biotite 0.38.0__cp310-cp310-macosx_11_0_arm64.whl → 0.40.0__cp310-cp310-macosx_11_0_arm64.whl

biotite/sequence/graphics/alignment.py

@@ -5,9 +5,9 @@
 __name__ = "biotite.sequence.graphics"
 __author__ = "Patrick Kunzmann"
 __all__ = ["SymbolPlotter", "LetterPlotter", "LetterSimilarityPlotter",
-           "LetterTypePlotter",
+           "LetterTypePlotter","ArrayPlotter",
            "plot_alignment", "plot_alignment_similarity_based",
-           "plot_alignment_type_based"]
+           "plot_alignment_type_based","plot_alignment_array"]
 
 import abc
 import numpy as np
@@ -345,6 +345,116 @@ class LetterTypePlotter(LetterPlotter):
         return self._colors[code]
 
 
+class ArrayPlotter(LetterPlotter):
+    '''
+    This :class:`SymbolPlotter` quantitatively decorates sequences alignments, with molecular
+    recognition data obtained from e.g. microarrays. Symbols are visualized as characters
+    on a colored background box. The color of a given box represents the recognition
+    signal. The intensity of the color, is proportional to the strenght of the
+    recognition.
+
+    Parameters
+    ----------
+    axes : Axes
+        A Matplotlib axes, that is used as plotting area.
+    fl_score : numpy.ndarray
+        The ndarray to store recognition values corresponding to the score residues.
+        By default, the normalized score is 1 for maximum recognition
+        and 0 for non-recognition (no color).
+    color_symbols : bool, optional
+        If true, the symbols themselves are colored.
+        If false, the symbols are black, and the boxes behind the
+        symbols are colored.
+    font_size : float, optional
+        Font size of the sequence symbols.
+    font_param : dict, optional
+        Additional parameters that is given to the
+        :class:`matplotlib.Text` instance of each symbol.
+
+    '''
+    def __init__(self, axes, fl_score, color_symbols=False,
+                 font_size=None, font_param=None):
+
+        super().__init__(axes, color_symbols, font_size, font_param)
+        self.fl_score = fl_score
+        self._cmap = self._generate_colormap(colors["dimorange"],
+                                             self._color_symbols)
+
+
+    def get_color(self, alignment, column_i, seq_i):
+        index1 = alignment.trace[column_i, seq_i]
+        if index1 == -1:
+            spot_signal = 0
+        else:
+            spot_signal = self._get_signal(self.fl_score, column_i, seq_i)
+        return self._cmap(spot_signal)
+
+
+    def _get_signal(self, fl_score, column_i, seq_i):
+        if fl_score is None:
+            signal = 0.0
+        else:
+            signal = fl_score[column_i, seq_i]
+        return signal
+
+    def get_cmap(self):
+        return self._cmap
+
+
+    def plot_symbol(self, bbox, alignment, column_i, seq_i):
+        from matplotlib.patches import Rectangle
+
+        trace = alignment.trace
+
+        if trace[column_i, seq_i] != -1:
+            key1 = alignment.sequences[1][trace[column_i, 1]]
+            key2 = alignment.sequences[0][trace[column_i, 0]]
+            if key1 == key2:
+                if seq_i == 1:
+                    symbol = "*"
+                else:
+                    symbol = alignment.sequences[seq_i][trace[column_i, seq_i]]
+            else:
+                symbol = alignment.sequences[seq_i][trace[column_i, seq_i]]
+        else:
+            symbol = "-"
+        color = self.get_color(alignment, column_i, seq_i)
+        box = Rectangle(bbox.p0, bbox.width, bbox.height)
+        self.axes.add_patch(box)
+        text = self.axes.text(
+            bbox.x0 + bbox.width/2, bbox.y0 + bbox.height/2,
+            symbol, color="black", ha="center", va="center",
+            size=self._font_size, **self._font_param)
+        text.set_clip_on(True)
+
+        if self._color_symbols:
+            box.set_color("None")
+            text.set_color(color)
+        else:
+            box.set_color(color)
+
+    @staticmethod
+    def _generate_colormap(color, to_black):
+        from matplotlib.colors import ListedColormap, to_rgb
+
+        color = to_rgb(color)
+        if to_black:
+            cmap_val = np.stack(
+                [
+                    np.interp(np.linspace(0, 1, 100), [0, 1], [color[i], 0])
+                    for i in range(len(color))
+                ]
+            ).transpose()
+        else:
+            cmap_val = np.stack(
+                [
+                    np.interp(np.linspace(0, 1, 100), [0, 1], [1, color[i]])
+                    for i in range(len(color))
+                ]
+            ).transpose()
+        return ListedColormap(cmap_val)
+
+
 def plot_alignment(axes, alignment, symbol_plotter, symbols_per_line=50,
                    show_numbers=False, number_size=None, number_functions=None,
                    labels=None, label_size=None,
@@ -800,6 +910,106 @@ def plot_alignment_type_based(axes, alignment, symbols_per_line=50,
         spacing=spacing, symbol_spacing=symbol_spacing
     )
 
+def plot_alignment_array(axes, alignment, fl_score, symbols_per_line=50,
+                         show_numbers=False, number_size=None,
+                         number_functions=None, labels=None, label_size=None,
+                         show_line_position=False, spacing=1, color=None,
+                         cmap=None, symbol_spacing=None,
+                         symbol_size=None, symbol_param=None):
+
+    '''
+    Plot a pairwise sequence alignment using an :class:`ArrayPlotter`
+    instance.
+
+    Highlights sequence recognition regions at the positions of the respective
+    score residue per alignment column.
+
+    Parameters
+    ----------
+    axes : Axes
+        A Matplotlib axes, that is used as plotting area.
+    alignment : Alignment
+        The pairwise sequence alignment to be plotted.
+    fl_score : ndarray
+        The array to map fluorescence values to score residues.
+        By default the normalized score is 1 for maximum recognition
+        and 0 for non-recognition (no color).
+    symbol_plotter : SymbolPlotter
+        Instance of ArrayPlotter. Defines how the symbols are drawn
+        in the alignment.
+    symbols_per_line : int, optional
+        The amount of alignment columns that are displayed per line.
+    show_numbers : bool, optional
+        If true, the sequence position of the symbols in the last
+        alignment column of a line is shown on the right side of the
+        plot.
+        If the last symbol is a gap, the position of the last actual
+        symbol before this gap is taken.
+        If the first symbol did not occur up to this point,
+        no number is shown for this line.
+        By default the first symbol of a sequence has the position 1,
+        but this behavior can be changed using the `number_functions`
+        parameter.
+    number_size : float, optional
+        The font size of the position numbers
+    number_functions : list of [(None or Callable(int -> int)], optional
+        By default the position of the first symbol in a sequence is 1,
+        i.e. the sequence position is the sequence index incremented by
+        1.
+        The behavior can be changed with this parameter:
+        If supplied, the length of the list must match the number of
+        sequences in the alignment.
+        Every entry is a function that maps a sequence index (*int*) to
+        a sequence position (*int*) for the respective sequence.
+        A `None` entry means, that the default numbering is applied
+        for the sequence.
+    labels : list of str, optional
+        The sequence labels.
+        Must be the same size and order as the sequences in the
+        alignment.
+    label_size : float, optional
+        Font size of the labels
+    show_line_position : bool, optional
+        If true the position within a line is plotted below the
+        alignment.
+    spacing : float, optional
+        The spacing between the alignment lines. 1.0 means that the size
+        is equal to the size of a symbol box.
+    color : tuple or str, optional
+        A *Matplotlib* compatible color.
+    cmap : Colormap or str, optional
+        The boxes are
+        colored based on the normalized intensity value on the
+        given *Matplotlib* Colormap.
+    symbol_size : float, optional
+        Font size of the sequence symbols.
+    symbol_param : dict
+        Additional parameters that is given to the
+        :class:`matplotlib.Text` instance of each symbol.
+    symbol_spacing : int, optional
+        A space is placed between each number of elements desired
+        by variable.
+
+    Notes
+    -----
+    A '*' represents a sequence match on the alignment
+    A '-' represents a sequence gap on the alignment
+
+    '''
+    symbol_plotter = ArrayPlotter(
+        axes, fl_score = fl_score, font_size = symbol_size, font_param = symbol_param,
+    )
+
+    plot_alignment(
+        axes=axes, alignment=alignment, symbol_plotter=symbol_plotter,
+        symbols_per_line=symbols_per_line,
+        show_numbers=show_numbers, number_size=number_size,
+        number_functions=number_functions,
+        labels=labels, label_size=label_size,
+        show_line_position=show_line_position,
+        spacing=spacing, symbol_spacing=symbol_spacing
+    )
+
 
 def _get_last_valid_index(alignment, column_i, seq_i):
     """

biotite/sequence/io/genbank/annotation.py

@@ -25,7 +25,7 @@ def get_annotation(gb_file, include_only=None):
     """
     Get the sequence annotation from the *FEATURES* field of a
     GenBank file.
-    
+
     Parameters
     ----------
     gb_file : GenBankFile
@@ -33,7 +33,7 @@ def get_annotation(gb_file, include_only=None):
     include_only : iterable object of str, optional
         List of names of feature keys, which should included
         in the annotation. By default all features are included.
-    
+
     Returns
     -------
     annotation : Annotation
@@ -45,11 +45,11 @@ def get_annotation(gb_file, include_only=None):
     if len(fields) > 1:
         raise InvalidFileError("File has multiple 'FEATURES' fields")
     lines, _ = fields[0]
-    
+
 
     ### Parse all lines to create an index of features,
     # i.e. pairs of the feature key
-    # and the text belonging to the respective feature 
+    # and the text belonging to the respective feature
     feature_list = []
     feature_key = None
     feature_value = ""
@@ -65,7 +65,7 @@ def get_annotation(gb_file, include_only=None):
         feature_value += line[_QUAL_START:] + " "
     # Store last feature key and value (loop already exited)
     feature_list.append((feature_key, feature_value))
-    
+
 
     ### Process only relevant features and put them into an Annotation
     annotation = Annotation()
@@ -74,7 +74,7 @@ def get_annotation(gb_file, include_only=None):
     for key, val in feature_list:
         if include_only is None or key in include_only:
             qual_dict = {}
-            
+
             # Split feature definition into parts
             # e.g.
             #
@@ -138,9 +138,9 @@ def get_annotation(gb_file, include_only=None):
                     _set_qual(qual_dict, qual_key, qual_val)
                     qual_key = None
                     qual_val = None
-            
+
             annotation.add_feature(Feature(key, locs, qual_dict))
-    
+
     return annotation
 
 
@@ -149,11 +149,11 @@ def _parse_locs(loc_str):
     if loc_str.startswith(("join", "order")):
         str_list = loc_str[loc_str.index("(")+1:loc_str.rindex(")")].split(",")
         for s in str_list:
-            locs.extend(_parse_locs(s))
+            locs.extend(_parse_locs(s.strip()))
     elif loc_str.startswith("complement"):
         compl_str = loc_str[loc_str.index("(")+1:loc_str.rindex(")")]
         compl_locs = [
-            Location(loc.first, loc.last, Location.Strand.REVERSE, loc.defect) 
+            Location(loc.first, loc.last, Location.Strand.REVERSE, loc.defect)
             for loc in _parse_locs(compl_str)
         ]
         locs.extend(compl_locs)
@@ -219,7 +219,7 @@ def _set_qual(qual_dict, key, val):
 def set_annotation(gb_file, annotation):
     """
     Set the *FEATURES* field of a GenBank file with an annotation.
-    
+
     Parameters
     ----------
     gb_file : GenBankFile