location_range())[0],
+        reverse = True
+    )
+    axes.add_artist(PlasmidMap(
+        axes, 0, features, plasmid_size, inner_radius, feature_width, spacing,
+        arrow_head_length, label, face_properties, label_properties,
+        omit_oversized_labels, feature_formatter
+    ))
+
+
+try:
+    # Only create these classes when matplotlib is installed
+    from matplotlib.artist import Artist
+    from matplotlib.transforms import Bbox
+    from matplotlib.patches import Rectangle, Polygon
+
+
+    class PlasmidMap(Artist):
+        def __init__(self, axes, zorder, features, plasmid_size, radius,
+                     feature_width, spacing, arrow_head_length, label,
+                     face_properties, label_properties, omit_oversized_labels,
+                     feature_formatter):
+            super().__init__()
+            self._axes = axes
+            self.zorder = zorder
+            self._features = features
+            self._plasmid_size = plasmid_size
+            self._radius = radius
+            self._feature_width = feature_width
+            self._spacing = spacing
+
+            self._all_indicators = []
+            for feature in features:
+                indicators_for_feature = []
+                for loc in feature.locs:
+                     # Set proper positions in 'draw()' method
+                    bbox = Bbox.from_extents(0, 0, 0, 0)
+                    # Draw features as curved arrows (feature indicator)
+                    indicator = axes.add_artist(Feature_Indicator(
+                        axes, self.zorder + 1, feature, loc, bbox,
+                        arrow_head_length, face_properties, label_properties,
+                        omit_oversized_labels, feature_formatter
+                    ))
+                    indicators_for_feature.append(indicator)
+                self._all_indicators.append(indicators_for_feature)
+
+        
+        def draw(self, renderer, *args, **kwargs):
+            # Find the maximum amount of feature rows
+            # (used for overlapping features)
+            row_count = int(
+                self._radius // (self._feature_width + self._spacing)
+            )
+            # Tracks the location ranges of feature that were added to
+            # a row in order to check if that row is occupied
+            ranges_in_row = [[] for i in range(row_count)]
+            # Stores the bottom coordinate (radius) for each row
+            row_bottoms = [
+                self._radius - (row+1) * (self._feature_width + self._spacing)
+                for row in range(row_count)
+            ]
+
+            # Arrange the feature indicators in an way,
+            # that there is no overlap between them
+            for feature, indicators_for_feature in zip(
+                self._features, self._all_indicators
+            ):
+                row_bottom = None
+                first, last = feature.get_location_range()
+
+                for row_i, curr_range in enumerate(ranges_in_row):
+                    is_occupied = False
+                    if curr_range is not None:
+                        # Check if row is occupied
+                        for curr_first, curr_last in curr_range:
+                            # If the location extends over periodic
+                            # boundary the 'first' location is negative
+                            if first > 0:
+                                # 'Normal feature'
+                                if first <= curr_last and last >= curr_first:
+                                    is_occupied = True
+                            else: # first < 1
+                                # Location is over periodic boundary
+                                if first + self._plasmid_size <= curr_last \
+                                   or last >= curr_first:
+                                        is_occupied = True
+                    if not is_occupied:
+                        # Row is not occupied by another feature
+                        # in the location range of the new feature
+                        # -> Use this row
+                        if first > 0:
+                            # 'Normal feature'
+                            ranges_in_row[row_i].append((first, last))
+                        else:
+                            # Location is over periodic boundary
+                            # Split into 'end' and 'start' part
+                            ranges_in_row[row_i].append((
+                                first + self._plasmid_size, self._plasmid_size
+                            ))
+                            ranges_in_row[row_i].append((
+                                1, last
+                            ))
+                        row_bottom = row_bottoms[row_i]
+                        break
+                if row_bottom is None:
+                    # No free row -> ignore feature and raise warning
+                    warnings.warn(
+                        "Too many feature overlaps, try to increase the "
+                        "radius or decrease the feature width or spacing"
+                    )
+                else:
+                    for loc, indicator in zip(
+                        feature.locs, indicators_for_feature
+                    ):
+                        # Calculate arrow shape parameters
+                        row_center = row_bottom + self._feature_width/2
+                        row_top = row_bottom + self._feature_width
+                        start_ang = _loc_to_rad(loc.first, self._plasmid_size)
+                        stop_ang  = _loc_to_rad(loc.last, self._plasmid_size)
+                        bbox = Bbox.from_extents(
+                            start_ang, row_bottom, stop_ang, row_top
+                        )
+                        indicator.set_bbox(bbox)
+
+
+    class Feature_Indicator(Artist):
+        def __init__(self, axes, zorder, feature, loc, bbox, head_length,
+                     arrow_properties, label_properties, omit_oversized_labels,
+                     feature_formatter):
+            super().__init__()
+            self._axes = axes
+            self.zorder = zorder
+            self._direction = loc.strand
+            self._bbox = bbox
+            self._head_length = head_length
+            self._omit_oversized_labels = omit_oversized_labels
+            
+            # Determine how to draw the feature
+            directional, face_color, label_color, label \
+                = feature_formatter(feature)
+            
+            # Draw arrow as composition of a rectangle and a triangle,
+            # as FancyArrow does not properly work for polar plots
+
+            self._arrow_tail = axes.add_patch(Rectangle(
+                # Set positions in 'draw()' method
+                (0, 0), 0, 0,
+                # Line width is set to 1 to avoid strange artifact in
+                # the transition from rectangle (tail) to polygon (head)
+                color=face_color, linewidth=1, zorder = self.zorder + 1,
+                **arrow_properties
+            ))
+            
+            if directional:
+                # Only draw any arrow head when feature has a direction,
+                # otherwise simply draw the tail (rectangle)
+                self._arrow_head = axes.add_patch(Polygon(
+                    # Set positions in 'draw()' method
+                    [(0, 0), (0, 0), (0, 0)],
+                    color=face_color, linewidth=1, zorder = self.zorder + 1,
+                    **arrow_properties
+                ))
+            else:
+                self._arrow_head = None
+
+            if label is not None:
+                label_properties["color"] = label_color
+                self._label = axes.add_artist(CurvedText(
+                    # Set positions in 'draw()' method
+                    axes, self.zorder + 1, 0, 0, label, label_properties
+                ))
+            else:
+                self._label = None
+        
+
+        def set_bbox(self, bbox):
+            self._bbox = bbox
+            center_x = (bbox.x0 + bbox.x1) / 2
+            center_y = (bbox.y0 + bbox.y1) / 2
+            if self._label is not None:
+                self._label.set_position(center_x, center_y)
+
+
+        def draw(self, renderer, *args, **kwargs):
+            bbox = self._bbox
+            center_x = (bbox.x0 + bbox.x1) / 2
+            center_y = (bbox.y0 + bbox.y1) / 2
+
+            # Constant absolute width for all arrows
+            # irrespective of the radius in the polar plot
+            # Calculate actual angle from given absolute width
+            head_length = self._head_length / center_y
+            
+            # Check if the head should be drawn
+            if self._arrow_head is None:
+                head_length = 0
+            # Check if the feature location is too small for
+            elif head_length > bbox.width:
+                # Limit size of arrow head to range of location
+                head_length = bbox.width
+
+            if self._direction == Location.Strand.FORWARD:
+                rect_pos = (bbox.x0, bbox.y0)
+                # (x0, y0), (x1, y1), (x2, y2)
+                triangle_coord = [
+                    (bbox.x1 - head_length, bbox.y0), # base 1
+                    (bbox.x1 - head_length, bbox.y1), # base 2
+                    (bbox.x1,              center_y) # tip
+                ]
+            else:
+                rect_pos = (bbox.x0+head_length, bbox.y0)
+                triangle_coord = [
+                    (bbox.x0 + head_length, bbox.y0), # base 1
+                    (bbox.x0 + head_length, bbox.y1), # base 2
+                    (bbox.x0,              center_y) # tip
+                ]
+            
+            # Update coordinates of sub-artists
+            self._arrow_tail.set_xy(rect_pos)
+            self._arrow_tail.set_width(bbox.width-head_length)
+            self._arrow_tail.set_height(bbox.height)
+            if self._arrow_head is not None:
+                self._arrow_head.set_xy(triangle_coord)
+            
+            if self._label is not None:
+                # Do not draw the labels if it is larger than the
+                # indicator
+                if self._omit_oversized_labels \
+                   and self._label.get_total_angle(renderer) > bbox.width:
+                        self._label.set_visible(False)
+                else:
+                    self._label.set_visible(True)
+
+
+
+    class CurvedText(Artist):
+        def __init__(self, axes, zorder, angle, radius, string,
+                     text_properties):
+            super().__init__()
+            self._axes = axes
+            self.zorder = zorder
+            self._angle = angle
+            self._radius = radius
+
+            self._texts = []
+            for word in _split_into_words(string):
+                text = axes.text(
+                    # Set position in 'draw()' method
+                    0, 0,
+                    word,
+                    ha="center", va="center",
+                    zorder=self.zorder + 1,
+                    **text_properties,
+                )
+                self._texts.append(text)
+        
+
+        def set_visible(self, visible):
+            super().set_visible(visible)
+            for text in self._texts:
+                text.set_visible(visible)
+
+
+        def set_position(self, angle, radius):
+            self._angle = angle
+            self._radius = radius
+        
+
+        def get_total_angle(self, renderer):
+            return np.sum(self.get_word_angles(renderer))
+        
+
+        def get_word_angles(self, renderer):
+            ax_px_radius = self._axes.get_window_extent(renderer).width / 2
+            ax_unit_radius = self._axes.get_ylim()[1]
+            circle_px_circumference = ax_px_radius * 2*np.pi \
+                                      * (self._radius / ax_unit_radius)
+
+            rad_angle = 360 - np.rad2deg(self._angle)
+            # Avoid to draw the text upside down, when drawn on the
+            # bottom half of the map
+            if rad_angle > 90 and rad_angle < 270:
+                turn_around = True
+            else:
+                turn_around = False
+            
+            angles = []
+            for text in self._texts:
+                orig_rot = text.get_rotation()
+                orig_visible = text.get_visible()
+                # Reset rotation and visibility
+                # for correct window extent calculation
+                text.set_rotation(0)
+                text.set_visible(True)
+                word_px_width = text.get_window_extent(renderer).width
+                # In some Matplotlib versions the window extent of
+                # whitespace characters is 'nan'
+                # In this case, assign a fixed width
+                if np.isnan(word_px_width):
+                    word_px_width = 5.0
+                word_angle \
+                    = 2*np.pi * word_px_width / circle_px_circumference
+                angles.append(word_angle)
+                # Restore
+                text.set_rotation(orig_rot)
+                text.set_visible(orig_visible)
+            return angles
+        
+
+        def draw(self, renderer, *args, **kwargs):
+            angles = self.get_word_angles(renderer)
+            total_angle = np.sum(angles)
+
+            rad_angle = 360 - np.rad2deg(self._angle)
+            # Avoid to draw the text upside down, when drawn on the
+            # bottom half of the map
+            if rad_angle > 90 and rad_angle < 270:
+                turn_around = True
+            else:
+                turn_around = False
+            
+            # Now that the angle for each word is known,
+            # the appropriate position and rotation can be set
+            if turn_around:
+                # curr_angle is the left-aligned position of the
+                # upcoming word
+                curr_angle = self._angle + total_angle / 2
+            else:
+                curr_angle = self._angle - total_angle / 2
+            for text, angle in zip(self._texts, angles):
+                if turn_around:
+                    # The text itself is centered
+                    # -> The position itself must be corrected with
+                    # half of the word angle
+                    angle_corrected = curr_angle - angle / 2
+                    text_rot = 360 - np.rad2deg(angle_corrected) + 180
+                    curr_angle -= angle
+                else:
+                    angle_corrected = curr_angle + angle / 2
+                    text_rot = 360 - np.rad2deg(angle_corrected)
+                    curr_angle += angle
+                text.set_position((angle_corrected, self._radius))
+                text.set_rotation(text_rot)
+
+
+except ImportError:
+    pass
+
+
+
+
+def _loc_to_rad(loc, plasmid_size):
+    if loc > plasmid_size:
+        raise ValueError(
+            f"Location {loc} is larger then the plasmid size of {plasmid_size}"
+        )
+    # Location starts at 1 -> (loc-1)
+    return ((loc-1) / plasmid_size) * 2*np.pi
+
+
+def _rad_to_loc(rad, plasmid_size):
+    # Location starts at 1 -> + 1
+    return rad / (2*np.pi) * plasmid_size + 1
+
+
+def _merge_over_periodic_boundary(feature, plasmid_size):
+    if len(feature.locs) == 1:
+        # Only one location -> no merge possible
+        return feature
+    first_loc = None
+    last_loc  = None
+    # Find total first location of the feature
+    for loc in feature.locs:
+        if first_loc is None or loc.first < first_loc.first:
+            first_loc = loc
+    # Find total last location of the feature
+    for loc in feature.locs:
+        if last_loc is None or loc.last > last_loc.last:
+            last_loc = loc
+    # If the first and last location meet at the periodic boundary of
+    # the plasmid -> merge them
+    if first_loc.first == 1 and last_loc.last == plasmid_size \
+        and first_loc.strand == last_loc.strand:
+            new_locs = set(feature.locs)
+            new_locs.remove(first_loc)
+            new_locs.remove(last_loc)
+            new_locs.add(Location(
+                # the fist base is now at negative location
+                # by shifting by one plasmid 'period'
+                first  = last_loc.first - plasmid_size,
+                last   = first_loc.last,
+                strand = first_loc.strand,
+                defect = first_loc.defect | last_loc.defect
+            ))
+            return Feature(feature.key, new_locs, feature.qual)
+    else:
+        return feature
+
+
+# ' ', '-' and '_' are word delimiters
+separators = re.compile(r"\s|_|-")
+def _split_into_words(string):
+    match_indices = sorted(
+        [match.start() for match in separators.finditer(string)]
+    )
+    current_index = 0
+    words = []
+    for i in match_indices:
+        # Add word up to delimiter
+        words.append(string[current_index : i])
+        # Add delimiter
+        words.append(string[i : i+1])
+        current_index = i+1
+    # If there is a word after the last delimiter, add it too
+    if current_index < len(string):
+        words.append(string[current_index:])
+    return words
+
+
+def _default_feature_formatter(f):
+    """
+    Returns
+    -------
+    directional : bool
+        True, if the direction of the feature should be indicated by
+        an arrow.
+    face_color: tuple or str, optional
+        A matplotlib compatible color for the feature indicator.
+    label_color: tuple or str, optional
+        A matplotlib compatible color for the feature label.
+    label: str or None
+        The label to be displayed for this feature.
+        None, if no label should be displayed.
+    """
+    # Source
+    if f.key == "source":
+        if f.qual.get("organism") is not None:
+            label = f"Source: {f.qual.get('organism')}"
+        else:
+            label = None
+        return False, "black", "white", label
+    
+    # Origin of Replication
+    elif f.key == "rep_origin":
+        return False, "indigo", "white", \
+               f.qual.get("standard_name", "ori")
+    
+    # Coding sequences
+    elif f.key in ["gene", "CDS", "rRNA"]:
+        label = f.qual.get("product")
+        if label is None:
+            label = f.qual.get("gene")
+        return True, colors["orange"], "black", label
+    
+    elif f.key == "regulatory":
+        # Promoters
+        if f.qual.get("regulatory_class") in [
+            "promoter",
+            "TATA_box",
+            "minus_35_signal",
+            "minus_10_signal"
+        ]:
+            return True, colors["dimgreen"], "black", f.qual.get("note")
+        
+        # Terminators
+        elif f.qual.get("regulatory_class") in "terminator":
+            return False, "firebrick", "white", f.qual.get("note")
+        
+        # RBS
+        elif f.qual.get("regulatory_class") == "ribosome_binding_site":
+            return False, colors["brightorange"], "white", None
+    
+    # Primers
+    elif f.key == "primer_bind":
+        return True, "royalblue", "black", f.qual.get("note")
+    
+    # Binding proteins
+    elif f.key == "protein_bind":
+        return False, colors["lightgreen"], "black", f.qual.get("note")
+    
+    # Misc
+    return True, "dimgray", "white", f.qual.get("note")

biotite/sequence/io/__init__.py

@@ -0,0 +1,12 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+A subpackage for reading and writing sequence related data.
+"""
+
+__name__ = "biotite.sequence.io"
+__author__ = "Patrick Kunzmann"
+
+from .general import *

biotite/sequence/io/fasta/__init__.py

@@ -0,0 +1,22 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+This subpackage is used for reading and writing sequence objects
+using the popular FASTA format.
+
+This package contains the :class:`FastaFile`, which provides a
+dictionary like interface to FASTA files, where the header lines are
+keys and the strings containing sequence data are the corresponding
+values.
+
+Furthermore, the package contains convenience functions for
+getting/setting directly :class:`Sequence` objects, rather than strings.
+"""
+
+__name__ = "biotite.sequence.io.fasta"
+__author__ = "Patrick Kunzmann"
+
+from .file import *
+from .convert import *