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uorf4u.drawing

This module provides visualisation of loci annotation.

AnnotationPlotManager

AnnotationPlotManager object holds needed information for annotation visualisation and controls it.

Note:

It's supposed that the AnnotationPlotManager' objects will not be used directly by API users since visualisation can be controlled by 'plot_annotation' method.

Attributes:

  • path (uorf4u.data_processing.Path) –

    Path class' objects that holds list of conserved ORFs.

  • upstream_sequences (list) –

    list of dicts with information about upstream sequences.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

  • coordinate_system (dict) –

    coordinate system of figure.

  • additional_data (dict) –

    dict with data for visualisation tracks.

Source code in uorf4u/drawing_annotation.py 
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class AnnotationPlotManager:
    """
    AnnotationPlotManager object holds needed information for annotation visualisation and controls it.

    Note:
        It's supposed that the AnnotationPlotManager' objects will not be used directly by API users since
            visualisation can be controlled by 'plot_annotation' method.

    Attributes:
        path (uorf4u.data_processing.Path): Path class' objects that holds list of conserved ORFs.
        upstream_sequences (list): list of dicts with information about upstream sequences.
        parameters (uorf4u.manager.Parameters): Parameters' class object.
        coordinate_system (dict): coordinate system of figure.
        additional_data (dict): dict with data for visualisation tracks.

    """

    def __init__(self, path, upstream_sequences: list, parameters: uorf4u.manager.Parameters):
        """Create a AnnotationPlotManager object.

        Arguments:
            path (uorf4u.data_processing.Path): Path class' objects that holds list of conserved ORFs.
            upstream_sequences (list): list of dicts with information about upstream sequences.
            parameters (uorf4u.manager.Parameters): Parameters' class object.

        """
        self.path = path
        self.upstream_sequences = upstream_sequences
        self.parameters = parameters
        self.coordinate_system = dict()
        self.additional_data = dict()

    def define_x_axis_coordinate_system(self) -> None:
        """Define coordinate system.

        Returns:
            None

        """

        label_height = self.parameters.arguments["label_height_to_orf_height"] * self.parameters.arguments[
            "orf_height"] * cm
        label_font_size = uorf4u.methods.string_height_to_font_size(label_height, "regular", self.parameters.arguments)
        self.additional_data["label_font_size"] = label_font_size
        self.additional_data["ordered_upstream_sequences"] = [self.upstream_sequences[i] for i in
                                                              [orf.useq_index for orf in self.path.path]]
        max_label_width = max([reportlab.pdfbase.pdfmetrics.stringWidth(i.annotations["label"], "regular",
                                                                        label_font_size)
                               for i in self.additional_data["ordered_upstream_sequences"]])
        self.additional_data["number_of_sequences"] = len(self.path)
        self.additional_data["max_upstream_sequence_length"] = max(
            i.annotations["upstream_region_length"] for i in self.additional_data["ordered_upstream_sequences"])
        self.additional_data["max_downstream_sequence_length"] = max(
            i.annotations["downstream_region_length"] for i in self.additional_data["ordered_upstream_sequences"])
        window_size_nt = self.additional_data["max_upstream_sequence_length"] + self.additional_data[
            "max_downstream_sequence_length"]
        if self.parameters.arguments["annotation_width"] == "auto":
            annotation_width = window_size_nt * self.parameters.arguments["mm_per_nt"] * mm
        else:
            annotation_width = self.parameters.arguments["annotation_width"] * cm
        self.coordinate_system["transformation_coef"] = annotation_width / window_size_nt
        self.coordinate_system["x_labels_start"] = self.parameters.arguments["margin"] * cm
        self.coordinate_system["x_labels_stop"] = self.coordinate_system["x_labels_start"] + max_label_width
        self.coordinate_system["x_annotation_start"] = self.coordinate_system["x_labels_stop"] + \
                                                       self.parameters.arguments["label_gap"] * cm
        self.coordinate_system["x_annotation_stop"] = self.coordinate_system["x_annotation_start"] + annotation_width
        self.coordinate_system["figure_width"] = 2 * self.parameters.arguments["margin"] * cm + annotation_width + \
                                                 max_label_width + self.parameters.arguments["label_gap"] * cm
        self.coordinate_system["figure_height"] = self.parameters.arguments["margin"] * cm

        return None

    def create_tracks(self) -> None:
        """Create visualisation tracks.

        Returns:
            None

        """
        self.tracks = []
        """
        title_loader = TitleLoader(self.parameters)
        title_loader.prepare_data(self.coordinate_system, self.additional_data)
        title_track = title_loader.create_track()
        self.tracks.append(title_track)
        self.coordinate_system["figure_height"] += title_track.needed_y_space()
        """
        for index in range(self.additional_data["number_of_sequences"]):
            upstream_sequence = self.additional_data["ordered_upstream_sequences"][index]
            conserved_orf = self.path.path[index]
            sequence_loader = SequencesLoader(self.parameters)
            sequence_loader.prepare_data(upstream_sequence, conserved_orf, self.coordinate_system, self.additional_data)
            track = sequence_loader.create_track()
            self.tracks.append(track)
            self.coordinate_system["figure_height"] += track.needed_y_space()
            self.coordinate_system["figure_height"] += self.parameters.arguments["gap"] * cm
            # if index < self.additional_data["number_of_sequences"] - 1:
        axis_tics_loader = AxisLoader(self.parameters)
        axis_tics_loader.prepare_data(self.coordinate_system, self.additional_data)
        axis_tics_track = axis_tics_loader.create_track()
        self.tracks.append(axis_tics_track)
        self.coordinate_system["figure_height"] += axis_tics_track.needed_y_space()
        self.coordinate_system["figure_height"] += self.parameters.arguments["margin"] * cm

    def plot(self, filename):
        image = Image(filename, self.coordinate_system["figure_width"], self.coordinate_system["figure_height"])
        current_y_top = self.coordinate_system["figure_height"] - self.parameters.arguments["margin"] * cm
        for track in self.tracks:
            track.visualisation_data["y_top"] = current_y_top
            track.draw(image.canvas)
            current_y_top -= (track.needed_space + self.parameters.arguments["gap"] * cm)
        image.save()
        return None

__init__(path, upstream_sequences, parameters)

Create a AnnotationPlotManager object.

Parameters:

  • path (uorf4u.data_processing.Path) –

    Path class' objects that holds list of conserved ORFs.

  • upstream_sequences (list) –

    list of dicts with information about upstream sequences.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

Source code in uorf4u/drawing_annotation.py 
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def __init__(self, path, upstream_sequences: list, parameters: uorf4u.manager.Parameters):
    """Create a AnnotationPlotManager object.

    Arguments:
        path (uorf4u.data_processing.Path): Path class' objects that holds list of conserved ORFs.
        upstream_sequences (list): list of dicts with information about upstream sequences.
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """
    self.path = path
    self.upstream_sequences = upstream_sequences
    self.parameters = parameters
    self.coordinate_system = dict()
    self.additional_data = dict()

create_tracks()

Create visualisation tracks.

Returns:

  • None –

    None

Source code in uorf4u/drawing_annotation.py 
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def create_tracks(self) -> None:
    """Create visualisation tracks.

    Returns:
        None

    """
    self.tracks = []
    """
    title_loader = TitleLoader(self.parameters)
    title_loader.prepare_data(self.coordinate_system, self.additional_data)
    title_track = title_loader.create_track()
    self.tracks.append(title_track)
    self.coordinate_system["figure_height"] += title_track.needed_y_space()
    """
    for index in range(self.additional_data["number_of_sequences"]):
        upstream_sequence = self.additional_data["ordered_upstream_sequences"][index]
        conserved_orf = self.path.path[index]
        sequence_loader = SequencesLoader(self.parameters)
        sequence_loader.prepare_data(upstream_sequence, conserved_orf, self.coordinate_system, self.additional_data)
        track = sequence_loader.create_track()
        self.tracks.append(track)
        self.coordinate_system["figure_height"] += track.needed_y_space()
        self.coordinate_system["figure_height"] += self.parameters.arguments["gap"] * cm
        # if index < self.additional_data["number_of_sequences"] - 1:
    axis_tics_loader = AxisLoader(self.parameters)
    axis_tics_loader.prepare_data(self.coordinate_system, self.additional_data)
    axis_tics_track = axis_tics_loader.create_track()
    self.tracks.append(axis_tics_track)
    self.coordinate_system["figure_height"] += axis_tics_track.needed_y_space()
    self.coordinate_system["figure_height"] += self.parameters.arguments["margin"] * cm

define_x_axis_coordinate_system()

Define coordinate system.

Returns:

  • None –

    None

Source code in uorf4u/drawing_annotation.py 
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def define_x_axis_coordinate_system(self) -> None:
    """Define coordinate system.

    Returns:
        None

    """

    label_height = self.parameters.arguments["label_height_to_orf_height"] * self.parameters.arguments[
        "orf_height"] * cm
    label_font_size = uorf4u.methods.string_height_to_font_size(label_height, "regular", self.parameters.arguments)
    self.additional_data["label_font_size"] = label_font_size
    self.additional_data["ordered_upstream_sequences"] = [self.upstream_sequences[i] for i in
                                                          [orf.useq_index for orf in self.path.path]]
    max_label_width = max([reportlab.pdfbase.pdfmetrics.stringWidth(i.annotations["label"], "regular",
                                                                    label_font_size)
                           for i in self.additional_data["ordered_upstream_sequences"]])
    self.additional_data["number_of_sequences"] = len(self.path)
    self.additional_data["max_upstream_sequence_length"] = max(
        i.annotations["upstream_region_length"] for i in self.additional_data["ordered_upstream_sequences"])
    self.additional_data["max_downstream_sequence_length"] = max(
        i.annotations["downstream_region_length"] for i in self.additional_data["ordered_upstream_sequences"])
    window_size_nt = self.additional_data["max_upstream_sequence_length"] + self.additional_data[
        "max_downstream_sequence_length"]
    if self.parameters.arguments["annotation_width"] == "auto":
        annotation_width = window_size_nt * self.parameters.arguments["mm_per_nt"] * mm
    else:
        annotation_width = self.parameters.arguments["annotation_width"] * cm
    self.coordinate_system["transformation_coef"] = annotation_width / window_size_nt
    self.coordinate_system["x_labels_start"] = self.parameters.arguments["margin"] * cm
    self.coordinate_system["x_labels_stop"] = self.coordinate_system["x_labels_start"] + max_label_width
    self.coordinate_system["x_annotation_start"] = self.coordinate_system["x_labels_stop"] + \
                                                   self.parameters.arguments["label_gap"] * cm
    self.coordinate_system["x_annotation_stop"] = self.coordinate_system["x_annotation_start"] + annotation_width
    self.coordinate_system["figure_width"] = 2 * self.parameters.arguments["margin"] * cm + annotation_width + \
                                             max_label_width + self.parameters.arguments["label_gap"] * cm
    self.coordinate_system["figure_height"] = self.parameters.arguments["margin"] * cm

    return None

AxisLoader

Bases: Loader

An AxisLoader object prepares data for an Axis track object.

Attributes:

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

  • prepared_data (dict) –

    dict with data needed for a visualisation track.

Source code in uorf4u/drawing_annotation.py 
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class AxisLoader(Loader):
    """An AxisLoader object prepares data for an Axis track object.


    Attributes:
        parameters (uorf4u.manager.Parameters): Parameters' class object.
        prepared_data (dict): dict with data needed for a visualisation track.

    """

    def __init__(self, parameters):
        """Create an AxisLoader object.

        Arguments:
            parameters (uorf4u.manager.Parameters): Parameters' class object.

        """
        super().__init__(parameters)

    def prepare_data(self, coordinate_system: dict, additional_data: dict):
        """Prepare data for an Axis visualisation track.

        Attributes:
            coordinate_system (dict): coordinate system of a figure page.
            additional_data (dict): data needed for a track initialisation.

        Returns:
            dict: dictionary with prepared data for visualisation.

        """
        prepared_data = dict()
        prepared_data["coordinate_system"] = coordinate_system
        prepared_data["max_upstream_sequence_length"] = additional_data["max_upstream_sequence_length"]
        prepared_data["max_downstream_sequence_length"] = additional_data["max_downstream_sequence_length"]
        step = int(round(additional_data["max_upstream_sequence_length"] / 2, -2))
        tics = [-additional_data["max_upstream_sequence_length"], 0, additional_data["max_downstream_sequence_length"]]
        x_tic_centred = int(round(-additional_data["max_upstream_sequence_length"] / 2, -2))
        tics.append(x_tic_centred)
        x_tic_left, x_tic_right = x_tic_centred - step, x_tic_centred + step
        while x_tic_right < 0 and x_tic_left > - additional_data["max_upstream_sequence_length"]:
            tics.append(x_tic_left)
            tics.append(x_tic_right)
            x_tic_left -= step
            x_tic_right += step
        tics.sort()
        tics_coordinates = [self.transform_relative_position_to_x_coordinate(i, coordinate_system, additional_data[
            "max_upstream_sequence_length"]) for i in tics]
        prepared_data["tics"] = {k: v for k, v in zip(tics, tics_coordinates)}
        self.prepared_data = prepared_data
        return prepared_data

    def transform_relative_position_to_x_coordinate(self, relative_position: int, coordinate_system: dict,
                                                    max_upstream_sequence_length: int) -> float:
        """Transform nucleotide x coordinate to pdf's.

        Arguments:
            relative_position (int): nucleotide position
            coordinate_system (dict): coordinate system of a figure.
            max_upstream_sequence_length (int): max length of upstream sequences for visualisation.

        Returns:
            float: transformed x coordinate.
        """
        return coordinate_system["x_annotation_start"] + (relative_position + max_upstream_sequence_length) * \
               coordinate_system["transformation_coef"]

    def create_track(self) -> TicsVis:
        """Initialise a Tics track object.

        Returns:
            TicsVis: visualisation track.

        """
        return TicsVis(self.prepared_data, self.parameters)

__init__(parameters)

Create an AxisLoader object.

Parameters:

Source code in uorf4u/drawing_annotation.py 
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def __init__(self, parameters):
    """Create an AxisLoader object.

    Arguments:
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """
    super().__init__(parameters)

create_track()

Initialise a Tics track object.

Returns:

  • TicsVis( TicsVis ) –

    visualisation track.

Source code in uorf4u/drawing_annotation.py 
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def create_track(self) -> TicsVis:
    """Initialise a Tics track object.

    Returns:
        TicsVis: visualisation track.

    """
    return TicsVis(self.prepared_data, self.parameters)

prepare_data(coordinate_system, additional_data)

Prepare data for an Axis visualisation track.

Attributes:

  • coordinate_system (dict) –

    coordinate system of a figure page.

  • additional_data (dict) –

    data needed for a track initialisation.

Returns:

  • dict –

    dictionary with prepared data for visualisation.

Source code in uorf4u/drawing_annotation.py 
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def prepare_data(self, coordinate_system: dict, additional_data: dict):
    """Prepare data for an Axis visualisation track.

    Attributes:
        coordinate_system (dict): coordinate system of a figure page.
        additional_data (dict): data needed for a track initialisation.

    Returns:
        dict: dictionary with prepared data for visualisation.

    """
    prepared_data = dict()
    prepared_data["coordinate_system"] = coordinate_system
    prepared_data["max_upstream_sequence_length"] = additional_data["max_upstream_sequence_length"]
    prepared_data["max_downstream_sequence_length"] = additional_data["max_downstream_sequence_length"]
    step = int(round(additional_data["max_upstream_sequence_length"] / 2, -2))
    tics = [-additional_data["max_upstream_sequence_length"], 0, additional_data["max_downstream_sequence_length"]]
    x_tic_centred = int(round(-additional_data["max_upstream_sequence_length"] / 2, -2))
    tics.append(x_tic_centred)
    x_tic_left, x_tic_right = x_tic_centred - step, x_tic_centred + step
    while x_tic_right < 0 and x_tic_left > - additional_data["max_upstream_sequence_length"]:
        tics.append(x_tic_left)
        tics.append(x_tic_right)
        x_tic_left -= step
        x_tic_right += step
    tics.sort()
    tics_coordinates = [self.transform_relative_position_to_x_coordinate(i, coordinate_system, additional_data[
        "max_upstream_sequence_length"]) for i in tics]
    prepared_data["tics"] = {k: v for k, v in zip(tics, tics_coordinates)}
    self.prepared_data = prepared_data
    return prepared_data

transform_relative_position_to_x_coordinate(relative_position, coordinate_system, max_upstream_sequence_length)

Transform nucleotide x coordinate to pdf's.

Parameters:

  • relative_position (int) –

    nucleotide position

  • coordinate_system (dict) –

    coordinate system of a figure.

  • max_upstream_sequence_length (int) –

    max length of upstream sequences for visualisation.

Returns:

  • float( float ) –

    transformed x coordinate.

Source code in uorf4u/drawing_annotation.py 
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def transform_relative_position_to_x_coordinate(self, relative_position: int, coordinate_system: dict,
                                                max_upstream_sequence_length: int) -> float:
    """Transform nucleotide x coordinate to pdf's.

    Arguments:
        relative_position (int): nucleotide position
        coordinate_system (dict): coordinate system of a figure.
        max_upstream_sequence_length (int): max length of upstream sequences for visualisation.

    Returns:
        float: transformed x coordinate.
    """
    return coordinate_system["x_annotation_start"] + (relative_position + max_upstream_sequence_length) * \
           coordinate_system["transformation_coef"]

Image

An Image object holds pdf.

Attributes:

  • canvas (reportlab.pdfgen.canvas.Canvas) –

    pdf object of the reportlab library.

Source code in uorf4u/drawing_annotation.py 
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class Image:
    """An Image object holds pdf.

    Attributes:
        canvas (reportlab.pdfgen.canvas.Canvas): pdf object of the reportlab library.

    """

    def __init__(self, filename: str, width: float, height: float):
        """Create an Image object.

        Arguments:
            filename (str): path and name of a pdf.
            width (float): width of a pdf.
            height (float): height of a pdf.

        """
        self.canvas = reportlab.pdfgen.canvas.Canvas(filename, pagesize=(width, height))

    def save(self) -> None:
        """Save a pdf file.

        Returns:
            None

        """
        self.canvas.save()
        return None

__init__(filename, width, height)

Create an Image object.

Parameters:

  • filename (str) –

    path and name of a pdf.

  • width (float) –

    width of a pdf.

  • height (float) –

    height of a pdf.

Source code in uorf4u/drawing_annotation.py 
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def __init__(self, filename: str, width: float, height: float):
    """Create an Image object.

    Arguments:
        filename (str): path and name of a pdf.
        width (float): width of a pdf.
        height (float): height of a pdf.

    """
    self.canvas = reportlab.pdfgen.canvas.Canvas(filename, pagesize=(width, height))

save()

Save a pdf file.

Returns:

  • None –

    None

Source code in uorf4u/drawing_annotation.py 
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def save(self) -> None:
    """Save a pdf file.

    Returns:
        None

    """
    self.canvas.save()
    return None

Loader

Parent class for tracks loaders.

Attributes:

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

  • prepared_data (dict) –

    dict with data needed for visualisation tracks.

Source code in uorf4u/drawing_annotation.py 
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class Loader:
    """Parent class for tracks loaders.

    Attributes:
        parameters (uorf4u.manager.Parameters): Parameters' class object.
        prepared_data (dict): dict with data needed for visualisation tracks.

    """

    def __init__(self, parameters: uorf4u.manager.Parameters):
        """Parent's constructor for creating a Loader class object.

        Arguments:
            parameters (uorf4u.manager.Parameters): Parameters' class object.
        """
        self.parameters = parameters
        self.prepared_data = None

    def prepare_data(self) -> None:
        """Empty parent's method for data preparation.

        Returns:
            None

        """
        pass

    def create_track(self) -> None:
        """Empty parent's method for initialisation of a track.

        Returns:
            None

        """
        pass

__init__(parameters)

Parent's constructor for creating a Loader class object.

Parameters:

Source code in uorf4u/drawing_annotation.py 
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def __init__(self, parameters: uorf4u.manager.Parameters):
    """Parent's constructor for creating a Loader class object.

    Arguments:
        parameters (uorf4u.manager.Parameters): Parameters' class object.
    """
    self.parameters = parameters
    self.prepared_data = None

create_track()

Empty parent's method for initialisation of a track.

Returns:

  • None –

    None

Source code in uorf4u/drawing_annotation.py 
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def create_track(self) -> None:
    """Empty parent's method for initialisation of a track.

    Returns:
        None

    """
    pass

prepare_data()

Empty parent's method for data preparation.

Returns:

  • None –

    None

Source code in uorf4u/drawing_annotation.py 
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def prepare_data(self) -> None:
    """Empty parent's method for data preparation.

    Returns:
        None

    """
    pass

SequenceVis

Bases: Track

SequenceVis track draws sequences and annotation.

Attributes:

  • visualisation_data (dict) –

    a dictionary with data needed for visualisation.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

  • needed_space (float) –

    needed vertical space for a track.

Source code in uorf4u/drawing_annotation.py 
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class SequenceVis(Track):
    """SequenceVis track draws sequences and annotation.

    Attributes:
        visualisation_data (dict): a dictionary with data needed for visualisation.
        parameters (uorf4u.manager.Parameters): Parameters' class object.
        needed_space (float): needed vertical space for a track.

    """

    def __init__(self, visualisation_data: dict, parameters: uorf4u.manager.Parameters):
        """Create a SequenceVis object.

        Arguments:
            visualisation_data (dict): a dictionary with data needed for visualisation.
            parameters (uorf4u.manager.Parameters): Parameters' class object.

        """
        super().__init__(visualisation_data, parameters)
        self.needed_space = None

    def needed_y_space(self) -> float:
        """Calculate needed vertical space for a SequenceVis track.

        Returns:
            float: needed vertical space.

        """
        self.needed_space = self.parameters.arguments["orf_height"] * cm
        return self.needed_space

    def draw(self, canvas: reportlab.pdfgen.canvas.Canvas) -> None:
        """Draw a Sequence track.

        Arguments:
            canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.

        Returns:
            None

        """
        orf_height = self.parameters.arguments["orf_height"] * cm
        y_c = self.visualisation_data["y_top"] - 0.5 * orf_height
        x_offset = 0.5 * self.parameters.arguments["upstream_seq_line_width"]
        canvas.setStrokeColorRGB(*uorf4u.methods.get_color("upstream_seq_line_color", self.parameters.arguments))
        canvas.setLineCap(0)
        canvas.setLineWidth(self.parameters.arguments["upstream_seq_line_width"])
        canvas.line(self.visualisation_data["upstream_sequence_line_start_x"], y_c,
                    self.visualisation_data["upstream_sequence_line_stop_x"] - x_offset, y_c)
        # Cleaning the space:
        canvas.setFillColorRGB
        canvas.setStrokeColorRGB(1, 1, 1, 1)

        for orf_dict in self.visualisation_data["orfs_coordinates_dict"].values():

            canvas.setLineWidth(self.parameters.arguments["upstream_seq_line_width"]*1.5)
            canvas.line(orf_dict["x_start"], y_c, orf_dict["x_stop"], y_c)
            #canvas.rect(orf_dict["x_start"], y_c - orf_height / 2, orf_dict["x_stop"] - orf_dict["x_start"], orf_height,
            #            stroke=0, fill=1)
        if self.parameters.arguments["check_assembly_annotation"] and \
                "fasta" not in self.parameters.cmd_arguments.keys():
            for protein_id, cds_dict in self.visualisation_data["CDSs_coordinates_dict"].items():
                canvas.line(cds_dict["x_start"], y_c, cds_dict["x_stop"], y_c)
        canvas.setLineWidth(self.parameters.arguments["upstream_seq_line_width"])

        # Labels
        canvas.setFillColorRGB(*uorf4u.methods.get_color("label_color", self.parameters.arguments))
        canvas.setFont("regular", self.visualisation_data["label_font_size"])
        y_l = y_c - 0.5 * (self.parameters.arguments["label_height_to_orf_height"] * orf_height)
        canvas.drawRightString(self.visualisation_data["coordinate_system"]["x_labels_stop"], y_l,
                               self.visualisation_data["useq_label"])

        # main_CDS
        canvas.setLineWidth(self.parameters.arguments["orf_line_width"])
        canvas.setStrokeColorRGB(*uorf4u.methods.get_color("cds_seq_stroke_color", self.parameters.arguments))
        canvas.setFillColorRGB(*uorf4u.methods.get_color("cds_seq_fill_color", self.parameters.arguments))
        p = canvas.beginPath()
        p.moveTo(self.visualisation_data["main_CDS_stop_x"], y_c - orf_height / 2)
        p.lineTo(self.visualisation_data["main_CDS_start_x"], y_c - orf_height / 2)
        p.lineTo(self.visualisation_data["main_CDS_start_x"], y_c + orf_height / 2)
        p.lineTo(self.visualisation_data["main_CDS_stop_x"], y_c + orf_height / 2)
        canvas.drawPath(p, stroke=1, fill=1)
        # Other ORFs:
        for orf in self.visualisation_data["annotated_orfs"]:
            orf_dict = self.visualisation_data["orfs_coordinates_dict"][orf]
            if orf != self.visualisation_data["conserved_orf"]:
                fill_color = None
                stroke_color = uorf4u.methods.get_color("other_uorfs_stroke_color", self.parameters.arguments)

            else:
                fill_color = uorf4u.methods.get_color("conserved_uorfs_fill_color", self.parameters.arguments)
                stroke_color = uorf4u.methods.get_color("conserved_uorfs_stroke_color", self.parameters.arguments)
            self.orf_object(canvas, orf_dict["x_start"], orf_dict["x_stop"], y_c, orf_dict["strand"], orf_height,
                            orf_dict["left_out"], orf_dict["right_out"], fill_color, stroke_color)

        # Annotated in RefSeq CDSs
        if self.parameters.arguments["check_assembly_annotation"] and \
                "fasta" not in self.parameters.cmd_arguments.keys():
            fill_color = None
            stroke_color = uorf4u.methods.get_color("annotated_orf_stroke_color", self.parameters.arguments)
            for protein_id, cds_dict in self.visualisation_data["CDSs_coordinates_dict"].items():
                self.orf_object(canvas, cds_dict["x_start"], cds_dict["x_stop"], y_c, cds_dict["strand"], orf_height,
                                cds_dict["left_out"], cds_dict["right_out"], fill_color, stroke_color)
        return None

    def orf_object(self, canvas: reportlab.pdfgen.canvas.Canvas, x_start: float, x_stop: float, y_c: float, strand: str,
                   height: float, left_out: bool, right_out: bool, fill_color: str, stroke_color: str) -> None:
        """Method for drawing an ORF's polygon.

        Arguments:
            canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.
            x_start (float): ORF's start coordinate (already transformed to pdf's)
            x_stop (float): ORF's stop coordinate (already transformed to pdf's)
            y_c: (float): centred y coordinate of a current track.
            strand (str): strand of an ORF.
            height (float): height of a polygon.
            left_out (bool): whether an ORF is out of range on the left.
            right_out (bool): whether an ORF is out of range on the right.
            fill_color (str): fill color of a polygon.
            stroke_color (str): stroke color of a polygon.

        Returns:
            None
        """
        fill, stroke = 0, 0
        if stroke_color:
            canvas.setStrokeColorRGB(*stroke_color)
            stroke = 1
        if fill_color:
            canvas.setFillColorRGB(*fill_color)
            fill = 1
        arrow_length = min(height, (x_stop - x_start))
        p = canvas.beginPath()
        if strand == "+" and not left_out and not right_out:
            p.moveTo(x_start, y_c)
            p.lineTo(x_start, y_c + height / 2)
            p.lineTo(x_stop - arrow_length, y_c + height / 2)
            p.lineTo(x_stop, y_c)
            p.lineTo(x_stop - arrow_length, y_c - height / 2)
            p.lineTo(x_start, y_c - height / 2)
            p.lineTo(x_start, y_c)
        elif strand == "+" and left_out and not right_out:
            p.moveTo(x_start, y_c + height / 2)
            p.lineTo(x_stop - arrow_length, y_c + height / 2)
            p.lineTo(x_stop, y_c)
            p.lineTo(x_stop - arrow_length, y_c - height / 2)
            p.lineTo(x_start, y_c - height / 2)
        elif strand == "+" and right_out and not left_out:
            p.moveTo(x_stop, y_c + height / 2)
            p.lineTo(x_start, y_c + height / 2)
            p.lineTo(x_start, y_c - height / 2)
            p.lineTo(x_stop, y_c - height / 2)
        elif strand == "-" and not left_out and not right_out:
            p.moveTo(x_stop, y_c)
            p.lineTo(x_stop, y_c + height / 2)
            p.lineTo(x_start + arrow_length, y_c + height / 2)
            p.lineTo(x_start, y_c)
            p.lineTo(x_start + arrow_length, y_c - height / 2)
            p.lineTo(x_stop, y_c - height / 2)
            p.lineTo(x_stop, y_c)
        elif strand == "-" and right_out and not left_out:
            p.moveTo(x_stop, y_c + height / 2)
            p.lineTo(x_start + arrow_length, y_c + height / 2)
            p.lineTo(x_start, y_c)
            p.lineTo(x_start + arrow_length, y_c - height / 2)
            p.lineTo(x_stop, y_c - height / 2)
        elif strand == "-" and left_out and not right_out:
            p.moveTo(x_start, y_c + height / 2)
            p.lineTo(x_stop, y_c + height / 2)
            p.lineTo(x_stop, y_c - height / 2)
            p.lineTo(x_start, y_c - height / 2)
        canvas.drawPath(p, stroke=stroke, fill=fill)

__init__(visualisation_data, parameters)

Create a SequenceVis object.

Parameters:

  • visualisation_data (dict) –

    a dictionary with data needed for visualisation.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

Source code in uorf4u/drawing_annotation.py 
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def __init__(self, visualisation_data: dict, parameters: uorf4u.manager.Parameters):
    """Create a SequenceVis object.

    Arguments:
        visualisation_data (dict): a dictionary with data needed for visualisation.
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """
    super().__init__(visualisation_data, parameters)
    self.needed_space = None

draw(canvas)

Draw a Sequence track.

Parameters:

  • canvas (reportlab.pdfgen.canvas.Canvas) –

    a pdf object.

Returns:

  • None –

    None

Source code in uorf4u/drawing_annotation.py 
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def draw(self, canvas: reportlab.pdfgen.canvas.Canvas) -> None:
    """Draw a Sequence track.

    Arguments:
        canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.

    Returns:
        None

    """
    orf_height = self.parameters.arguments["orf_height"] * cm
    y_c = self.visualisation_data["y_top"] - 0.5 * orf_height
    x_offset = 0.5 * self.parameters.arguments["upstream_seq_line_width"]
    canvas.setStrokeColorRGB(*uorf4u.methods.get_color("upstream_seq_line_color", self.parameters.arguments))
    canvas.setLineCap(0)
    canvas.setLineWidth(self.parameters.arguments["upstream_seq_line_width"])
    canvas.line(self.visualisation_data["upstream_sequence_line_start_x"], y_c,
                self.visualisation_data["upstream_sequence_line_stop_x"] - x_offset, y_c)
    # Cleaning the space:
    canvas.setFillColorRGB
    canvas.setStrokeColorRGB(1, 1, 1, 1)

    for orf_dict in self.visualisation_data["orfs_coordinates_dict"].values():

        canvas.setLineWidth(self.parameters.arguments["upstream_seq_line_width"]*1.5)
        canvas.line(orf_dict["x_start"], y_c, orf_dict["x_stop"], y_c)
        #canvas.rect(orf_dict["x_start"], y_c - orf_height / 2, orf_dict["x_stop"] - orf_dict["x_start"], orf_height,
        #            stroke=0, fill=1)
    if self.parameters.arguments["check_assembly_annotation"] and \
            "fasta" not in self.parameters.cmd_arguments.keys():
        for protein_id, cds_dict in self.visualisation_data["CDSs_coordinates_dict"].items():
            canvas.line(cds_dict["x_start"], y_c, cds_dict["x_stop"], y_c)
    canvas.setLineWidth(self.parameters.arguments["upstream_seq_line_width"])

    # Labels
    canvas.setFillColorRGB(*uorf4u.methods.get_color("label_color", self.parameters.arguments))
    canvas.setFont("regular", self.visualisation_data["label_font_size"])
    y_l = y_c - 0.5 * (self.parameters.arguments["label_height_to_orf_height"] * orf_height)
    canvas.drawRightString(self.visualisation_data["coordinate_system"]["x_labels_stop"], y_l,
                           self.visualisation_data["useq_label"])

    # main_CDS
    canvas.setLineWidth(self.parameters.arguments["orf_line_width"])
    canvas.setStrokeColorRGB(*uorf4u.methods.get_color("cds_seq_stroke_color", self.parameters.arguments))
    canvas.setFillColorRGB(*uorf4u.methods.get_color("cds_seq_fill_color", self.parameters.arguments))
    p = canvas.beginPath()
    p.moveTo(self.visualisation_data["main_CDS_stop_x"], y_c - orf_height / 2)
    p.lineTo(self.visualisation_data["main_CDS_start_x"], y_c - orf_height / 2)
    p.lineTo(self.visualisation_data["main_CDS_start_x"], y_c + orf_height / 2)
    p.lineTo(self.visualisation_data["main_CDS_stop_x"], y_c + orf_height / 2)
    canvas.drawPath(p, stroke=1, fill=1)
    # Other ORFs:
    for orf in self.visualisation_data["annotated_orfs"]:
        orf_dict = self.visualisation_data["orfs_coordinates_dict"][orf]
        if orf != self.visualisation_data["conserved_orf"]:
            fill_color = None
            stroke_color = uorf4u.methods.get_color("other_uorfs_stroke_color", self.parameters.arguments)

        else:
            fill_color = uorf4u.methods.get_color("conserved_uorfs_fill_color", self.parameters.arguments)
            stroke_color = uorf4u.methods.get_color("conserved_uorfs_stroke_color", self.parameters.arguments)
        self.orf_object(canvas, orf_dict["x_start"], orf_dict["x_stop"], y_c, orf_dict["strand"], orf_height,
                        orf_dict["left_out"], orf_dict["right_out"], fill_color, stroke_color)

    # Annotated in RefSeq CDSs
    if self.parameters.arguments["check_assembly_annotation"] and \
            "fasta" not in self.parameters.cmd_arguments.keys():
        fill_color = None
        stroke_color = uorf4u.methods.get_color("annotated_orf_stroke_color", self.parameters.arguments)
        for protein_id, cds_dict in self.visualisation_data["CDSs_coordinates_dict"].items():
            self.orf_object(canvas, cds_dict["x_start"], cds_dict["x_stop"], y_c, cds_dict["strand"], orf_height,
                            cds_dict["left_out"], cds_dict["right_out"], fill_color, stroke_color)
    return None

needed_y_space()

Calculate needed vertical space for a SequenceVis track.

Returns:

  • float( float ) –

    needed vertical space.

Source code in uorf4u/drawing_annotation.py 
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def needed_y_space(self) -> float:
    """Calculate needed vertical space for a SequenceVis track.

    Returns:
        float: needed vertical space.

    """
    self.needed_space = self.parameters.arguments["orf_height"] * cm
    return self.needed_space

orf_object(canvas, x_start, x_stop, y_c, strand, height, left_out, right_out, fill_color, stroke_color)

Method for drawing an ORF's polygon.

Parameters:

  • canvas (reportlab.pdfgen.canvas.Canvas) –

    a pdf object.

  • x_start (float) –

    ORF's start coordinate (already transformed to pdf's)

  • x_stop (float) –

    ORF's stop coordinate (already transformed to pdf's)

  • y_c (float) –

    (float): centred y coordinate of a current track.

  • strand (str) –

    strand of an ORF.

  • height (float) –

    height of a polygon.

  • left_out (bool) –

    whether an ORF is out of range on the left.

  • right_out (bool) –

    whether an ORF is out of range on the right.

  • fill_color (str) –

    fill color of a polygon.

  • stroke_color (str) –

    stroke color of a polygon.

Returns:

  • None –

    None

Source code in uorf4u/drawing_annotation.py 
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def orf_object(self, canvas: reportlab.pdfgen.canvas.Canvas, x_start: float, x_stop: float, y_c: float, strand: str,
               height: float, left_out: bool, right_out: bool, fill_color: str, stroke_color: str) -> None:
    """Method for drawing an ORF's polygon.

    Arguments:
        canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.
        x_start (float): ORF's start coordinate (already transformed to pdf's)
        x_stop (float): ORF's stop coordinate (already transformed to pdf's)
        y_c: (float): centred y coordinate of a current track.
        strand (str): strand of an ORF.
        height (float): height of a polygon.
        left_out (bool): whether an ORF is out of range on the left.
        right_out (bool): whether an ORF is out of range on the right.
        fill_color (str): fill color of a polygon.
        stroke_color (str): stroke color of a polygon.

    Returns:
        None
    """
    fill, stroke = 0, 0
    if stroke_color:
        canvas.setStrokeColorRGB(*stroke_color)
        stroke = 1
    if fill_color:
        canvas.setFillColorRGB(*fill_color)
        fill = 1
    arrow_length = min(height, (x_stop - x_start))
    p = canvas.beginPath()
    if strand == "+" and not left_out and not right_out:
        p.moveTo(x_start, y_c)
        p.lineTo(x_start, y_c + height / 2)
        p.lineTo(x_stop - arrow_length, y_c + height / 2)
        p.lineTo(x_stop, y_c)
        p.lineTo(x_stop - arrow_length, y_c - height / 2)
        p.lineTo(x_start, y_c - height / 2)
        p.lineTo(x_start, y_c)
    elif strand == "+" and left_out and not right_out:
        p.moveTo(x_start, y_c + height / 2)
        p.lineTo(x_stop - arrow_length, y_c + height / 2)
        p.lineTo(x_stop, y_c)
        p.lineTo(x_stop - arrow_length, y_c - height / 2)
        p.lineTo(x_start, y_c - height / 2)
    elif strand == "+" and right_out and not left_out:
        p.moveTo(x_stop, y_c + height / 2)
        p.lineTo(x_start, y_c + height / 2)
        p.lineTo(x_start, y_c - height / 2)
        p.lineTo(x_stop, y_c - height / 2)
    elif strand == "-" and not left_out and not right_out:
        p.moveTo(x_stop, y_c)
        p.lineTo(x_stop, y_c + height / 2)
        p.lineTo(x_start + arrow_length, y_c + height / 2)
        p.lineTo(x_start, y_c)
        p.lineTo(x_start + arrow_length, y_c - height / 2)
        p.lineTo(x_stop, y_c - height / 2)
        p.lineTo(x_stop, y_c)
    elif strand == "-" and right_out and not left_out:
        p.moveTo(x_stop, y_c + height / 2)
        p.lineTo(x_start + arrow_length, y_c + height / 2)
        p.lineTo(x_start, y_c)
        p.lineTo(x_start + arrow_length, y_c - height / 2)
        p.lineTo(x_stop, y_c - height / 2)
    elif strand == "-" and left_out and not right_out:
        p.moveTo(x_start, y_c + height / 2)
        p.lineTo(x_stop, y_c + height / 2)
        p.lineTo(x_stop, y_c - height / 2)
        p.lineTo(x_start, y_c - height / 2)
    canvas.drawPath(p, stroke=stroke, fill=fill)

SequencesLoader

Bases: Loader

A SequencesLoader object prepares data for a Sequence track object.

Attributes:

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

  • prepared_data (dict) –

    dict with data needed for a visualisation track.

Source code in uorf4u/drawing_annotation.py 
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class SequencesLoader(Loader):
    """A SequencesLoader object prepares data for a Sequence track object.


    Attributes:
        parameters (uorf4u.manager.Parameters): Parameters' class object.
        prepared_data (dict): dict with data needed for a visualisation track.

    """

    def __init__(self, parameters):
        """Create a SequenceLoader object.

        Arguments:
            parameters (uorf4u.manager.Parameters): Parameters' class object.

        """
        super().__init__(parameters)

    def prepare_data(self, upstream_sequence: Bio.SeqRecord.SeqRecord, conserved_orf, coordinate_system: dict,
                     additional_data: dict) -> dict:
        """Prepare data for a Title visualisation track.

        Attributes:
            upstream_sequence (dict): upstream sequence' data.
            conserved_orf (uorf4u.data_processing.ORF): conserved ORF on the upstream sequence.
            coordinate_system (dict): coordinate system of a figure page.
            additional_data (dict): data needed for a track initialisation.

        Returns:
            dict: dictionary with prepared data for visualisation.

        """
        prepared_data = dict()
        max_upstream_sequence_length = additional_data["max_upstream_sequence_length"]
        prepared_data["coordinate_system"] = coordinate_system
        prepared_data["label_font_size"] = additional_data["label_font_size"]
        prepared_data["label_right_border"] = coordinate_system["x_labels_stop"]
        prepared_data["upstream_sequence_line_start_x"] = coordinate_system["x_annotation_start"] + \
                                                          ((max_upstream_sequence_length -
                                                            upstream_sequence.annotations["upstream_region_length"]) * \
                                                           coordinate_system["transformation_coef"])
        prepared_data["upstream_sequence_line_stop_x"] = coordinate_system["x_annotation_start"] + \
                                                         (max_upstream_sequence_length *
                                                          coordinate_system["transformation_coef"])
        prepared_data["main_CDS_start_x"] = coordinate_system["x_annotation_start"] + \
                                            (max_upstream_sequence_length *
                                             coordinate_system["transformation_coef"])
        prepared_data["main_CDS_stop_x"] = coordinate_system["x_annotation_start"] + \
                                           ((max_upstream_sequence_length +
                                             upstream_sequence.annotations["downstream_region_length"]) *
                                            coordinate_system["transformation_coef"])

        prepared_data["orfs_coordinates_dict"] = {k: v for k, v in
                                                  zip(upstream_sequence.annotations["ORFs"],
                                                      [self.calculate_orf_position(i.start, i.stop, "+",
                                                                                   upstream_sequence,
                                                                                   max_upstream_sequence_length,
                                                                                   coordinate_system) for i in
                                                       upstream_sequence.annotations["ORFs"]])}
        prepared_data["useq_label"] = upstream_sequence.annotations["label"]
        prepared_data["annotated_orfs"] = [orf for orf in upstream_sequence.annotations["ORFs"] if orf != conserved_orf]
        prepared_data["annotated_orfs"].append(conserved_orf)
        prepared_data["conserved_orf"] = conserved_orf
        if self.parameters.arguments["check_assembly_annotation"] and upstream_sequence.annotations["RefSeq"]:
            prepared_data["CDSs"] = [i for i in upstream_sequence.annotations["locus_annotation"].CDSs if
                                     i["relative_start"] != upstream_sequence.annotations["upstream_region_length"]]
            prepared_data["CDSs_coordinates_dict"] = {k: v for k, v in
                                                      zip([i["protein_id"] for i in
                                                           prepared_data["CDSs"]],
                                                          [self.calculate_orf_position(i["relative_start"],
                                                                                       i["relative_stop"],
                                                                                       i["relative_strand"],
                                                                                       upstream_sequence,
                                                                                       max_upstream_sequence_length,
                                                                                       coordinate_system) for i in
                                                           prepared_data["CDSs"]])}
        else:
            prepared_data["CDSs"] = None
        self.prepared_data = prepared_data

        return prepared_data

    def calculate_orf_position(self, start: int, stop: int, strand: str, useq: Bio.SeqRecord.SeqRecord,
                               max_upstream_sequence_length: int, coordinate_system: dict) -> dict:
        """Transform an ORF's nucleotide coordinates to pdf's coordinates.

        Arguments:
            start (int): start coordinate in nt.
            stop (int): stop coordinate in nt.
            strand (str): strand of an ORF.
            useq (dict): current upstream sequence.
            max_upstream_sequence_length (int): max length of upstream sequences for visualisation.
            coordinate_system (dict): coordinate system of a figure.

        Returns:
            dict: transformed orf's coordinates.
        """
        orf_coordinates = dict()
        orf_coordinates["x_start"] = coordinate_system["x_annotation_start"] + (
                max(0, start) + (max_upstream_sequence_length - useq.annotations["upstream_region_length"])) * \
                                     coordinate_system["transformation_coef"]
        orf_coordinates["x_stop"] = coordinate_system["x_annotation_start"] + (
                min(stop, useq.annotations["length"]) + (
                max_upstream_sequence_length - useq.annotations["upstream_region_length"])) * \
                                    coordinate_system["transformation_coef"]
        orf_coordinates["strand"] = strand
        orf_coordinates["left_out"] = start < 0
        orf_coordinates["right_out"] = stop > useq.annotations["length"]
        return orf_coordinates

    def create_track(self) -> SequenceVis:
        """Initialise a Sequence track object.

        Returns:
            SequenceVis: visualisation track.

        """
        return SequenceVis(self.prepared_data, self.parameters)

__init__(parameters)

Create a SequenceLoader object.

Parameters:

Source code in uorf4u/drawing_annotation.py 
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def __init__(self, parameters):
    """Create a SequenceLoader object.

    Arguments:
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """
    super().__init__(parameters)

calculate_orf_position(start, stop, strand, useq, max_upstream_sequence_length, coordinate_system)

Transform an ORF's nucleotide coordinates to pdf's coordinates.

Parameters:

  • start (int) –

    start coordinate in nt.

  • stop (int) –

    stop coordinate in nt.

  • strand (str) –

    strand of an ORF.

  • useq (dict) –

    current upstream sequence.

  • max_upstream_sequence_length (int) –

    max length of upstream sequences for visualisation.

  • coordinate_system (dict) –

    coordinate system of a figure.

Returns:

  • dict( dict ) –

    transformed orf's coordinates.

Source code in uorf4u/drawing_annotation.py 
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def calculate_orf_position(self, start: int, stop: int, strand: str, useq: Bio.SeqRecord.SeqRecord,
                           max_upstream_sequence_length: int, coordinate_system: dict) -> dict:
    """Transform an ORF's nucleotide coordinates to pdf's coordinates.

    Arguments:
        start (int): start coordinate in nt.
        stop (int): stop coordinate in nt.
        strand (str): strand of an ORF.
        useq (dict): current upstream sequence.
        max_upstream_sequence_length (int): max length of upstream sequences for visualisation.
        coordinate_system (dict): coordinate system of a figure.

    Returns:
        dict: transformed orf's coordinates.
    """
    orf_coordinates = dict()
    orf_coordinates["x_start"] = coordinate_system["x_annotation_start"] + (
            max(0, start) + (max_upstream_sequence_length - useq.annotations["upstream_region_length"])) * \
                                 coordinate_system["transformation_coef"]
    orf_coordinates["x_stop"] = coordinate_system["x_annotation_start"] + (
            min(stop, useq.annotations["length"]) + (
            max_upstream_sequence_length - useq.annotations["upstream_region_length"])) * \
                                coordinate_system["transformation_coef"]
    orf_coordinates["strand"] = strand
    orf_coordinates["left_out"] = start < 0
    orf_coordinates["right_out"] = stop > useq.annotations["length"]
    return orf_coordinates

create_track()

Initialise a Sequence track object.

Returns:

Source code in uorf4u/drawing_annotation.py 
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def create_track(self) -> SequenceVis:
    """Initialise a Sequence track object.

    Returns:
        SequenceVis: visualisation track.

    """
    return SequenceVis(self.prepared_data, self.parameters)

prepare_data(upstream_sequence, conserved_orf, coordinate_system, additional_data)

Prepare data for a Title visualisation track.

Attributes:

  • upstream_sequence (dict) –

    upstream sequence' data.

  • conserved_orf (uorf4u.data_processing.ORF) –

    conserved ORF on the upstream sequence.

  • coordinate_system (dict) –

    coordinate system of a figure page.

  • additional_data (dict) –

    data needed for a track initialisation.

Returns:

  • dict( dict ) –

    dictionary with prepared data for visualisation.

Source code in uorf4u/drawing_annotation.py 
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def prepare_data(self, upstream_sequence: Bio.SeqRecord.SeqRecord, conserved_orf, coordinate_system: dict,
                 additional_data: dict) -> dict:
    """Prepare data for a Title visualisation track.

    Attributes:
        upstream_sequence (dict): upstream sequence' data.
        conserved_orf (uorf4u.data_processing.ORF): conserved ORF on the upstream sequence.
        coordinate_system (dict): coordinate system of a figure page.
        additional_data (dict): data needed for a track initialisation.

    Returns:
        dict: dictionary with prepared data for visualisation.

    """
    prepared_data = dict()
    max_upstream_sequence_length = additional_data["max_upstream_sequence_length"]
    prepared_data["coordinate_system"] = coordinate_system
    prepared_data["label_font_size"] = additional_data["label_font_size"]
    prepared_data["label_right_border"] = coordinate_system["x_labels_stop"]
    prepared_data["upstream_sequence_line_start_x"] = coordinate_system["x_annotation_start"] + \
                                                      ((max_upstream_sequence_length -
                                                        upstream_sequence.annotations["upstream_region_length"]) * \
                                                       coordinate_system["transformation_coef"])
    prepared_data["upstream_sequence_line_stop_x"] = coordinate_system["x_annotation_start"] + \
                                                     (max_upstream_sequence_length *
                                                      coordinate_system["transformation_coef"])
    prepared_data["main_CDS_start_x"] = coordinate_system["x_annotation_start"] + \
                                        (max_upstream_sequence_length *
                                         coordinate_system["transformation_coef"])
    prepared_data["main_CDS_stop_x"] = coordinate_system["x_annotation_start"] + \
                                       ((max_upstream_sequence_length +
                                         upstream_sequence.annotations["downstream_region_length"]) *
                                        coordinate_system["transformation_coef"])

    prepared_data["orfs_coordinates_dict"] = {k: v for k, v in
                                              zip(upstream_sequence.annotations["ORFs"],
                                                  [self.calculate_orf_position(i.start, i.stop, "+",
                                                                               upstream_sequence,
                                                                               max_upstream_sequence_length,
                                                                               coordinate_system) for i in
                                                   upstream_sequence.annotations["ORFs"]])}
    prepared_data["useq_label"] = upstream_sequence.annotations["label"]
    prepared_data["annotated_orfs"] = [orf for orf in upstream_sequence.annotations["ORFs"] if orf != conserved_orf]
    prepared_data["annotated_orfs"].append(conserved_orf)
    prepared_data["conserved_orf"] = conserved_orf
    if self.parameters.arguments["check_assembly_annotation"] and upstream_sequence.annotations["RefSeq"]:
        prepared_data["CDSs"] = [i for i in upstream_sequence.annotations["locus_annotation"].CDSs if
                                 i["relative_start"] != upstream_sequence.annotations["upstream_region_length"]]
        prepared_data["CDSs_coordinates_dict"] = {k: v for k, v in
                                                  zip([i["protein_id"] for i in
                                                       prepared_data["CDSs"]],
                                                      [self.calculate_orf_position(i["relative_start"],
                                                                                   i["relative_stop"],
                                                                                   i["relative_strand"],
                                                                                   upstream_sequence,
                                                                                   max_upstream_sequence_length,
                                                                                   coordinate_system) for i in
                                                       prepared_data["CDSs"]])}
    else:
        prepared_data["CDSs"] = None
    self.prepared_data = prepared_data

    return prepared_data

TicsVis

Bases: Track

TicsVis track draws axis tics.

Attributes:

  • visualisation_data (dict) –

    a dictionary with data needed for visualisation.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

  • needed_space (float) –

    needed vertical space for a track.

Source code in uorf4u/drawing_annotation.py 
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class TicsVis(Track):
    """TicsVis track draws axis tics.

    Attributes:
        visualisation_data (dict): a dictionary with data needed for visualisation.
        parameters (uorf4u.manager.Parameters): Parameters' class object.
        needed_space (float): needed vertical space for a track.

    """

    def __init__(self, visualisation_data: dict, parameters: uorf4u.manager.Parameters):
        """Create a TicsVis object.

        Arguments:
            visualisation_data (dict): a dictionary with data needed for visualisation.
            parameters (uorf4u.manager.Parameters): Parameters' class object.

        """
        super().__init__(visualisation_data, parameters)
        self.needed_space = None

    def needed_y_space(self) -> float:
        """Calculate needed vertical space for a SequenceVis track.

        Returns:
            float: needed vertical space.

        """
        font_type = "regular"
        reportlab.pdfbase.pdfmetrics.registerFont(
            reportlab.pdfbase.ttfonts.TTFont(font_type, self.parameters.arguments[f"font_{font_type}"]))
        face = reportlab.pdfbase.pdfmetrics.getFont("regular").face
        if self.parameters.arguments["axis_tics_font_size"] == "auto":
            text_height = self.parameters.arguments["label_height_to_orf_height"] * self.parameters.arguments[
                "orf_height"] * cm
            font_size = uorf4u.methods.string_height_to_font_size(text_height, "regular", self.parameters.arguments)
            self.parameters.arguments["axis_tics_font_size"] = font_size
        else:
            text_height = (self.parameters.arguments["axis_tics_font_size"] * (face.ascent - face.descent)) / (
                    1000 * 1.38)
        self.visualisation_data["tics_height"] = 0.7 * text_height
        self.visualisation_data["text_space"] = 1.2 * text_height
        self.needed_space = self.visualisation_data["tics_height"] + self.visualisation_data["text_space"]
        return self.needed_space

    def draw(self, canvas: reportlab.pdfgen.canvas.Canvas) -> None:
        """Draw an AxisTics track.

        Arguments:
            canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.

        Returns:
            None

        """
        y_top = self.visualisation_data["y_top"]
        canvas.setLineCap(2)
        canvas.setLineWidth(self.parameters.arguments["axis_tics_line_width"])
        canvas.setStrokeColorRGB(*uorf4u.methods.get_color("label_color", self.parameters.arguments))
        canvas.setFillColorRGB(*uorf4u.methods.get_color("label_color", self.parameters.arguments))
        canvas.setFont("regular", self.parameters.arguments["axis_tics_font_size"])
        canvas.line(self.visualisation_data["coordinate_system"]["x_annotation_start"], y_top,
                    self.visualisation_data["coordinate_system"]["x_annotation_stop"], y_top)
        for tic_label, tic_position in self.visualisation_data["tics"].items():
            canvas.line(tic_position, y_top, tic_position, y_top - self.visualisation_data["tics_height"])
            if tic_label == -self.visualisation_data["max_upstream_sequence_length"]:
                canvas.drawString(tic_position,
                                  y_top - (self.visualisation_data["tics_height"] + self.visualisation_data[
                                      "text_space"]), str(tic_label))
            elif tic_label == self.visualisation_data["max_downstream_sequence_length"]:
                canvas.drawRightString(tic_position,
                                       y_top - (self.visualisation_data["tics_height"] + self.visualisation_data[
                                           "text_space"]), str(tic_label))
            else:
                canvas.drawCentredString(tic_position,
                                         y_top - (self.visualisation_data["tics_height"] + self.visualisation_data[
                                             "text_space"]), str(tic_label))

__init__(visualisation_data, parameters)

Create a TicsVis object.

Parameters:

  • visualisation_data (dict) –

    a dictionary with data needed for visualisation.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

Source code in uorf4u/drawing_annotation.py 
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def __init__(self, visualisation_data: dict, parameters: uorf4u.manager.Parameters):
    """Create a TicsVis object.

    Arguments:
        visualisation_data (dict): a dictionary with data needed for visualisation.
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """
    super().__init__(visualisation_data, parameters)
    self.needed_space = None

draw(canvas)

Draw an AxisTics track.

Parameters:

  • canvas (reportlab.pdfgen.canvas.Canvas) –

    a pdf object.

Returns:

  • None –

    None

Source code in uorf4u/drawing_annotation.py 
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def draw(self, canvas: reportlab.pdfgen.canvas.Canvas) -> None:
    """Draw an AxisTics track.

    Arguments:
        canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.

    Returns:
        None

    """
    y_top = self.visualisation_data["y_top"]
    canvas.setLineCap(2)
    canvas.setLineWidth(self.parameters.arguments["axis_tics_line_width"])
    canvas.setStrokeColorRGB(*uorf4u.methods.get_color("label_color", self.parameters.arguments))
    canvas.setFillColorRGB(*uorf4u.methods.get_color("label_color", self.parameters.arguments))
    canvas.setFont("regular", self.parameters.arguments["axis_tics_font_size"])
    canvas.line(self.visualisation_data["coordinate_system"]["x_annotation_start"], y_top,
                self.visualisation_data["coordinate_system"]["x_annotation_stop"], y_top)
    for tic_label, tic_position in self.visualisation_data["tics"].items():
        canvas.line(tic_position, y_top, tic_position, y_top - self.visualisation_data["tics_height"])
        if tic_label == -self.visualisation_data["max_upstream_sequence_length"]:
            canvas.drawString(tic_position,
                              y_top - (self.visualisation_data["tics_height"] + self.visualisation_data[
                                  "text_space"]), str(tic_label))
        elif tic_label == self.visualisation_data["max_downstream_sequence_length"]:
            canvas.drawRightString(tic_position,
                                   y_top - (self.visualisation_data["tics_height"] + self.visualisation_data[
                                       "text_space"]), str(tic_label))
        else:
            canvas.drawCentredString(tic_position,
                                     y_top - (self.visualisation_data["tics_height"] + self.visualisation_data[
                                         "text_space"]), str(tic_label))

needed_y_space()

Calculate needed vertical space for a SequenceVis track.

Returns:

  • float( float ) –

    needed vertical space.

Source code in uorf4u/drawing_annotation.py 
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def needed_y_space(self) -> float:
    """Calculate needed vertical space for a SequenceVis track.

    Returns:
        float: needed vertical space.

    """
    font_type = "regular"
    reportlab.pdfbase.pdfmetrics.registerFont(
        reportlab.pdfbase.ttfonts.TTFont(font_type, self.parameters.arguments[f"font_{font_type}"]))
    face = reportlab.pdfbase.pdfmetrics.getFont("regular").face
    if self.parameters.arguments["axis_tics_font_size"] == "auto":
        text_height = self.parameters.arguments["label_height_to_orf_height"] * self.parameters.arguments[
            "orf_height"] * cm
        font_size = uorf4u.methods.string_height_to_font_size(text_height, "regular", self.parameters.arguments)
        self.parameters.arguments["axis_tics_font_size"] = font_size
    else:
        text_height = (self.parameters.arguments["axis_tics_font_size"] * (face.ascent - face.descent)) / (
                1000 * 1.38)
    self.visualisation_data["tics_height"] = 0.7 * text_height
    self.visualisation_data["text_space"] = 1.2 * text_height
    self.needed_space = self.visualisation_data["tics_height"] + self.visualisation_data["text_space"]
    return self.needed_space

TitleLoader

Bases: Loader

A TitleLoader object prepares data for a Title track object.

Note:

Title track currently is not available.

Attributes:

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

  • prepared_data (dict) –

    dict with data needed for a visualisation track.

Source code in uorf4u/drawing_annotation.py 
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class TitleLoader(Loader):
    """A TitleLoader object prepares data for a Title track object.

    Note:
        Title track currently is not available.

    Attributes:
        parameters (uorf4u.manager.Parameters): Parameters' class object.
        prepared_data (dict): dict with data needed for a visualisation track.

    """

    def __init__(self, parameters):
        """Create a TitleLoader object.

        Arguments:
            parameters (uorf4u.manager.Parameters): Parameters' class object.

        """
        super().__init__(parameters)

    def prepare_data(self, coordinate_system: dict, additional_data: dict) -> dict:
        """Prepare data for Title visualisation track.

        Attributes:
            coordinate_system (dict): coordinate system of a figure page.
            additional_data (dict): data needed for a track initialisation.

        Returns:
            dict: dictionary with prepared data for visualisation.

        """
        prepared_data = dict()
        prepared_data["title"] = "Title Testing"
        prepared_data["coordinate_system"] = coordinate_system
        self.prepared_data = prepared_data
        return prepared_data

    def create_track(self) -> TitleVis:
        """Initialise a Title track object.

        Returns:
            TitleVis: visualisation track.

        """
        return TitleVis(self.prepared_data, self.parameters)

__init__(parameters)

Create a TitleLoader object.

Parameters:

Source code in uorf4u/drawing_annotation.py 
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def __init__(self, parameters):
    """Create a TitleLoader object.

    Arguments:
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """
    super().__init__(parameters)

create_track()

Initialise a Title track object.

Returns:

  • TitleVis( TitleVis ) –

    visualisation track.

Source code in uorf4u/drawing_annotation.py 
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def create_track(self) -> TitleVis:
    """Initialise a Title track object.

    Returns:
        TitleVis: visualisation track.

    """
    return TitleVis(self.prepared_data, self.parameters)

prepare_data(coordinate_system, additional_data)

Prepare data for Title visualisation track.

Attributes:

  • coordinate_system (dict) –

    coordinate system of a figure page.

  • additional_data (dict) –

    data needed for a track initialisation.

Returns:

  • dict( dict ) –

    dictionary with prepared data for visualisation.

Source code in uorf4u/drawing_annotation.py 
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def prepare_data(self, coordinate_system: dict, additional_data: dict) -> dict:
    """Prepare data for Title visualisation track.

    Attributes:
        coordinate_system (dict): coordinate system of a figure page.
        additional_data (dict): data needed for a track initialisation.

    Returns:
        dict: dictionary with prepared data for visualisation.

    """
    prepared_data = dict()
    prepared_data["title"] = "Title Testing"
    prepared_data["coordinate_system"] = coordinate_system
    self.prepared_data = prepared_data
    return prepared_data

TitleVis

Bases: Track

Title visualisation track object draws figure's title.

Note:

This track currently is not supported.

Attributes:

  • visualisation_data (dict) –

    a dictionary with data needed for visualisation.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

Source code in uorf4u/drawing_annotation.py 
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class TitleVis(Track):
    """Title visualisation track object draws figure's title.

    Note:
        This track currently is not supported.

    Attributes:
        visualisation_data (dict): a dictionary with data needed for visualisation.
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """

    def __init__(self, visualisation_data: dict, parameters: uorf4u.manager.Parameters):
        """Create TitleVis object.

        Arguments:
            visualisation_data (dict): a dictionary with data needed for visualisation.
            parameters (uorf4u.manager.Parameters): Parameters' class object.

        """
        self.visualisation_data = visualisation_data
        self.parameters = parameters

    def needed_y_space(self) -> float:
        """Calculate needed vertical space for a Title track.

        Returns:
            float: needed vertical space.

        """
        font_type = self.parameters.arguments["title_font_type"]
        reportlab.pdfbase.pdfmetrics.registerFont(
            reportlab.pdfbase.ttfonts.TTFont(font_type, self.parameters.arguments[f"font_{font_type}"]))
        face = reportlab.pdfbase.pdfmetrics.getFont(font_type).face
        if self.parameters.arguments["title_font_size"] == "auto":
            text_height = self.parameters.arguments["orf_height"] * cm
            font_size = uorf4u.methods.string_height_to_font_size(text_height, font_type, self.parameters.arguments)
            self.parameters.arguments["title_font_size"] = font_size
        else:
            text_height = (self.parameters.arguments["title_font_size"] * (face.ascent - face.descent)) / (
                    1000 * 1.38)
        self.visualisation_data["text_height"] = text_height
        self.needed_space = text_height * 1.2
        return self.needed_space

    def draw(self, canvas: reportlab.pdfgen.canvas.Canvas) -> None:
        """Draw a Title track.

        Arguments:
            canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.

        Returns:
            None

        """
        x_left_border = self.visualisation_data["coordinate_system"]["x_labels_start"]
        # x_left_border = self.visualisation_data["coordinate_system"]["x_annotation_start"]
        canvas.setFillColorRGB(*uorf4u.methods.get_color("label_color", self.parameters.arguments))
        canvas.setFont(self.parameters.arguments["title_font_type"], self.parameters.arguments["title_font_size"])
        canvas.drawString(x_left_border, self.visualisation_data["y_top"] - self.visualisation_data["text_height"],
                          self.visualisation_data["title"])

__init__(visualisation_data, parameters)

Create TitleVis object.

Parameters:

  • visualisation_data (dict) –

    a dictionary with data needed for visualisation.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

Source code in uorf4u/drawing_annotation.py 
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def __init__(self, visualisation_data: dict, parameters: uorf4u.manager.Parameters):
    """Create TitleVis object.

    Arguments:
        visualisation_data (dict): a dictionary with data needed for visualisation.
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """
    self.visualisation_data = visualisation_data
    self.parameters = parameters

draw(canvas)

Draw a Title track.

Parameters:

  • canvas (reportlab.pdfgen.canvas.Canvas) –

    a pdf object.

Returns:

  • None –

    None

Source code in uorf4u/drawing_annotation.py 
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def draw(self, canvas: reportlab.pdfgen.canvas.Canvas) -> None:
    """Draw a Title track.

    Arguments:
        canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.

    Returns:
        None

    """
    x_left_border = self.visualisation_data["coordinate_system"]["x_labels_start"]
    # x_left_border = self.visualisation_data["coordinate_system"]["x_annotation_start"]
    canvas.setFillColorRGB(*uorf4u.methods.get_color("label_color", self.parameters.arguments))
    canvas.setFont(self.parameters.arguments["title_font_type"], self.parameters.arguments["title_font_size"])
    canvas.drawString(x_left_border, self.visualisation_data["y_top"] - self.visualisation_data["text_height"],
                      self.visualisation_data["title"])

needed_y_space()

Calculate needed vertical space for a Title track.

Returns:

  • float( float ) –

    needed vertical space.

Source code in uorf4u/drawing_annotation.py 
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def needed_y_space(self) -> float:
    """Calculate needed vertical space for a Title track.

    Returns:
        float: needed vertical space.

    """
    font_type = self.parameters.arguments["title_font_type"]
    reportlab.pdfbase.pdfmetrics.registerFont(
        reportlab.pdfbase.ttfonts.TTFont(font_type, self.parameters.arguments[f"font_{font_type}"]))
    face = reportlab.pdfbase.pdfmetrics.getFont(font_type).face
    if self.parameters.arguments["title_font_size"] == "auto":
        text_height = self.parameters.arguments["orf_height"] * cm
        font_size = uorf4u.methods.string_height_to_font_size(text_height, font_type, self.parameters.arguments)
        self.parameters.arguments["title_font_size"] = font_size
    else:
        text_height = (self.parameters.arguments["title_font_size"] * (face.ascent - face.descent)) / (
                1000 * 1.38)
    self.visualisation_data["text_height"] = text_height
    self.needed_space = text_height * 1.2
    return self.needed_space

Track

Parent clas for visualisation Tracks.

Attributes:

  • visualisation_data (dict) –

    a dictionary with data needed for visualisation.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

Source code in uorf4u/drawing_annotation.py 
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class Track:
    """Parent clas for visualisation Tracks.

    Attributes:
        visualisation_data (dict): a dictionary with data needed for visualisation.
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """

    def __init__(self, visualisation_data: dict, parameters: uorf4u.manager.Parameters):
        """Parent's constructor for creating a Track object.

        Arguments:
            visualisation_data (dict): a dictionary with data needed for visualisation.
            parameters (uorf4u.manager.Parameters): Parameters' class object.

        """
        self.visualisation_data = visualisation_data
        self.parameters = parameters

    def needed_y_space(self) -> None:
        """Empy parent's method for calculation needed vertical space for a track.

        Returns:
            None

        """
        pass

    def draw(self, canvas: reportlab.pdfgen.canvas.Canvas) -> None:
        """Empy parent's method for track visualisation.

        Arguments:
            canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.

        Returns:
            None
        """
        pass

__init__(visualisation_data, parameters)

Parent's constructor for creating a Track object.

Parameters:

  • visualisation_data (dict) –

    a dictionary with data needed for visualisation.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

Source code in uorf4u/drawing_annotation.py 
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def __init__(self, visualisation_data: dict, parameters: uorf4u.manager.Parameters):
    """Parent's constructor for creating a Track object.

    Arguments:
        visualisation_data (dict): a dictionary with data needed for visualisation.
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """
    self.visualisation_data = visualisation_data
    self.parameters = parameters

draw(canvas)

Empy parent's method for track visualisation.

Parameters:

  • canvas (reportlab.pdfgen.canvas.Canvas) –

    a pdf object.

Returns:

  • None –

    None

Source code in uorf4u/drawing_annotation.py 
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def draw(self, canvas: reportlab.pdfgen.canvas.Canvas) -> None:
    """Empy parent's method for track visualisation.

    Arguments:
        canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.

    Returns:
        None
    """
    pass

needed_y_space()

Empy parent's method for calculation needed vertical space for a track.

Returns:

  • None –

    None

Source code in uorf4u/drawing_annotation.py 
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def needed_y_space(self) -> None:
    """Empy parent's method for calculation needed vertical space for a track.

    Returns:
        None

    """
    pass

This module provides visualisation of loci annotation.

Image

An Image object holds pdf.

Attributes:

  • canvas (reportlab.pdfgen.canvas.Canvas) –

    pdf object of the reportlab library.

Source code in uorf4u/drawing_msa.py 
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class Image:
    """An Image object holds pdf.

    Attributes:
        canvas (reportlab.pdfgen.canvas.Canvas): pdf object of the reportlab library.

    """

    def __init__(self, filename: str, width: float, height: float):
        """Create an Image object.

        Arguments:
            filename (str): path and name of a pdf.
            width (float): width of a pdf.
            height (float): height of a pdf.

        """
        self.canvas = reportlab.pdfgen.canvas.Canvas(filename, pagesize=(width, height))

    def save(self) -> None:
        """Save a pdf file.

        Returns:
            None

        """
        self.canvas.save()
        return None

__init__(filename, width, height)

Create an Image object.

Parameters:

  • filename (str) –

    path and name of a pdf.

  • width (float) –

    width of a pdf.

  • height (float) –

    height of a pdf.

Source code in uorf4u/drawing_msa.py 
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def __init__(self, filename: str, width: float, height: float):
    """Create an Image object.

    Arguments:
        filename (str): path and name of a pdf.
        width (float): width of a pdf.
        height (float): height of a pdf.

    """
    self.canvas = reportlab.pdfgen.canvas.Canvas(filename, pagesize=(width, height))

save()

Save a pdf file.

Returns:

  • None –

    None

Source code in uorf4u/drawing_msa.py 
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def save(self) -> None:
    """Save a pdf file.

    Returns:
        None

    """
    self.canvas.save()
    return None

Loader

Parent class for tracks loaders.

Attributes:

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

  • prepared_data (dict) –

    dict with data needed for visualisation tracks.

Source code in uorf4u/drawing_msa.py 
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class Loader:
    """Parent class for tracks loaders.

    Attributes:
        parameters (uorf4u.manager.Parameters): Parameters' class object.
        prepared_data (dict): dict with data needed for visualisation tracks.

    """

    def __init__(self, parameters: uorf4u.manager.Parameters):
        """Parent's constructor for creating a Loader class object.

        Arguments:
            parameters (uorf4u.manager.Parameters): Parameters' class object.
        """
        self.parameters = parameters
        self.prepared_data = None

    def prepare_data(self) -> None:
        """Empty parent's method for data preparation.

        Returns:
            None

        """
        pass

    def create_track(self) -> None:
        """Empty parent's method for initialisation of a track.

        Returns:
            None

        """
        pass

__init__(parameters)

Parent's constructor for creating a Loader class object.

Parameters:

Source code in uorf4u/drawing_msa.py 
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def __init__(self, parameters: uorf4u.manager.Parameters):
    """Parent's constructor for creating a Loader class object.

    Arguments:
        parameters (uorf4u.manager.Parameters): Parameters' class object.
    """
    self.parameters = parameters
    self.prepared_data = None

create_track()

Empty parent's method for initialisation of a track.

Returns:

  • None –

    None

Source code in uorf4u/drawing_msa.py 
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def create_track(self) -> None:
    """Empty parent's method for initialisation of a track.

    Returns:
        None

    """
    pass

prepare_data()

Empty parent's method for data preparation.

Returns:

  • None –

    None

Source code in uorf4u/drawing_msa.py 
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def prepare_data(self) -> None:
    """Empty parent's method for data preparation.

    Returns:
        None

    """
    pass

MSAPlotManager

AnnotationPlotManager object holds needed information for annotation visualisation and controls it.

Note:

It's supposed that the AnnotationPlotManager' objects will not be used directly by API users since visualisation can be controlled by 'plot_annotation' method.

Attributes:

  • msa (FILL IN) –

    Path class' multiple sequence alignment.

  • upstream_sequences (list) –

    list of dicts with information about upstream sequences.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

  • coordinate_system (dict) –

    coordinate system of figure.

  • additional_data (dict) –

    dict with data for visualisation tracks.

Source code in uorf4u/drawing_msa.py 
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class MSAPlotManager:
    """
    AnnotationPlotManager object holds needed information for annotation visualisation and controls it.

    Note:
        It's supposed that the AnnotationPlotManager' objects will not be used directly by API users since
            visualisation can be controlled by 'plot_annotation' method.

    Attributes:
        msa (FILL IN): Path class' multiple sequence alignment.
        upstream_sequences (list): list of dicts with information about upstream sequences.
        parameters (uorf4u.manager.Parameters): Parameters' class object.
        coordinate_system (dict): coordinate system of figure.
        additional_data (dict): dict with data for visualisation tracks.

    """

    def __init__(self, msa, parameters: uorf4u.manager.Parameters, type: str):
        """Create a AnnotationPlotManager object.

        Arguments:
            path (uorf4u.data_processing.Path): Path class' objects that holds list of conserved ORFs.
            upstream_sequences (list): list of dicts with information about upstream sequences.
            parameters (uorf4u.manager.Parameters): Parameters' class object.
            type (str): type of sequences (sd, nt, aa)

        """
        self.msa = msa
        self.parameters = parameters
        self.coordinate_system = dict()
        self.additional_data = dict()
        self.type = type

    def define_x_axis_coordinate_system(self) -> None:
        """Define coordinate system.

        Returns:
            None

        """

        label_height = self.parameters.arguments["label_size"] * self.parameters.arguments["tile_size"] * cm
        label_font_size = uorf4u.methods.string_height_to_font_size(label_height, "regular", self.parameters.arguments)
        self.additional_data["label_font_size"] = label_font_size
        msa_length = self.msa.get_alignment_length()
        max_label_width = max([reportlab.pdfbase.pdfmetrics.stringWidth(i.description, "regular",
                                                                        label_font_size) for i in self.msa])

        char_height = self.parameters.arguments["char_size"] * self.parameters.arguments["tile_size"] * cm
        char_font_size = uorf4u.methods.string_height_to_font_size(char_height, "mono", self.parameters.arguments)
        self.additional_data["char_font_size"] = char_font_size

        self.additional_data["number_of_sequences"] = len(self.msa)
        self.coordinate_system["x_labels_start"] = self.parameters.arguments["margin"] * cm
        self.coordinate_system["x_labels_stop"] = self.coordinate_system["x_labels_start"] + max_label_width
        self.coordinate_system["x_msa_start"] = self.coordinate_system["x_labels_stop"] + \
                                                self.parameters.arguments["label_gap"] * cm
        msa_width = self.parameters.arguments["tile_size"] * msa_length * cm
        self.coordinate_system["x_msa_stop"] = self.coordinate_system["x_msa_start"] + msa_width
        self.coordinate_system["figure_width"] = 2 * self.parameters.arguments["margin"] * cm + msa_width + \
                                                 max_label_width + self.parameters.arguments["label_gap"] * cm
        self.coordinate_system["figure_height"] = self.parameters.arguments["margin"] * cm
        self.additional_data["palette"] = self.parameters.arguments[f"colors_{self.type}"]
        self.additional_data["palette"] = {k: uorf4u.methods.color_name_to_hex(v, self.parameters.arguments) for k, v in
                                           self.additional_data["palette"].items()}

        return None

    def create_tracks(self) -> None:
        """Create visualisation tracks.

        Returns:
            None

        """
        self.tracks = []
        """
        title_loader = TitleLoader(self.parameters)
        title_loader.prepare_data(self.coordinate_system, self.additional_data)
        title_track = title_loader.create_track()
        self.tracks.append(title_track)
        self.coordinate_system["figure_height"] += title_track.needed_y_space()
        """
        for record in self.msa:
            sequence_loader = SequencesLoader(self.parameters)
            sequence_loader.prepare_data(record, self.coordinate_system, self.additional_data)
            track = sequence_loader.create_track()
            self.tracks.append(track)
            self.coordinate_system["figure_height"] += track.needed_y_space()
            # self.coordinate_system["figure_height"] += self.parameters.arguments["gap"] * cm
            # if index < self.additional_data["number_of_sequences"] - 1:
        self.coordinate_system["figure_height"] += self.parameters.arguments["margin"] * cm

    def plot(self, filename):
        image = Image(filename, self.coordinate_system["figure_width"], self.coordinate_system["figure_height"])
        current_y_top = self.coordinate_system["figure_height"] - self.parameters.arguments["margin"] * cm
        for track in self.tracks:
            track.visualisation_data["y_top"] = current_y_top
            track.draw(image.canvas)
            current_y_top -= (track.needed_space)
        image.save()
        return None

__init__(msa, parameters, type)

Create a AnnotationPlotManager object.

Parameters:

  • path (uorf4u.data_processing.Path) –

    Path class' objects that holds list of conserved ORFs.

  • upstream_sequences (list) –

    list of dicts with information about upstream sequences.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

  • type (str) –

    type of sequences (sd, nt, aa)

Source code in uorf4u/drawing_msa.py 
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def __init__(self, msa, parameters: uorf4u.manager.Parameters, type: str):
    """Create a AnnotationPlotManager object.

    Arguments:
        path (uorf4u.data_processing.Path): Path class' objects that holds list of conserved ORFs.
        upstream_sequences (list): list of dicts with information about upstream sequences.
        parameters (uorf4u.manager.Parameters): Parameters' class object.
        type (str): type of sequences (sd, nt, aa)

    """
    self.msa = msa
    self.parameters = parameters
    self.coordinate_system = dict()
    self.additional_data = dict()
    self.type = type

create_tracks()

Create visualisation tracks.

Returns:

  • None –

    None

Source code in uorf4u/drawing_msa.py 
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def create_tracks(self) -> None:
    """Create visualisation tracks.

    Returns:
        None

    """
    self.tracks = []
    """
    title_loader = TitleLoader(self.parameters)
    title_loader.prepare_data(self.coordinate_system, self.additional_data)
    title_track = title_loader.create_track()
    self.tracks.append(title_track)
    self.coordinate_system["figure_height"] += title_track.needed_y_space()
    """
    for record in self.msa:
        sequence_loader = SequencesLoader(self.parameters)
        sequence_loader.prepare_data(record, self.coordinate_system, self.additional_data)
        track = sequence_loader.create_track()
        self.tracks.append(track)
        self.coordinate_system["figure_height"] += track.needed_y_space()
        # self.coordinate_system["figure_height"] += self.parameters.arguments["gap"] * cm
        # if index < self.additional_data["number_of_sequences"] - 1:
    self.coordinate_system["figure_height"] += self.parameters.arguments["margin"] * cm

define_x_axis_coordinate_system()

Define coordinate system.

Returns:

  • None –

    None

Source code in uorf4u/drawing_msa.py 
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def define_x_axis_coordinate_system(self) -> None:
    """Define coordinate system.

    Returns:
        None

    """

    label_height = self.parameters.arguments["label_size"] * self.parameters.arguments["tile_size"] * cm
    label_font_size = uorf4u.methods.string_height_to_font_size(label_height, "regular", self.parameters.arguments)
    self.additional_data["label_font_size"] = label_font_size
    msa_length = self.msa.get_alignment_length()
    max_label_width = max([reportlab.pdfbase.pdfmetrics.stringWidth(i.description, "regular",
                                                                    label_font_size) for i in self.msa])

    char_height = self.parameters.arguments["char_size"] * self.parameters.arguments["tile_size"] * cm
    char_font_size = uorf4u.methods.string_height_to_font_size(char_height, "mono", self.parameters.arguments)
    self.additional_data["char_font_size"] = char_font_size

    self.additional_data["number_of_sequences"] = len(self.msa)
    self.coordinate_system["x_labels_start"] = self.parameters.arguments["margin"] * cm
    self.coordinate_system["x_labels_stop"] = self.coordinate_system["x_labels_start"] + max_label_width
    self.coordinate_system["x_msa_start"] = self.coordinate_system["x_labels_stop"] + \
                                            self.parameters.arguments["label_gap"] * cm
    msa_width = self.parameters.arguments["tile_size"] * msa_length * cm
    self.coordinate_system["x_msa_stop"] = self.coordinate_system["x_msa_start"] + msa_width
    self.coordinate_system["figure_width"] = 2 * self.parameters.arguments["margin"] * cm + msa_width + \
                                             max_label_width + self.parameters.arguments["label_gap"] * cm
    self.coordinate_system["figure_height"] = self.parameters.arguments["margin"] * cm
    self.additional_data["palette"] = self.parameters.arguments[f"colors_{self.type}"]
    self.additional_data["palette"] = {k: uorf4u.methods.color_name_to_hex(v, self.parameters.arguments) for k, v in
                                       self.additional_data["palette"].items()}

    return None

SequenceVis

Bases: Track

SequenceVis track draws sequences and annotation.

Attributes:

  • visualisation_data (dict) –

    a dictionary with data needed for visualisation.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

  • needed_space (float) –

    needed vertical space for a track.

Source code in uorf4u/drawing_msa.py 
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class SequenceVis(Track):
    """SequenceVis track draws sequences and annotation.

    Attributes:
        visualisation_data (dict): a dictionary with data needed for visualisation.
        parameters (uorf4u.manager.Parameters): Parameters' class object.
        needed_space (float): needed vertical space for a track.

    """

    def __init__(self, visualisation_data: dict, parameters: uorf4u.manager.Parameters):
        """Create a SequenceVis object.

        Arguments:
            visualisation_data (dict): a dictionary with data needed for visualisation.
            parameters (uorf4u.manager.Parameters): Parameters' class object.

        """
        super().__init__(visualisation_data, parameters)
        self.needed_space = None

    def needed_y_space(self) -> float:
        """Calculate needed vertical space for a SequenceVis track.

        Returns:
            float: needed vertical space.

        """
        self.needed_space = self.parameters.arguments["tile_size"] * cm
        return self.needed_space

    def draw(self, canvas: reportlab.pdfgen.canvas.Canvas) -> None:
        """Draw a Sequence track.

        Arguments:
            canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.

        Returns:
            None

        """
        tile_size = self.parameters.arguments["tile_size"] * cm
        y_c = self.visualisation_data["y_top"] - (tile_size * 0.5)
        y_l = self.visualisation_data["y_top"] - tile_size

        y_gap_label = tile_size * (1 - self.parameters.arguments["label_size"]) * 0.5
        y_gap_char = tile_size * (1 - self.parameters.arguments["char_size"]) * 0.5
        # Labels
        canvas.setFillColorRGB(*uorf4u.methods.get_color("label_color", self.parameters.arguments))
        canvas.setFont("regular", self.visualisation_data["label_font_size"])
        canvas.drawRightString(self.visualisation_data["coordinate_system"]["x_labels_stop"], y_l + y_gap_label,
                               self.visualisation_data["label"])

        canvas.setLineWidth(0.05 * tile_size)
        canvas.setStrokeColorRGB(1, 1, 1)
        canvas.setFont("mono", self.visualisation_data["char_font_size"])
        x = self.visualisation_data['msa_left_border']
        for symbol in self.visualisation_data["sequence"]:
            x_c = x + tile_size * 0.5
            symbol = symbol.upper()
            try:
                color = self.visualisation_data["palette"][symbol]
            except:
                color = "#FFFFFF"
            canvas.setFillColorRGB(*uorf4u.methods.hex_to_rgb(color), self.parameters.arguments["tile_alpha"])
            canvas.rect(x, y_l, tile_size, tile_size, fill=1)
            canvas.setFillColorRGB(0, 0, 0, 0.8)  # to change
            canvas.drawCentredString(x_c, y_l + y_gap_char, symbol)
            x += tile_size

        return None

__init__(visualisation_data, parameters)

Create a SequenceVis object.

Parameters:

  • visualisation_data (dict) –

    a dictionary with data needed for visualisation.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

Source code in uorf4u/drawing_msa.py 
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def __init__(self, visualisation_data: dict, parameters: uorf4u.manager.Parameters):
    """Create a SequenceVis object.

    Arguments:
        visualisation_data (dict): a dictionary with data needed for visualisation.
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """
    super().__init__(visualisation_data, parameters)
    self.needed_space = None

draw(canvas)

Draw a Sequence track.

Parameters:

  • canvas (reportlab.pdfgen.canvas.Canvas) –

    a pdf object.

Returns:

  • None –

    None

Source code in uorf4u/drawing_msa.py 
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def draw(self, canvas: reportlab.pdfgen.canvas.Canvas) -> None:
    """Draw a Sequence track.

    Arguments:
        canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.

    Returns:
        None

    """
    tile_size = self.parameters.arguments["tile_size"] * cm
    y_c = self.visualisation_data["y_top"] - (tile_size * 0.5)
    y_l = self.visualisation_data["y_top"] - tile_size

    y_gap_label = tile_size * (1 - self.parameters.arguments["label_size"]) * 0.5
    y_gap_char = tile_size * (1 - self.parameters.arguments["char_size"]) * 0.5
    # Labels
    canvas.setFillColorRGB(*uorf4u.methods.get_color("label_color", self.parameters.arguments))
    canvas.setFont("regular", self.visualisation_data["label_font_size"])
    canvas.drawRightString(self.visualisation_data["coordinate_system"]["x_labels_stop"], y_l + y_gap_label,
                           self.visualisation_data["label"])

    canvas.setLineWidth(0.05 * tile_size)
    canvas.setStrokeColorRGB(1, 1, 1)
    canvas.setFont("mono", self.visualisation_data["char_font_size"])
    x = self.visualisation_data['msa_left_border']
    for symbol in self.visualisation_data["sequence"]:
        x_c = x + tile_size * 0.5
        symbol = symbol.upper()
        try:
            color = self.visualisation_data["palette"][symbol]
        except:
            color = "#FFFFFF"
        canvas.setFillColorRGB(*uorf4u.methods.hex_to_rgb(color), self.parameters.arguments["tile_alpha"])
        canvas.rect(x, y_l, tile_size, tile_size, fill=1)
        canvas.setFillColorRGB(0, 0, 0, 0.8)  # to change
        canvas.drawCentredString(x_c, y_l + y_gap_char, symbol)
        x += tile_size

    return None

needed_y_space()

Calculate needed vertical space for a SequenceVis track.

Returns:

  • float( float ) –

    needed vertical space.

Source code in uorf4u/drawing_msa.py 
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def needed_y_space(self) -> float:
    """Calculate needed vertical space for a SequenceVis track.

    Returns:
        float: needed vertical space.

    """
    self.needed_space = self.parameters.arguments["tile_size"] * cm
    return self.needed_space

SequencesLoader

Bases: Loader

A SequencesLoader object prepares data for a Sequence track object.

Attributes:

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

  • prepared_data (dict) –

    dict with data needed for a visualisation track.

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class SequencesLoader(Loader):
    """A SequencesLoader object prepares data for a Sequence track object.


    Attributes:
        parameters (uorf4u.manager.Parameters): Parameters' class object.
        prepared_data (dict): dict with data needed for a visualisation track.

    """

    def __init__(self, parameters):
        """Create a SequenceLoader object.

        Arguments:
            parameters (uorf4u.manager.Parameters): Parameters' class object.

        """
        super().__init__(parameters)

    def prepare_data(self, record, coordinate_system: dict, additional_data: dict) -> dict:
        """Prepare data for a Title visualisation track.

        Attributes:
            record (FILL in): record of blablabla
            coordinate_system (dict): coordinate system of a figure page.
            additional_data (dict): data needed for a track initialisation.

        Returns:
            dict: dictionary with prepared data for visualisation.

        """
        prepared_data = dict()
        prepared_data["coordinate_system"] = coordinate_system
        prepared_data["label_font_size"] = additional_data["label_font_size"]
        prepared_data["char_font_size"] = additional_data["char_font_size"]
        prepared_data["label_right_border"] = coordinate_system["x_labels_stop"]
        prepared_data["msa_left_border"] = coordinate_system["x_msa_start"]
        prepared_data["sequence"] = record.seq
        prepared_data["label"] = record.description
        prepared_data["palette"] = additional_data["palette"]
        self.prepared_data = prepared_data

        return prepared_data

    def create_track(self) -> SequenceVis:
        """Initialise a Sequence track object.

        Returns:
            SequenceVis: visualisation track.

        """
        return SequenceVis(self.prepared_data, self.parameters)

__init__(parameters)

Create a SequenceLoader object.

Parameters:

Source code in uorf4u/drawing_msa.py 
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def __init__(self, parameters):
    """Create a SequenceLoader object.

    Arguments:
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """
    super().__init__(parameters)

create_track()

Initialise a Sequence track object.

Returns:

Source code in uorf4u/drawing_msa.py 
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def create_track(self) -> SequenceVis:
    """Initialise a Sequence track object.

    Returns:
        SequenceVis: visualisation track.

    """
    return SequenceVis(self.prepared_data, self.parameters)

prepare_data(record, coordinate_system, additional_data)

Prepare data for a Title visualisation track.

Attributes:

  • record (FILL in) –

    record of blablabla

  • coordinate_system (dict) –

    coordinate system of a figure page.

  • additional_data (dict) –

    data needed for a track initialisation.

Returns:

  • dict( dict ) –

    dictionary with prepared data for visualisation.

Source code in uorf4u/drawing_msa.py 
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def prepare_data(self, record, coordinate_system: dict, additional_data: dict) -> dict:
    """Prepare data for a Title visualisation track.

    Attributes:
        record (FILL in): record of blablabla
        coordinate_system (dict): coordinate system of a figure page.
        additional_data (dict): data needed for a track initialisation.

    Returns:
        dict: dictionary with prepared data for visualisation.

    """
    prepared_data = dict()
    prepared_data["coordinate_system"] = coordinate_system
    prepared_data["label_font_size"] = additional_data["label_font_size"]
    prepared_data["char_font_size"] = additional_data["char_font_size"]
    prepared_data["label_right_border"] = coordinate_system["x_labels_stop"]
    prepared_data["msa_left_border"] = coordinate_system["x_msa_start"]
    prepared_data["sequence"] = record.seq
    prepared_data["label"] = record.description
    prepared_data["palette"] = additional_data["palette"]
    self.prepared_data = prepared_data

    return prepared_data

Track

Parent clas for visualisation Tracks.

Attributes:

  • visualisation_data (dict) –

    a dictionary with data needed for visualisation.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

Source code in uorf4u/drawing_msa.py 
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class Track:
    """Parent clas for visualisation Tracks.

    Attributes:
        visualisation_data (dict): a dictionary with data needed for visualisation.
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """

    def __init__(self, visualisation_data: dict, parameters: uorf4u.manager.Parameters):
        """Parent's constructor for creating a Track object.

        Arguments:
            visualisation_data (dict): a dictionary with data needed for visualisation.
            parameters (uorf4u.manager.Parameters): Parameters' class object.

        """
        self.visualisation_data = visualisation_data
        self.parameters = parameters

    def needed_y_space(self) -> None:
        """Empy parent's method for calculation needed vertical space for a track.

        Returns:
            None

        """
        pass

    def draw(self, canvas: reportlab.pdfgen.canvas.Canvas) -> None:
        """Empy parent's method for track visualisation.

        Arguments:
            canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.

        Returns:
            None
        """
        pass

__init__(visualisation_data, parameters)

Parent's constructor for creating a Track object.

Parameters:

  • visualisation_data (dict) –

    a dictionary with data needed for visualisation.

  • parameters (uorf4u.manager.Parameters) –

    Parameters' class object.

Source code in uorf4u/drawing_msa.py 
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def __init__(self, visualisation_data: dict, parameters: uorf4u.manager.Parameters):
    """Parent's constructor for creating a Track object.

    Arguments:
        visualisation_data (dict): a dictionary with data needed for visualisation.
        parameters (uorf4u.manager.Parameters): Parameters' class object.

    """
    self.visualisation_data = visualisation_data
    self.parameters = parameters

draw(canvas)

Empy parent's method for track visualisation.

Parameters:

  • canvas (reportlab.pdfgen.canvas.Canvas) –

    a pdf object.

Returns:

  • None –

    None

Source code in uorf4u/drawing_msa.py 
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def draw(self, canvas: reportlab.pdfgen.canvas.Canvas) -> None:
    """Empy parent's method for track visualisation.

    Arguments:
        canvas (reportlab.pdfgen.canvas.Canvas): a pdf object.

    Returns:
        None
    """
    pass

needed_y_space()

Empy parent's method for calculation needed vertical space for a track.

Returns:

  • None –

    None

Source code in uorf4u/drawing_msa.py 
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def needed_y_space(self) -> None:
    """Empy parent's method for calculation needed vertical space for a track.

    Returns:
        None

    """
    pass