| Previous changeset 0:621754dd31f8 (2022-06-17) Next changeset 2:b36bdd17d99a (2024-06-28) |
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Commit message:
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c |
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added:
dna_features_viewer/BiopythonTranslator/BiopythonTranslator.py dna_features_viewer/BiopythonTranslator/BiopythonTranslatorBase.py dna_features_viewer/BiopythonTranslator/BlackBoxlessLabelTranslator.py dna_features_viewer/BiopythonTranslator/__init__.py dna_features_viewer/CircularGraphicRecord/ArrowWedge.py dna_features_viewer/CircularGraphicRecord/CircularGraphicRecord.py dna_features_viewer/CircularGraphicRecord/__init__.py dna_features_viewer/GraphicFeature.py dna_features_viewer/GraphicRecord/BokehPlottableMixin.py dna_features_viewer/GraphicRecord/GraphicRecord.py dna_features_viewer/GraphicRecord/MatplotlibPlottableMixin.py dna_features_viewer/GraphicRecord/MultilinePlottableMixin.py dna_features_viewer/GraphicRecord/SequenceAndTranslationMixin.py dna_features_viewer/GraphicRecord/__init__.py dna_features_viewer/README.md dna_features_viewer/__init__.py dna_features_viewer/biotools.py dna_features_viewer/compute_features_levels.py dna_features_viewer/version.py linear_genome_plot.py linear_genome_plot.xml macros.xml test-data/Mu50-profile.xml.xml test-data/Mu50.sam test-data/mga.fa test-data/mu_reanno.gb test-data/out_img.svg test-data/out_img_multi.svg test-data/out_img_zoom.svg test-data/out_stats.txt test-data/out_stats_multi.txt test-data/out_stats_zoom.txt test-data/tmp.svg test-data/tmp_multi.svg test-data/tmp_zoom.svg |
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removed:
cpt_linear_genome_plot/dna_features_viewer/BiopythonTranslator/BiopythonTranslator.py cpt_linear_genome_plot/dna_features_viewer/BiopythonTranslator/BiopythonTranslatorBase.py cpt_linear_genome_plot/dna_features_viewer/BiopythonTranslator/BlackBoxlessLabelTranslator.py cpt_linear_genome_plot/dna_features_viewer/BiopythonTranslator/__init__.py cpt_linear_genome_plot/dna_features_viewer/CircularGraphicRecord/ArrowWedge.py cpt_linear_genome_plot/dna_features_viewer/CircularGraphicRecord/CircularGraphicRecord.py cpt_linear_genome_plot/dna_features_viewer/CircularGraphicRecord/__init__.py cpt_linear_genome_plot/dna_features_viewer/GraphicFeature.py cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/BokehPlottableMixin.py cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/GraphicRecord.py cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/MatplotlibPlottableMixin.py cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/MultilinePlottableMixin.py cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/SequenceAndTranslationMixin.py cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/__init__.py cpt_linear_genome_plot/dna_features_viewer/README.md cpt_linear_genome_plot/dna_features_viewer/__init__.py cpt_linear_genome_plot/dna_features_viewer/biotools.py cpt_linear_genome_plot/dna_features_viewer/compute_features_levels.py cpt_linear_genome_plot/dna_features_viewer/version.py cpt_linear_genome_plot/linear_genome_plot.py cpt_linear_genome_plot/linear_genome_plot.xml cpt_linear_genome_plot/macros.xml cpt_linear_genome_plot/test-data/Mu50-profile.xml.xml cpt_linear_genome_plot/test-data/Mu50.sam cpt_linear_genome_plot/test-data/mga.fa cpt_linear_genome_plot/test-data/mu_reanno.gb cpt_linear_genome_plot/test-data/out_img.svg cpt_linear_genome_plot/test-data/out_img_multi.svg cpt_linear_genome_plot/test-data/out_img_zoom.svg cpt_linear_genome_plot/test-data/out_stats.txt cpt_linear_genome_plot/test-data/out_stats_multi.txt cpt_linear_genome_plot/test-data/out_stats_zoom.txt cpt_linear_genome_plot/test-data/tmp.svg cpt_linear_genome_plot/test-data/tmp_multi.svg cpt_linear_genome_plot/test-data/tmp_zoom.svg |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/BiopythonTranslator/BiopythonTranslator.py --- a/cpt_linear_genome_plot/dna_features_viewer/BiopythonTranslator/BiopythonTranslator.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,130 +0,0 @@ -from .BiopythonTranslatorBase import BiopythonTranslatorBase - - -class BiopythonTranslator(BiopythonTranslatorBase): - """A translator from SeqRecords to dna_features_viewer GraphicRecord. - - This can be subclassed to create custom "themes" (see the example - ``custom_biopython_translator.py`` in the docs). - - This class is meant to be customized by subclassing and changing the - methods (``compute_feature_label``, etc.) and/or the attributes - (``default_feature_color`` etc). - - Attributes - ---------- - - default_feature_color = "#7245dc" - graphic_record_parameters - Dictionnary containing keyword arguments that will be passed to the - (Circular)GraphicRecord constructor - - ignored_features_types - A list or tuple of strings indicating all the feature types that should - always be ignored (i.e. not included in the graphic record) by the - translator - - label_fields - This list of strings provides the order in which the different - attributes of a Genbank feature will be considered, when automatically - determining the feature label. For instance if the list is - ["label", "source", "locus_tag"] and a feature has no label but has a - "source", the "source" will be displayed in the plots. - - Parameters - ---------- - - features_filters - List of filters (some_biopython_feature) => True/False. - Only features passing all the filters are kept. - This only works if you haven't redefined ``compute_filtered_features`` - - features_properties - A function (feature)=> properties_dict - - """ - - default_feature_color = "#7245dc" - ignored_features_types = () - label_fields = [ - "label", - "name", - "gene", - "product", - "source", - "locus_tag", - "note", - ] - - def __init__(self, features_filters=(), features_properties=None): - self.features_filters = features_filters - self.features_properties = features_properties - - def compute_feature_color(self, feature): - """Compute a color for this feature. - - If the feature has a ``color`` qualifier it will be used. Otherwise, - the classe's ``default_feature_color`` is used. - - To change the behaviour, create a subclass of ``BiopythonTranslator`` - and overwrite this method. - """ - if "color" in feature.qualifiers: - color = feature.qualifiers["color"] - if isinstance(color[0], str): - return "".join(feature.qualifiers["color"]) - else: - return color - else: - return self.default_feature_color - - def compute_feature_fontdict(self, feature): - """Compute a font dict for this feature.""" - return None - - def compute_feature_box_linewidth(self, feature): - """Compute a box_linewidth for this feature.""" - return 0.3 - - def compute_feature_box_color(self, feature): - """Compute a box_color for this feature.""" - return "auto" - - def compute_feature_label_link_color(self, feature): - """Compute the color of the line linking the label to its feature.""" - return "black" - - def compute_filtered_features(self, features): - """Return the list of features minus the ignored ones. - - By the method keeps any feature whose type is not in - ignored_features_types and for which all filter(f) pass - """ - return [ - f - for f in features - if all([fl(f) for fl in self.features_filters]) - and f.type not in self.ignored_features_types - ] - - def compute_feature_label(self, feature): - """Compute the label of the feature.""" - label = feature.type - for key in self.label_fields: - if key in feature.qualifiers and len(feature.qualifiers[key]): - label = feature.qualifiers[key] - break - if isinstance(label, list): - label = "|".join(label) - return label - - def compute_feature_linewidth(self, feature): - """Compute the edge width of the feature's arrow/rectangle.""" - return 1.0 - - def compute_feature_legend_text(self, feature): - return None - - def compute_feature_html(self, feature): - """Gets the 'label' of the feature.""" - return self.compute_feature_label(feature) |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/BiopythonTranslator/BiopythonTranslatorBase.py --- a/cpt_linear_genome_plot/dna_features_viewer/BiopythonTranslator/BiopythonTranslatorBase.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,119 +0,0 @@ -from ..biotools import load_record -from ..GraphicRecord import GraphicRecord -from ..CircularGraphicRecord import CircularGraphicRecord -from ..GraphicFeature import GraphicFeature - - -class BiopythonTranslatorBase: - """Base class for all BiopythonTranslators. - - This class needs to be complemented with methods compute_feature_label, - compute_features_color, etc. to be usable. See BiopythonTranslator for - an example of minimal working subclass. - - Parameters - ---------- - - features_filters - List of filters (some_biopython_feature) => True/False. - Only features passing all the filters are kept. - This only works if you haven't redefined ``compute_filtered_features`` - - features_properties - A function (feature)=> properties_dict - - """ - graphic_record_parameters = {} - - def __init__(self, features_filters=(), features_properties=None): - self.features_filters = features_filters - self.features_properties = features_properties - - def translate_feature(self, feature): - """Translate a Biopython feature into a Dna Features Viewer feature.""" - properties = dict( - label=self.compute_feature_label(feature), - color=self.compute_feature_color(feature), - html=self.compute_feature_html(feature), - fontdict=self.compute_feature_fontdict(feature), - box_linewidth=self.compute_feature_box_linewidth(feature), - box_color=self.compute_feature_box_color(feature), - linewidth=self.compute_feature_linewidth(feature), - label_link_color=self.compute_feature_label_link_color(feature), - legend_text=self.compute_feature_legend_text(feature) - ) - if self.features_properties is not None: - other_properties = self.features_properties - if hasattr(other_properties, '__call__'): - other_properties = other_properties(feature) - properties.update(other_properties) - - return GraphicFeature( - start=feature.location.start, - end=feature.location.end, - strand=feature.location.strand, - **properties - ) - - def translate_record(self, record, record_class=None): - """Create a new GraphicRecord from a BioPython Record object. - - Parameters - ---------- - - record - A BioPython Record object or the path to a Genbank or a GFF file. - - record_class - The graphic record class to use, e.g. GraphicRecord (default) or - CircularGraphicRecord. Strings 'circular' and 'linear' can also be - provided. - """ - classes = { - "linear": GraphicRecord, - "circular": CircularGraphicRecord, - None: GraphicRecord, - } - if record_class in classes: - record_class = classes[record_class] - - if isinstance(record, str) or hasattr(record, 'read'): - record = load_record(record) - filtered_features = self.compute_filtered_features(record.features) - return record_class( - sequence_length=len(record), - sequence=str(record.seq), - features=[ - self.translate_feature(feature) - for feature in filtered_features - if feature.location is not None - ], - **self.graphic_record_parameters - ) - - @classmethod - def quick_class_plot(cls, record, figure_width=12, **kwargs): - """Allows super quick and dirty plotting of Biopython records. - - This is really meant for use in a Jupyter/Ipython notebook with - the "%matplotlib inline" setting. - - >>> from dna_features_viewer import BiopythonTranslator - >>> BiopythonTranslator.quick_plot(my_record) - """ - graphic_record = cls().translate_record(record) - ax, _ = graphic_record.plot(figure_width=figure_width, **kwargs) - return ax - - def quick_plot(self, record, figure_width=12, **kwargs): - """Allows super quick and dirty plotting of Biopython records. - - This is really meant for use in a Jupyter/Ipython notebook with - the "%matplotlib inline" setting. - - >>> from dna_features_viewer import BiopythonTranslator - >>> BiopythonTranslator.quick_plot(my_record) - """ - graphic_record = self.translate_record(record) - ax, _ = graphic_record.plot(figure_width=figure_width, **kwargs) - return ax |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/BiopythonTranslator/BlackBoxlessLabelTranslator.py --- a/cpt_linear_genome_plot/dna_features_viewer/BiopythonTranslator/BlackBoxlessLabelTranslator.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,13 +0,0 @@ -from .BiopythonTranslator import BiopythonTranslator - -class BlackBoxlessLabelTranslator(BiopythonTranslator): - """Translates Biopython records into GraphicRecords where annotations - appear black on a white background with no box. Which can be cleaner.""" - - def compute_feature_box_linewidth(self, feature): - """Return 0 as this translator doesn't show a box.""" - return 0 - - def compute_feature_box_color(self, feature): - """Return white.""" - return "white" \ No newline at end of file |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/BiopythonTranslator/__init__.py --- a/cpt_linear_genome_plot/dna_features_viewer/BiopythonTranslator/__init__.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -from .BiopythonTranslator import BiopythonTranslator -from .BlackBoxlessLabelTranslator import BlackBoxlessLabelTranslator - -__all__ = ["BiopythonTranslator", "BlackBoxlessLabelTranslator"] \ No newline at end of file |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/CircularGraphicRecord/ArrowWedge.py --- a/cpt_linear_genome_plot/dna_features_viewer/CircularGraphicRecord/ArrowWedge.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,110 +0,0 @@ -"""Implements the missing Matplotlib ArrowWedge patch class. - -This is a plain arrow curved alongside a protion of circle, like you would -expect a circular genetic feature to look. -""" -import numpy as np -import matplotlib.patches as mpatches - - -class ArrowWedge(mpatches.Wedge): - """Matplotlib patch shaped as a tick fraction of circle with a pointy end. - - This is the patch used by CircularGraphicRecord to draw features. - - Parameters - ---------- - - center - Center of the circle around which the arrow-wedge is drawn. - - radius - Radius of the circle around which the arrow-wedge is drawn. - - theta1 - Start angle of the wedge - - theta2 - End angle of the wedge - - width - Width or thickness of the arrow-wedge. - - direction - Determines whether the pointy end points in direct sense (+1) or - indirect sense (-1) or no sense at all (0) - """ - - def __init__( - self, center, radius, theta1, theta2, width, direction=+1, **kwargs - ): - - self.direction = direction - self.radius = radius - mpatches.Wedge.__init__( - self, center, radius, theta1, theta2, width, **kwargs - ) - self._recompute_path() - - def _recompute_path(self): - """Recompute the full path forming the "tick" arrowed wedge - - This method overwrites "mpatches.Wedge._recompute_path" in the - super-class. - """ - - if self.direction not in [-1, +1]: - return mpatches.Wedge._recompute_path(self) - - theta1, theta2 = self.theta1, self.theta2 - arrow_angle = min(5, abs(theta2 - theta1) / 2) - normalized_arrow_width = self.width / 2.0 / self.radius - if self.direction == +1: - angle_start_arrow = theta1 + arrow_angle - arc = mpatches.Path.arc(angle_start_arrow, theta2) - outer_arc = arc.vertices[::-1] * (1 + normalized_arrow_width) - inner_arc = arc.vertices * (1 - normalized_arrow_width) - arrow_vertices = [ - outer_arc[-1], - np.array( - [np.cos(np.deg2rad(theta1)), np.sin(np.deg2rad(theta1))] - ), - inner_arc[0], - ] - else: - angle_start_arrow = theta2 - arrow_angle - arc = mpatches.Path.arc(theta1, angle_start_arrow) - outer_arc = ( - arc.vertices * (self.radius + self.width / 2.0) / self.radius - ) - inner_arc = ( - arc.vertices[::-1] - * (self.radius - self.width / 2.0) - / self.radius - ) - arrow_vertices = [ - outer_arc[-1], - np.array( - [np.cos(np.deg2rad(theta2)), np.sin(np.deg2rad(theta2))] - ), - inner_arc[0], - ] - p = np.vstack([outer_arc, arrow_vertices, inner_arc]) - - path_vertices = np.vstack([p, inner_arc[-1, :], (0, 0)]) - - path_codes = np.hstack( - [ - arc.codes, - 4 * [mpatches.Path.LINETO], - arc.codes[1:], - mpatches.Path.LINETO, - mpatches.Path.CLOSEPOLY, - ] - ) - path_codes[len(arc.codes)] = mpatches.Path.LINETO - - # Shift and scale the wedge to the final location. - path_vertices *= self.r - path_vertices += np.asarray(self.center) - self._path = mpatches.Path(path_vertices, path_codes) |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/CircularGraphicRecord/CircularGraphicRecord.py --- a/cpt_linear_genome_plot/dna_features_viewer/CircularGraphicRecord/CircularGraphicRecord.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,171 +0,0 @@ -"""Implements the CircularGraphicRecord class. -""" - -import matplotlib.patches as mpatches -import numpy as np - -from ..GraphicRecord import GraphicRecord -from .ArrowWedge import ArrowWedge - - -class CircularGraphicRecord(GraphicRecord): - """Set of Genetic Features of a same DNA sequence, to be plotted together. - - Parameters - ---------- - - sequence_length - Length of the DNA sequence, in number of nucleotides - - features - list of GraphicalFeature objects. - - top_position - The index in the sequence that will end up at the top of the circle - - feature_level_height - Width in inches of one "level" for feature arrows. - - annotation_height - Width in inches of one "level" for feature annotations. - - labels_spacing - Distance in basepairs to keep between labels to avoid "quasi-collisions" - - **kw - Other keyword arguments - do not use, these parameters are allowed for - making it easier to use GraphicRecord and CircularGraphicRecord - interchangeably. - - """ - - default_elevate_outline_annotations = True - min_y_height_of_text_line = 0.1 - - def __init__( - self, - sequence_length, - features, - top_position=0, - feature_level_height=0.2, - annotation_height="auto", - labels_spacing=12, - **kw - ): - - self.radius = 1.0 - self.sequence_length = sequence_length - self.features = features - self.top_position = top_position - self.feature_level_height = feature_level_height - self.annotation_height = annotation_height - self.labels_spacing = labels_spacing - - def initialize_ax(self, ax, draw_line, with_ruler): - """Initialize the ax with a circular line, sets limits, aspect etc. - """ - - if draw_line: - circle = mpatches.Circle( - (0, -self.radius), self.radius, facecolor="none", edgecolor="k" - ) - ax.add_patch(circle) - ax.axis("off") - if with_ruler: - # only display the xaxis ticks - ax.set_frame_on(False) - ax.yaxis.set_visible(False) - ax.xaxis.tick_bottom() - else: - # don't display anything - ax.axis("off") - - ax.set_xlim(-1.1 * self.radius, 1.1 * self.radius) - ax.set_ylim(-self.radius, 3 * self.radius) - ax.set_aspect("equal") - - def finalize_ax( - self, - ax, - features_levels, - annotations_max_level, - auto_figure_height=False, - ideal_yspan=None, - annotations_are_elevated=True - ): - """Final display range and figure dimension tweakings.""" - annotation_height = self.determine_annotation_height( - annotations_max_level - ) - ymin = -2 * self.radius - self.feature_level_height * ( - features_levels + 1 - ) - ymax = ( - self.feature_level_height * (features_levels + 1) - + annotation_height * (annotations_max_level + 1) - ) - if ideal_yspan is not None: - ymax = max(annotation_height * ideal_yspan + ymin, ymax) - xmin = -self.radius - self.feature_level_height * (features_levels + 1) - xmax = -xmin - ax.set_xlim(xmin, xmax) - ax.set_ylim(ymin, ymax) - ratio = 1.0 * (ymax - ymin) / (xmax - xmin) - - if auto_figure_height: - figure_width = ax.figure.get_size_inches()[0] - ax.figure.set_size_inches(figure_width, figure_width * ratio) - - def plot_feature(self, ax, feature, level): - """Plot an ArrowWedge representing the feature at the giben height - level. - - - """ - a_start = self.position_to_angle(feature.start) - a_end = self.position_to_angle(feature.end) - a_start, a_end = sorted([a_start, a_end]) - r = self.radius + level * self.feature_level_height - patch = ArrowWedge( - center=(0, -self.radius), - radius=r, - theta1=a_start, - theta2=a_end, - width=0.7 * self.feature_level_height, - direction=feature.strand, - edgecolor=feature.linecolor, - linewidth=feature.linewidth, - facecolor=feature.color, - zorder=1, - ) - ax.add_patch(patch) - - def position_to_angle(self, position): - """Convert a sequence position into an angle in the figure.""" - a = 360.0 * (position - self.top_position) / self.sequence_length - return 90 - a - - def coordinates_in_plot(self, position, level): - """Convert a sequence position and height level to (x, y) coordinates. - """ - r = self.radius + level * self.feature_level_height - angle = self.position_to_angle(position) - rad_angle = np.deg2rad(angle) - return np.array( - [r * np.cos(rad_angle), r * np.sin(rad_angle) - self.radius] - ) - - def determine_annotation_height(self, max_annotations_level): - """Auto-select the annotations height. - - Annotation height is 0.2 at most, or else whatever will make - the figure a 5*radius tall rectangle where the circular plasmid - occupies the bottom-2 5th and the annotations occupy the top-3 5th. - """ - return min(0.25, 3.0 * self.radius / (1.0 + max_annotations_level)) - - def compute_padding(self, ax): - "" - ax_width = ax.get_window_extent(ax.figure.canvas.get_renderer()).width - xmin, xmax = ax.get_xlim() - return 3 * self.labels_spacing * (xmax - xmin) / (1.0 * ax_width) \ No newline at end of file |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/CircularGraphicRecord/__init__.py --- a/cpt_linear_genome_plot/dna_features_viewer/CircularGraphicRecord/__init__.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -from .CircularGraphicRecord import CircularGraphicRecord - -__all__ = ["CircularGraphicRecord"] |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/GraphicFeature.py --- a/cpt_linear_genome_plot/dna_features_viewer/GraphicFeature.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,162 +0,0 @@ -from copy import deepcopy - -class GraphicFeature: - """Genetic Feature to be plotted. - - Parameters - ---------- - - start, end - Coordinates of the feature in the final sequence. - - strand - Directionality of the feature. can be +1/-1/0 for direct sense, - anti-sense, or no directionality. - - label - Short descriptive text associated and plotted with the feature - - color - Color of the feature, any Matplotlib-compatible format is accepted, - such as "white", "w", "#ffffff", (1,1,1), etc. - - linecolor - Color of the feature's border, any Matplotlib-compatible format is - accepted, such as "white", "w", "#ffffff", (1,1,1), etc. - - linewidth - Width of the line (=edge) surrounding the graphic feature, in pixels. - - thickness - Vertical span of the feature - - box_color - Color of the label box. Set to None for no box around the label. - Leave to "auto" for a box color that is a lightened version of the - feature's color. - - data - Any other keyword is kept into the feature.data[] dictionary. - - fontdict - A Matplotlib fontdict for the font to be used in the label, e.g. - ``size=11``, ``weight='bold'``, ``family='Helvetica'``, etc. - - open_left, open_right - Set to True if this feature does not end on the right or left because it - is a cropped version of a bigger feature. - - box_linewidth - Width of the line delimiting the text box when the annotation is outside - the graphic feature. Set to 0 for no box borders - - box_color - Background color of the annotation's text box. If left to "auto" the - color will be a lighter version of the feature's color. - - label_link_color - Color of the line linking the text annotation to its respective graphic - feature. Set to auto for the line to automatically be a darker version - of the feature's color. - """ - - feature_type = "feature" - - def __init__( - self, - start=None, - end=None, - strand=None, - label=None, - color="#000080", - thickness=14, - linewidth=1.0, - linecolor="#000000", - fontdict=None, - html=None, - open_left=False, - open_right=False, - box_linewidth=1, - box_color="auto", - legend_text=None, - label_link_color="black", - **data - ): - self.start = start - self.end = end - self.strand = strand - self.label = label - self.color = color - self.linecolor = linecolor - self.data = data - self.thickness = thickness - self.linewidth = linewidth - self.box_linewidth = box_linewidth - self.box_color = box_color - self.label_link_color = label_link_color - self.fontdict = dict( - [("fontsize", 11)] + list((fontdict or {}).items()) - ) - self.html = html - self.open_left = open_left - self.open_right = open_right - self.legend_text = legend_text - - def split_in_two(self, x_coord=0): - """Return two features by cutting this feature at x_coord.""" - copy1 = deepcopy(self) - copy2 = deepcopy(self) - copy1.end = x_coord - copy2.start = x_coord + 1 - return copy1, copy2 - - def crop(self, window): - """Return a the fragment of the feature that is in the window. - - If there is no overlap between the feature location and the window, - None is returned. - """ - s, e = window - if (s > self.end) or (e < self.start): - return None - copy = deepcopy(self) - if s > self.start: - copy.start = s - copy.open_left = True - if e < self.end: - copy.end = e - copy.open_right = True - return copy - - def overlaps_with(self, other): - """Return whether the feature's location overlaps with feature `other` - """ - loc1, loc2 = (self.start, self.end), (other.start, other.end) - loc1, loc2 = sorted(loc1), sorted(loc2) - loc1, loc2 = sorted([loc1, loc2], key=lambda loc: loc[0]) - return loc1[1] > loc2[0] - - @property - def length(self): - """Return the length of the feature (end-start)""" - return abs(self.end - self.start) - - @property - def x_center(self): - """Return the x-center of the feature, (start+end)/2""" - return 0.5 * (self.start + self.end - 1) - - @staticmethod - def from_biopython_feature(feature, **props): - """Create a GraphicalFeature from a Biopython.Feature object.""" - return GraphicFeature( - start=feature.location.start, - end=feature.location.end, - strand=feature.location.strand, - **props - ) - - def __repr__(self): - return ("GF(%(label)s, %(start)d-%(end)d " % self.__dict__) + ( - ")" if self.strand is None else "(%d))" % self.strand - ) |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/BokehPlottableMixin.py --- a/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/BokehPlottableMixin.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,174 +0,0 @@ -try: - from bokeh.plotting import figure, ColumnDataSource - from bokeh.models import Range1d, HoverTool - - BOKEH_AVAILABLE = True -except ImportError: - BOKEH_AVAILABLE = False - -try: - import pandas as pd - - PANDAS_AVAILABLE = True -except ImportError: - PANDAS_AVAILABLE = False - -import matplotlib.pyplot as plt - - -class BokehPlottableMixin: - def bokeh_feature_patch( - self, - start, - end, - strand, - figure_width=5, - width=0.4, - level=0, - arrow_width_inches=0.05, - **kwargs - ): - """Return a dict with points coordinates of a Bokeh Feature arrow. - - Parameters - ---------- - - start, end, strand - - """ - hw = width / 2.0 - x1, x2 = (start, end) if (strand >= 0) else (end, start) - bp_per_width = figure_width / self.sequence_length - delta = arrow_width_inches / bp_per_width - if strand >= 0: - head_base = max(x1, x2 - delta) - else: - head_base = min(x1, x2 + delta) - result = dict( - xs=[x1, x1, head_base, x2, head_base, x1], - ys=[e + level for e in [-hw, hw, hw, 0, -hw, -hw]], - ) - result.update(kwargs) - return result - - def plot_with_bokeh(self, figure_width=5, figure_height="auto", tools="auto"): - """Plot the graphic record using Bokeh. - - Examples - -------- - - >>> - - - """ - if not BOKEH_AVAILABLE: - raise ImportError("``plot_with_bokeh`` requires Bokeh installed.") - if not PANDAS_AVAILABLE: - raise ImportError("``plot_with_bokeh`` requires Pandas installed.") - - # Set up default tools - if tools == "auto": - tools = [HoverTool(tooltips="@hover_html"), "xpan,xwheel_zoom,reset,tap"] - - # FIRST PLOT WITH MATPLOTLIB AND GATHER INFOS ON THE PLOT - ax, (features_levels, plot_data) = self.plot(figure_width=figure_width) - width, height = [int(100 * e) for e in ax.figure.get_size_inches()] - plt.close(ax.figure) - if figure_height == "auto": - height = int(0.5 * height) - else: - height = 100 * figure_height - height = max(height, 185) # Minimal height to see all icons - - max_y = max( - [data["annotation_y"] for f, data in plot_data.items()] - + list(features_levels.values()) - ) - - # BUILD THE PLOT () - plot = figure( - plot_width=width, - plot_height=height, - tools=tools, - x_range=Range1d(0, self.sequence_length), - y_range=Range1d(-1, max_y + 1), - ) - plot.patches( - xs="xs", - ys="ys", - color="color", - line_color="#000000", - source=ColumnDataSource( - pd.DataFrame.from_records( - [ - self.bokeh_feature_patch( - feature.start, - feature.end, - feature.strand, - figure_width=figure_width, - level=level, - color=feature.color, - label=feature.label, - hover_html=( - feature.html - if feature.html is not None - else feature.label - ), - ) - for feature, level in features_levels.items() - ] - ) - ), - ) - - if plot_data != {}: - plot.text( - x="x", - y="y", - text="text", - text_align="center", - text_font_size="12px", - text_font="arial", - text_font_style="normal", - source=ColumnDataSource( - pd.DataFrame.from_records( - [ - dict( - x=feature.x_center, - y=pdata["annotation_y"], - text=feature.label, - color=feature.color, - ) - for feature, pdata in plot_data.items() - ] - ) - ), - ) - plot.segment( - x0="x0", - x1="x1", - y0="y0", - y1="y1", - line_width=0.5, - color="#000000", - source=ColumnDataSource( - pd.DataFrame.from_records( - [ - dict( - x0=feature.x_center, - x1=feature.x_center, - y0=pdata["annotation_y"], - y1=pdata["feature_y"], - ) - for feature, pdata in plot_data.items() - ] - ) - ), - ) - - plot.yaxis.visible = False - plot.outline_line_color = None - plot.grid.grid_line_color = None - plot.toolbar.logo = None - - return plot |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/GraphicRecord.py --- a/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/GraphicRecord.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,199 +0,0 @@ -from ..biotools import find_narrowest_text_wrap - -from Bio.Seq import Seq -from Bio.SeqRecord import SeqRecord -from Bio.SeqFeature import FeatureLocation, SeqFeature -from Bio.Alphabet import DNAAlphabet - -from .MatplotlibPlottableMixin import MatplotlibPlottableMixin -from .BokehPlottableMixin import BokehPlottableMixin - - -class GraphicRecord(MatplotlibPlottableMixin, BokehPlottableMixin): - """Set of Genetic Features of a same DNA sequence, to be plotted together. - - Parameters - ---------- - - sequence_length - Length of the DNA sequence, in number of nucleotides - - features - list of GraphicalFeature objects. - - feature_level_height - Width in inches of one "level" for feature arrows. - - annotation_height - Width in inches of one "level" for feature annotations. - - first_index - Indicates the first index to plot in case the sequence is actually a - subsequence of a larger one. For instance, if the Graphic record - represents the segment (400, 420) of a sequence, we will have - ``first_index=400`` and ``sequence_length=20``. - - plots_indexing - Indicates which standard to use to show nucleotide indices in the plots. - If 'biopython', the standard python indexing is used (starting at 0). - If 'genbank', the indexing follows the Genbank standard (starting at 1). - - labels_spacing - Number of pixels that will "pad" every labels to force some horizontal - space between two labels or between a label and the borders of a feature. - - ticks_resolution - Leave to "auto" for an auto-selected number of ticks on the ruler, or set - to e.g. 50 for a tick every 50 nucleotide. - - Attributes - ---------- - - default_font_family - Default font to use for a feature that doesn't declare a font. - - default_ruler_color - Default ruler color to use when no color is given at plot() time. - - default_box_color - Default box color for non-inline annotations. If set to None, no - boxes will be drawn unless the features declare a box_color. - If "auto", a color (clearer version of the feature's color) will be - computed, for all features also declaring their box_color as "auto". - - default_elevate_outline_annotations - Value to use for elevate_outline_annotations when no specific value is - given at ``graphic_record.plot(...)`` time. Set to true to have all - text annotations appears above all features, or false else. - """ - - default_font_family = None - default_ruler_color = "grey" - default_box_color = "auto" - min_y_height_of_text_line = 0.5 - - def __init__( - self, - sequence_length=None, - sequence=None, - features=(), - feature_level_height=1, - first_index=0, - plots_indexing="biopython", - labels_spacing=8, - ticks_resolution='auto' - ): - if sequence_length is None: - sequence_length = len(sequence) - self.features = features - self.sequence_length = sequence_length - self.feature_level_height = feature_level_height - self.sequence = sequence - self.first_index = first_index - self.plots_indexing = plots_indexing - self.labels_spacing = labels_spacing - self.ticks_resolution = ticks_resolution - - @property - def last_index(self): - return self.first_index + self.sequence_length - - @property - def span(self): - """Return the display span (start, end) accounting for first_index.""" - return self.first_index, self.last_index - - def to_biopython_record(self, sequence): - """ - Example - ------- - from Bio import SeqIO - gr_record = GraphicRecord(features=features, sequence_length=len(seq), - sequence=seq) - bio_record = gr_record.to_biopython_record() - with open("example.gb", "w+") as f: - SeqIO.write(record, f, "genbank") - """ - features = [ - SeqFeature( - FeatureLocation(f.start, f.end, f.strand), - type=f.feature_type, - qualifiers={"label": f.label}, - ) - for f in self.features - ] - if not isinstance(sequence, Seq): - sequence = Seq(sequence, alphabet=DNAAlphabet()) - return SeqRecord(seq=sequence, features=features) - - def crop(self, window): - start, end = window - first_index = self.first_index - if (start < first_index) or (end > self.last_index): - raise ValueError("out-of-bound cropping") - new_features = [] - for f in self.features: - cropped_feature = f.crop(window) - if cropped_feature is not None: # = has ovelap with the window - new_features.append(cropped_feature) - - return GraphicRecord( - sequence=self.sequence[start - first_index : end - first_index] - if self.sequence is not None - else None, - sequence_length=end - start, - features=new_features, - feature_level_height=self.feature_level_height, - first_index=start, - plots_indexing=self.plots_indexing, - labels_spacing=self.labels_spacing, - ticks_resolution=self.ticks_resolution - ) - - def determine_annotation_height(self, levels): - """By default the ideal annotation level height is the same as the - feature_level_height.""" - # TODO: Improve me! ideally, annotation width would be linked to the - # height of one line of text, so dependent on font size and ax - # height/span. - return self.feature_level_height - - def coordinates_in_plot(self, x, level): - """Convert a sequence position and height level into a (x, y) position. - """ - return (x, level * self.feature_level_height) - - def split_overflowing_features_circularly(self): - """Split the features that overflow over the edge for circular - constructs (inplace).""" - new_features = [] - for f in self.features: - if f.start < 0 < f.end: - f1, f2 = f.split_in_two(-1) - f1.start, f1.end = ( - f1.start + self.sequence_length, - f1.end + self.sequence_length, - ) - new_features += [f1, f2] - elif f.start < self.sequence_length < f.end: - f1, f2 = f.split_in_two(self.sequence_length - 1) - f2.start, f2.end = ( - f2.start - self.sequence_length, - f2.end - self.sequence_length, - ) - new_features += [f1, f2] - else: - new_features.append(f) - self.features = new_features - - def _format_label(self, label, max_label_length=50, max_line_length=40): - if len(label) > max_label_length: - label = label[: max_label_length - 1] + "…" - if len(label) > max_line_length: - label = find_narrowest_text_wrap(label, max_line_length) - return label - - def compute_padding(self, ax): - ax_width = ax.get_window_extent(ax.figure.canvas.get_renderer()).width - xmin, xmax = ax.get_xlim() - return self.labels_spacing * (xmax - xmin) / (1.0 * ax_width) |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/MatplotlibPlottableMixin.py --- a/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/MatplotlibPlottableMixin.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,651 +0,0 @@\n-"""Useful functions for the library"""\n-\n-import colorsys\n-\n-import matplotlib.pyplot as plt\n-import matplotlib.patches as mpatches\n-from matplotlib.patches import Patch\n-import matplotlib.ticker as ticker\n-\n-from ..compute_features_levels import compute_features_levels\n-from ..GraphicFeature import GraphicFeature\n-from matplotlib.colors import colorConverter\n-from .MultilinePlottableMixin import MultilinePlottableMixin\n-from .SequenceAndTranslationMixin import SequenceAndTranslationMixin\n-\n-\n-class MatplotlibPlottableMixin(\n- MultilinePlottableMixin, SequenceAndTranslationMixin\n-):\n- """Class mixin for matplotlib-related methods."""\n-\n- default_elevate_outline_annotations = False\n- default_strand_in_label_threshold = None\n-\n- def initialize_ax(self, ax, draw_line, with_ruler, ruler_color=None):\n- """Initialize the ax: remove axis, draw a horizontal line, etc.\n-\n- Parameters\n- ----------\n-\n- draw_line\n- True/False to draw the horizontal line or not.\n-\n- with_ruler\n- True/False to draw the indices indicators along the line.\n-\n- """\n- ruler_color = ruler_color or self.default_ruler_color\n- start, end = self.span\n- plot_start, plot_end = start - 0.8, end - 0.2\n- if draw_line:\n- ax.plot([plot_start, plot_end], [0, 0], zorder=-1000, c="k")\n-\n- if with_ruler: # only display the xaxis ticks\n- ax.set_frame_on(False)\n- ax.yaxis.set_visible(False)\n- ax.xaxis.tick_bottom()\n- if ruler_color is not None:\n- ax.tick_params(axis="x", colors=ruler_color)\n- else: # don\'t display anything\n- ax.axis("off")\n-\n- ax.set_xlim(plot_start, plot_end)\n- if self.first_index != 0:\n- ax.ticklabel_format(useOffset=False, style="plain")\n- fmt = lambda x, p: "{:,}".format(int(x))\n- ax.xaxis.set_major_formatter(ticker.FuncFormatter(fmt))\n- if self.ticks_resolution == "auto":\n- ax.xaxis.set_major_locator(ticker.MaxNLocator(integer=True))\n- else:\n- locator = ticker.MultipleLocator(self.ticks_resolution)\n- ax.xaxis.set_major_locator(locator)\n-\n- def finalize_ax(\n- self,\n- ax,\n- features_levels,\n- annotations_max_level,\n- auto_figure_height=False,\n- ideal_yspan=None,\n- annotations_are_elevated=True,\n- ):\n- """Prettify the figure with some last changes.\n- \n- Changes include redefining y-bounds and figure height.\n-\n- Parameters\n- ==========\n- ax\n- ax on which the record was plotted\n- \n- features_levels\n- \n- annotations_max_level\n- Number indicating to the method the maximum height for an\n- annotation, so the method can set ymax accordingly\n-\n- auto_figure_height\n- If true, the figure\'height will be automatically re-set to a nice\n- value (counting ~0.4inch per level in the figure).\n-\n- ideal_yspan\n- if provided, can help the method select a better ymax to make sure\n- all constraints fit.\n-\n- """\n-\n- # Compute the "natural" ymax\n- annotation_height = self.determine_annotation_height(None)\n- features_ymax = self.feature_level_height * (features_levels + 1)\n- annotations_ymax = annotation_height * annotations_max_level\n- if annotations_are_elevated:\n- ymax = features_ymax + annotations_ymax\n- else:\n- ymax = max(features_ymax, annotations_ymax) + 1\n- ymin = min(ax.get_ylim()[0], -0.5)\n-\n- # ymax could be even bigger if a "ideal_yspan" has been set.\n- if (ideal_yspan is not None) and not (auto_figure_height):\n- ymax = max(ideal_yspan + ymin, ymax)\n- ax.set_ylim(ymin, ymax)\n- if auto_figure_height:\n- figure_width = ax.figure.get_size_inches()[0]\n- '..b'ature_level"]\n- )\n-\n- # PLOT THE LABEL-TO-FEATURE LINK\n- link_color = feature.label_link_color\n- if link_color == "auto":\n- link_color = change_luminosity(feature.color, luminosity=0.2)\n- ax.plot([x, fx], [new_y, fy], c=link_color, lw=0.5, zorder=-10)\n- labels_data[feature.data["feature"]] = dict(\n- feature_y=fy, annotation_y=new_y\n- )\n-\n- if plot_sequence:\n- self.plot_sequence(ax, **(sequence_params or {}))\n-\n- self.finalize_ax(\n- ax=ax,\n- features_levels=max([1] + list(features_levels.values())),\n- annotations_max_level=max_annotations_level,\n- auto_figure_height=auto_figure_height,\n- ideal_yspan=ideal_yspan,\n- annotations_are_elevated=elevate_outline_annotations,\n- )\n- return ax, (features_levels, labels_data)\n-\n- def plot_legend(\n- self, ax, allow_ambiguity=False, include_edge=True, **legend_kwargs\n- ):\n- handles = []\n- features_parameters = {}\n- for feature in self.features:\n- text = feature.legend_text\n- if text is None:\n- continue\n- parameters = dict(\n- label=text, facecolor=feature.color, edgecolor="black",\n- )\n- if include_edge:\n- parameters.update(\n- dict(\n- linewidth=feature.linewidth,\n- edgecolor=feature.linecolor,\n- )\n- )\n- if text in features_parameters:\n- previous_parameters = features_parameters[text]\n- if (not allow_ambiguity) and any(\n- [\n- parameters[k] != previous_parameters[k]\n- for k in parameters\n- ]\n- ):\n- raise ValueError(\n- "Cannot generate an unambiguous legend as two"\n- )\n- continue\n- features_parameters[text] = parameters\n- handles.append(Patch(**parameters))\n- ax.legend(handles=handles, **legend_kwargs)\n-\n-\n-def change_luminosity(\n- color, luminosity=None, min_luminosity=None, factor=None\n-):\n- """Return a version of the color with different luminosity.\n-\n- Parameters\n- ----------\n- color\n- A color in any Matplotlib-compatible format such as "white", "w",\n- (1,1,1), "#ffffff", etc.\n- luminosity\n- A float in 0-1. If provided, the returned color has this level of\n- luminosity.\n- factor\n- Only used if `luminosity` is not set. Positive factors increase\n- luminosity and negative factors decrease it. More precisely, the\n- luminosity of the new color is L^(-factor), where L is the current\n- luminosity, between 0 and 1. \n- """\n- r, g, b = colorConverter.to_rgb(color)\n- h, l, s = colorsys.rgb_to_hls(r, g, b)\n- new_l = l\n- if luminosity is not None:\n- new_l = luminosity\n- if factor is not None:\n- new_l = l ** (-factor)\n- if min_luminosity is not None:\n- new_l = max(new_l, min_luminosity)\n-\n- return colorsys.hls_to_rgb(h, new_l, s)\n-\n-\n-def get_text_box(text, margin=0):\n- """Return the coordinates of a Matplotlib Text.\n-\n- `text` is a Matplotlib text obtained with ax.text().\n- This returns `(x1,y1, x2, y2)` where (x1,y1) is the lower left corner\n- and (x2, y2) is the upper right corner of the text, in data coordinates.\n- If a margin m is supplied, the returned result is (x1-m, y1-m, x2+m, y2+m)\n- """\n- renderer = text.axes.figure.canvas.get_renderer()\n- bbox = text.get_window_extent(renderer) # bounding box\n- __x1, y1, __x2, y2 = bbox.get_points().flatten()\n- bbox = bbox.transformed(text.axes.transData.inverted())\n- x1, __y1, x2, __y2 = bbox.get_points().flatten()\n- return [x1, y1, x2, y2]\n' |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/MultilinePlottableMixin.py --- a/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/MultilinePlottableMixin.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,153 +0,0 @@ -import matplotlib.pyplot as plt -from matplotlib.backends.backend_pdf import PdfPages -import numpy - - -class MultilinePlottableMixin: - def plot_on_multiple_lines( - self, - n_lines=None, - nucl_per_line=None, - plot_sequence=False, - figure_width="auto", - **plot_params - ): - """Plot the features on different lines (one Matplotlib ax per line) - - Parameters - ---------- - - n_lines - Number of lines on which the record will be plotted. A number of - nucleotides per line can be provided instead (see below). - - nucl_per_line - Number of nucleotides to be represented on every line (determines - the number of lines ``n_lines``). - - plot_sequence - Whether to plot the nucleotide sequence on each line - - figure_width - Width of the figure in inches. Leave to auto for a width of either 10 - (if not sequence is plotted) or 0.15*nucl_per_line inches - (if a sequence is plotted). - - **plot_params - Parameters from ``graphic_record.plot()`` to be used in the plotting - of the individual lines. This includes ``draw_line``, ``with_ruler``, - ``annotate_inline``, ``plot_sequence``, - ``evelate_outline_annotations``, ``strand_in_label_pixel_threshold`` - - Returns - ------- - - figure, axes - The matplotlib figure and axes generated. - """ - - if n_lines is None: - n_lines = int(numpy.ceil(self.sequence_length / nucl_per_line)) - else: - nucl_per_line = self.sequence_length // n_lines + 1 - - if figure_width == "auto": - if plot_sequence: - figure_width = 0.15 * nucl_per_line - else: - figure_width = 10 - - figures_heights = [] - - def plot_line(line_index, ax=None): - first, last = self.first_index, self.last_index - line_start = first + line_index * nucl_per_line - line_virtual_end = first + (line_index + 1) * nucl_per_line - line_end = min(last, line_virtual_end) - line_record = self.crop((line_start, line_end)) - line_ax, _ = line_record.plot( - figure_width=figure_width, - x_lim=(line_start, line_virtual_end), - ax=ax, - plot_sequence=plot_sequence, - **plot_params - ) - return line_ax - - for line_index in range(n_lines): - line_ax = plot_line(line_index) - figures_heights.append(line_ax.figure.get_figheight()) - plt.close(line_ax.figure) - fig, axes = plt.subplots( - n_lines, - 1, - gridspec_kw={"height_ratios": figures_heights}, - figsize=(figure_width, 0.9 * sum(figures_heights)), - ) - if n_lines == 1: - axes = [axes] - for line_index, ax in enumerate(axes): - plot_line(line_index, ax=ax) - fig.tight_layout() - return fig, axes - - def plot_on_multiple_pages( - self, - pdf_target, - n_lines=None, - nucl_per_line=None, - lines_per_page=5, - figure_width="auto", - **plot_params - ): - """Plot the features on different lines on different pages of a PDF. - - This function returns None - - Parameters - ---------- - - pdf_target - Either a path to a PDF, or a file(-like) handle. - - n_lines - Number of lines on which the record will be plotted. A number of - nucleotides per line can be provided instead (see below). - - nucl_per_line - Number of nucleotides to be represented on every line (determines - the number of lines ``n_lines``). - - lines_per_page - Number of lines on each page - - plot_sequence - Whether to plot the nucleotide sequence on each line - - figure_width - Width of the figure in inches. Leave to auto for a width of either 10 - (if not sequence is plotted) or 0.15*nucl_per_line inches - (if a sequence is plotted). - - **plot_params - Parameters from ``graphic_record.plot()`` to be used in the plotting - of the individual lines. This includes ``draw_line``, ``with_ruler``, - ``annotate_inline``, ``plot_sequence``, - ``evelate_outline_annotations``, ``strand_in_label_pixel_threshold`` - """ - nucl_per_page = nucl_per_line * lines_per_page - number_of_pages = int(numpy.ceil(self.sequence_length / nucl_per_page)) - with PdfPages(pdf_target) as pdf: - for page_index in range(number_of_pages): - first, last = self.first_index, self.last_index - page_start = first + page_index * nucl_per_page - page_end = first + (page_index + 1) * nucl_per_page - page_end = min(last, page_end) - page_record = self.crop((page_start, page_end)) - fig, axes = page_record.plot_on_multiple_lines( - nucl_per_line=nucl_per_line, - figure_width=figure_width, - **plot_params - ) - pdf.savefig(fig) - plt.close(fig) |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/SequenceAndTranslationMixin.py --- a/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/SequenceAndTranslationMixin.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,145 +0,0 @@ -from ..biotools import extract_graphical_translation - - -class SequenceAndTranslationMixin: - def plot_sequence( - self, ax, location=None, y_offset=1, fontdict=None, guides_intensity=0 - ): - """Plot a sequence of nucleotides at the bottom of the plot. - - Parameters - ---------- - - ax - Which axes the translation should be plotted to - - location - location of the segment to translate, either (start, end) or - (start, end, strand) - - y_offset - Number of text levels under the plot's base line where to draw the - nucleotides. Should be 1 if the nucleotide sequence is to be plotted - directly under the main line. - - fontdict - Matplotlib fontdict for the text, e.g. - ``{'size': 11, 'weight':'bold'}`` - - background - tuple (color1, color2) of alternate colors to plot behind each - nucleotide position to guide vision. Leave to None for no background. - - guides_intensity - Intensity of the vertical guides marking the different nucleotides - (0 = no guides) - """ - if self.sequence is None: - raise ValueError("No sequence in the graphic record") - if location is None: - location = self.span - location_start, location_end = location - fontdict = dict(size=11) - fontdict.update(fontdict or {}) - for i, nucleotide in enumerate(self.sequence): - index = i + location_start - if location_start <= index <= location_end: - ax.text( - index, - -0.7 * self.feature_level_height * y_offset, - nucleotide, - ha="center", - va="center", - fontdict=fontdict, - ) - if guides_intensity: - color = (0, 0, 0, guides_intensity) - for i in range(location_start, location_end + 1): - ax.axvline(i - 0.5, linewidth=0.1, color=color, zorder=-10000) - ymin = ax.get_ylim()[0] - if ymin < -500: - ymin = 0 - ax.set_ylim(bottom=min(ymin, -y_offset * self.feature_level_height)) - - def plot_translation( - self, - ax, - location=None, - y_offset=2, - fontdict=None, - guides_intensity=0.5, - translation=None, - long_form_translation=True, - ): - """Plot a sequence of amino-acids at the bottom of the plot. - - Parameters - ---------- - - ax - Which axes the translation should be plotted to - - location - location of the segment to translate (start, end) - - y_offset - Number of text levels under the plot's base line where to draw the - amino acid names. Should be 2 if the nucleotide sequence is also - plotted at level 1. - - fontdict - Matplotlib fontdict for the text, e.g. - ``{'size': 11, 'weight':'bold'}`` - - background - tuple (color1, color2) of alternate colors to plot behind each - amino acid position to guide vision. Leave to None for no background. - - translation - Sequence of amino acids either as a string ``'MAKG...'`` or as a list - ``['Met', 'Ala', ...]`` - - - """ - start, end = location[0], location[1] - strand = location[2] if (len(location) == 3) else 1 - s, e = self.span - start = max(start, s + ((start - s) % 3)) - end = min(end, e - ((end - e) % 3)) - if translation is None: - new_loc = start - self.first_index, end - self.first_index, strand - translation = extract_graphical_translation( - self.sequence, - location=new_loc, - long_form=long_form_translation, - ) - texts = [ - ((start + 3 * i, start + 3 * (i + 1)), aa) - for i, aa in enumerate(translation) - ] - - y = -0.7 * y_offset * self.feature_level_height - ymin = ax.get_ylim()[0] - ax.set_ylim(bottom=min(ymin, -y_offset * self.feature_level_height)) - fontdict = fontdict or {} - guides_color = (0, 0, 0, guides_intensity) - for i, ((start, end), text) in enumerate(texts): - ax.text( - 0.5 * (start + end - 1), - y, - text, - ha="center", - va="center", - fontdict=fontdict, - ) - if guides_intensity: - ax.axvline( - start - 0.5, - linewidth=0.1, - color=guides_color, - zorder=-10000, - ) - if guides_intensity: - ax.axvline( - end - 0.5, linewidth=0.1, color=guides_color, zorder=-10000 - ) |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/__init__.py --- a/cpt_linear_genome_plot/dna_features_viewer/GraphicRecord/__init__.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -from .GraphicRecord import GraphicRecord - -__all__ = ['GraphicRecord'] |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/README.md --- a/cpt_linear_genome_plot/dna_features_viewer/README.md Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,13 +0,0 @@ -# Code organization - -This document walks you trough the Geneblocks code. Please request changes if anything is unclear. - -- **GraphicFeature.py** implements a class for defining a *GraphicFeature*, which is an annotation (start, end, strand, label) with graphical properties (color, line width, font family...) - -- **GraphicRecord/** implements the *GraphicRecord* class, which can plot a set of *GraphicFeatures* using Matplotlib or Bokeh. To keep file sizes acceptable, many methods are implemented in separate files (*bokeh_plots.py*, *matplotlib_plots.py*) and added to *GraphicRecord* via class mixins. - -- **CircularGraphicRecord/** implements the *GraphicRecord* class, which inherits from *GraphicRecord* but draws features circularly using custom Matplotlib patches called "arrow-wedge" (defined in file *ArrowWedge.py*). - -- **compute_features_levels.py** implements the algorithm for deciding the levels on which the different features (and annotations) are drawn - -- **biotools.py** implements generic biology-related methods (reverse_complement, annotation of Biopython records, etc.) |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/__init__.py --- a/cpt_linear_genome_plot/dna_features_viewer/__init__.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,22 +0,0 @@ -""" dna_features_viewer/__init__.py """ - -from .GraphicRecord import GraphicRecord -from .CircularGraphicRecord import CircularGraphicRecord -from .GraphicFeature import GraphicFeature -from .BiopythonTranslator import ( - BiopythonTranslator, - BlackBoxlessLabelTranslator, -) -from .biotools import load_record, annotate_biopython_record - -from .version import __version__ - -__all__ = [ - "GraphicRecord", - "CircularGraphicRecord", - "GraphicFeature", - "BiopythonTranslator", - "BlackBoxlessLabelTranslator", - "annotate_biopython_record", - "__version__", -] |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/biotools.py --- a/cpt_linear_genome_plot/dna_features_viewer/biotools.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,170 +0,0 @@ -import textwrap -from Bio.Seq import Seq -from Bio.SeqFeature import SeqFeature, FeatureLocation -from Bio.PDB.Polypeptide import aa1, aa3 -from Bio import SeqIO - -try: - from BCBio import GFF -except ImportError: - - class GFF: - def parse(*a): - """Not available. Please install bcbio-gff.""" - raise ImportError( - "Please install the bcbio-gff library to parse GFF data" - ) - - -def complement(dna_sequence): - """Return the complement of the DNA sequence. - - For instance ``complement("ATGCCG")`` returns ``"TACGGC"``. - - Uses BioPython for speed. - """ - return str(Seq(dna_sequence).complement()) - - -def reverse_complement(sequence): - """Return the reverse-complement of the DNA sequence. - - For instance ``complement("ATGCCG")`` returns ``"GCCGTA"``. - - Uses BioPython for speed. - """ - return complement(sequence)[::-1] - - -aa_short_to_long_form_dict = { - _aa1: _aa3[0] + _aa3[1:].lower() - for (_aa1, _aa3) in zip(aa1 + "*", aa3 + ["*"]) -} - - -def translate(dna_sequence, long_form=False): - """Translate the DNA sequence into an amino-acids sequence MLKYQT... - - If long_form is true, a list of 3-letter amino acid representations - is returned instead (['Ala', 'Ser', ...]). - """ - result = str(Seq(dna_sequence).translate()) - if long_form: - result = [aa_short_to_long_form_dict[aa] for aa in result] - return result - - -def extract_graphical_translation(sequence, location, long_form=False): - """Return a string of the "graphical" translation of a sequence's subsegment. - - Here "graphical" means that the amino acid sequence is always given - left-to-right, as it will appear under the sequence in the plot. This matters - when the location is on the -1 strand. In this case, the amino-acids are - determined by (part of) the reverse-complement of the sequence, however - the sequence returned will be the mirror of the translated sequence, as - this is the left-to-right order in which the codons corresponding to the - amino-acids appear in the sequence. - - Parameters - ---------- - sequence - An "ATGC" string. - - location - Either (start, end) or (start, end, strand), with strand in (0, 1, -1). - - long_form - if True, a list of 3-letter amino acid representations is returned instead - (['Ala', 'Ser', ...]). - - """ - if len(location) == 3: - start, end, strand = location - else: - start, end = location - strand = 1 - subsequence = sequence[start:end] - if strand == -1: - subsequence = reverse_complement(subsequence) - translation = translate(subsequence, long_form=long_form) - if strand == -1: - translation = translation[::-1] - return translation - - -def load_record(path): - """Load a Genbank file """ - if isinstance(path, str): - # Input is a file path - if path.lower().endswith('.gff'): - return list(GFF.parse(path))[0] - else: - return SeqIO.read(path, "genbank") - else: - # Input is a file-like object - try: - return SeqIO.read(path, "genbank") - except: - path.seek(0) - return list(GFF.parse(path))[0] - - -def annotate_biopython_record( - seqrecord, - location="full", - feature_type="misc_feature", - margin=0, - **qualifiers -): - """Add a feature to a Biopython SeqRecord. - - Parameters - ---------- - - seqrecord - The biopython seqrecord to be annotated. - - location - Either (start, end) or (start, end, strand). (strand defaults to +1) - - feature_type - The type associated with the feature - - margin - Number of extra bases added on each side of the given location. - - qualifiers - Dictionnary that will be the Biopython feature's `qualifiers` attribute. - """ - if location == "full": - location = (margin, len(seqrecord) - margin) - - strand = location[2] if len(location) == 3 else 1 - seqrecord.features.append( - SeqFeature( - FeatureLocation(location[0], location[1], strand), - qualifiers=qualifiers, - type=feature_type, - ) - ) - - -def find_narrowest_text_wrap(text, max_line_length): - """Wrap the text into a multi-line text minimizing the longest line length. - - This is done by first wrapping the text using max_line_length, then - attempt new wraps by iteratively decreasing the line_length, as long as the - number of lines stays the same as with max_line_length. - """ - narrowest_wrap = textwrap.wrap(text, max_line_length) - narrowest_width = max([len(l) for l in narrowest_wrap]) - for line_length in range(max_line_length - 1, 0, -1): - wrap = textwrap.wrap(text, line_length) - if len(wrap) <= len(narrowest_wrap): - width = max([len(l) for l in wrap]) - if width < narrowest_width: - narrowest_wrap = wrap - narrowest_width = width - else: - break - return "\n".join(narrowest_wrap) |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/compute_features_levels.py --- a/cpt_linear_genome_plot/dna_features_viewer/compute_features_levels.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,75 +0,0 @@ -"""Implements the method used for deciding which feature goes to which level -when plotting.""" - -import itertools -import math - - -class Graph: - """Minimal implementation of non-directional graphs. - - Parameters - ---------- - - nodes - A list of objects. They must be hashable - edges - A list of the form [(n1,n2), (n3,n4)...] where (n1, n2) represents - an edge between nodes n1 and n2 - """ - - def __init__(self, nodes, edges): - self.nodes = nodes - self.neighbors = {n: [] for n in nodes} - for n1, n2 in edges: - self.neighbors[n1].append(n2) - self.neighbors[n2].append(n1) - - -def compute_features_levels(features): - """Compute the vertical levels on which the features should be displayed - in order to avoid collisions. - - `features` must be a list of `dna_features_viewer.GraphicFeature`. - - The method used is basically a graph coloring: - - The nodes of the graph are features and they will be colored with a level - - Two nodes are neighbors if and only if their features's locations overlap - - Levels are attributed to nodes iteratively starting with the nodes - corresponding to the largest features. - - A node receives the lowest level (starting at 0) that is not already - the level of one of its neighbors. - """ - edges = [ - (f1, f2) - for f1, f2 in itertools.combinations(features, 2) - if f1.overlaps_with(f2) - ] - graph = Graph(features, edges) - levels = { - n: n.data.get("fixed_level", None) - for n in graph.nodes - } - - def collision(node, level): - """Return whether the node placed at base_level collides with its - neighbors in the graph.""" - line_factor = 0.5 - nlines = node.data.get("nlines", 1) - for neighbor in graph.neighbors[node]: - neighbor_level = levels[neighbor] - if neighbor_level is None: - continue - neighbor_lines = neighbor.data.get("nlines", 1) - min_distance = line_factor * (nlines + neighbor_lines) - if abs(level - neighbor_level) < min_distance: - return True - return False - - for node in sorted(graph.nodes, key=lambda f: -f.length): - if levels[node] is None: - level = 0 - while collision(node, level): - level += 0.5 - levels[node] = level - return levels |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/dna_features_viewer/version.py --- a/cpt_linear_genome_plot/dna_features_viewer/version.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -__version__ = "3.0.1" |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/linear_genome_plot.py --- a/cpt_linear_genome_plot/linear_genome_plot.py Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,281 +0,0 @@\n-#!/usr/bin/env python\n-from Bio import SeqIO\n-from dna_features_viewer import BiopythonTranslator, GraphicRecord\n-from matplotlib import rc_context\n-import matplotlib\n-import matplotlib.pyplot as plt\n-from itertools import cycle\n-import re\n-import sys\n-import argparse\n-\n-class CPTTranslator(BiopythonTranslator):\n- """\n- This is a customized translator from the dna_features_viewer module to fit Galaxy\n- """\n-\n- global custom_feature_colors\n- global box_status\n- global label_fields\n- global custom_name_colors\n- global ignored_features_types\n- global ignored_gene_labels\n- global ignored_feature_labels\n-\n- def compute_feature_color(self, feature):\n- if feature.type == "CDS":\n- if "product" in feature.qualifiers:\n- color_specific = any(re.search(("(\\\\b"+str(item)+"\\\\b)"),feature.qualifiers["product"][0]) for item in custom_name_colors.keys()) or any(re.search((item),feature.qualifiers["product"][0]) for item in custom_name_colors.keys())\n- if color_specific:\n- try:\n- return custom_name_colors[feature.qualifiers["product"][0]]\n- except KeyError:\n- for item in custom_name_colors.keys():\n- if item in feature.qualifiers["product"][0]:\n- custom_name_colors[feature.qualifiers["product"][0]] = custom_name_colors[item]\n- return custom_name_colors[feature.qualifiers["product"][0]]\n- #print(feature.qualifiers["product"][0])\n- else:\n- try:\n- return custom_feature_colors[feature.type]\n- except KeyError:\n- return BiopythonTranslator.compute_feature_color(self, feature)\n- else:\n- if feature.type not in ignored_features_types:\n- try:\n- return custom_feature_colors[feature.type]\n- except KeyError:\n- return BiopythonTranslator.compute_feature_color(self, feature)\n-\n- def compute_feature_label(self, feature): # remove the chop_blocks\n- self.label_fields = label_fields\n- if feature.type == "CDS":\n- if "product" in feature.qualifiers:\n- if ignored_gene_labels: # product name drop\n- verify_chops = any(re.search(("(\\\\b"+str(item)+"\\\\b)"),feature.qualifiers["product"][0]) for item in ignored_gene_labels) or any(re.search((item), feature.qualifiers["product"][0]) for item in ignored_gene_labels)\n- if verify_chops:\n- return None\n- else:\n- return BiopythonTranslator.compute_feature_label(self, feature)\n- else:\n- return BiopythonTranslator.compute_feature_label(self, feature)\n- elif feature.type in ignored_feature_labels:\n- return None\n- else:\n- return BiopythonTranslator.compute_feature_label(self, feature)\n-\n- def compute_filtered_features(self, features):\n- return [\n- feature for feature in features if feature.type not in ignored_features_types\n- ]\n-\n- def compute_feature_legend_text(self, feature):\n- return feature.type\n-\n- def compute_feature_box_color(self, feature):\n- if feature.type == "CDS":\n- return "white"\n-\n- def compute_feature_label_link_color(self, feature):\n- return "black"\n-\n- def compute_feature_box_linewidth(self, feature):\n- if box_status:\n- return 0.5\n- else:\n- return 0\n-\n-def parse_gbk(file):\n- """ simple function to parse out the feature information AND products """\n-\n- record = SeqIO.read(file,"genbank")\n- count = 0\n- feature_types = {}\n- product_names = []\n- for feat in record.features:\n- if feat.type not in f'..b'gene_ids,gene_ids_colors))\n- else:\n- custom_name_colors = {}\n-\n- ## Ignored Features\n- #ignored_features_types = str.split(args.features_excluded,",")\n- if args.common_features_excluded:\n- ignored_features_types = str.split(args.common_features_excluded, ",")\n- if args.features_excluded:\n- ignored_features_types += str.split(args.features_excluded,",")\n- elif args.features_excluded:\n- ignored_features_types = str.split(args.features_excluded,",")\n- else:\n- ignored_features_types = False\n-\n- print(ignored_features_types)\n- \n- ## product labels\n- if args.common_ignore_product_labels:\n- ignored_gene_labels = str.split(args.common_ignore_product_labels,",")\n- if args.ignore_labeling:\n- ignored_gene_labels += str.split(args.ignore_labeling,",")\n- elif args.ignore_labeling:\n- ignored_gene_labels = str.split(args.ignore_labeling,",")\n- else:\n- ignored_gene_labels = False\n- \n- print(ignored_gene_labels)\n-\n- if args.feature_label_order != [\'\']:\n- label_fields = str.split(args.feature_label_order,",")\n-\n- #if ignored_gene_labels == [\'\']:\n- # ignored_gene_labels = False\n-\n- ## Ignored Labeling\n- if args.common_ignore_feature_labels:\n- ignored_feature_labels = str.split(args.common_ignore_feature_labels,",")\n- if args.ignored_feature_labels:\n- ignored_feature_labels += str.split(args.ignored_feature_labels,",")\n- elif args.ignored_feature_labels:\n- ignored_feature_labels = str.split(args.ignored_feature_labels,",")\n- else:\n- ignored_feature_labels = False\n- \n- print(ignored_feature_labels)\n- ## Print Statements for Debugging\n- #print(custom_feature_colors)\n- #print(custom_name_colors)\n- #print(ignored_features_types)\n- #print(ignored_gene_labels)\n- #print(label_fields)\n-\n- ## Part III ; PLOT\n- # Housekeeping\n- rc_context({"font.family": ["monospace"],}) # courier-like\n- matplotlib.use(\'Agg\') # I think this has to be used...\n-\n- if args.label_algo:\n- lab_algo = True\n- else:\n- lab_algo = False\n-\n- translator = CPTTranslator()\n- graphic_record = translator.translate_record(genome)\n-\n- with open("tmp.svg", "wb") as img:\n- img.truncate(0)\n- img.close()\n-\n- if args.sz and not args.multiline: # if user is wanting to look at a subset region of the genome\n- zoom_start, zoom_end = args.sz, args.ez\n- cropped = graphic_record.crop((zoom_start,zoom_end))\n- ax, _ = cropped.plot(figure_width=args.plot_width, annotate_inline=lab_algo,figure_height=None)\n- if args.translation_on:\n- crop_seq = (args.st - 1, args.et)\n- cropped.plot_translation(ax, location=crop_seq, fontdict={\'size\':8, \'weight\':\'bold\'},y_offset=1)\n- ax.set_title(args.title)\n- # Galaxy specific shenanigans\n- tmp_fig = "./tmp.svg"\n- plt.savefig(tmp_fig)\n- plt.close()\n- elif args.multiline:\n- if args.sz:\n- zoom_start, zoom_end = args.sz, args.ez\n- else:\n- zoom_start, zoom_end = 1, graphic_record.sequence_length\n- cropped = graphic_record.crop((zoom_start,zoom_end))\n- ax, _ = cropped.plot_on_multiple_lines(\n- figure_width=args.plot_width,\n- annotate_inline=lab_algo,\n- figure_height=None,\n- nucl_per_line=args.nucl_per_line,\n- plot_sequence=False\n- )\n- #ax.set_title(args.title)\n- tmp_fig = "./tmp.svg"\n- plt.savefig(tmp_fig)\n- plt.close()\n- else:\n- ax, _ = graphic_record.plot(figure_width=args.plot_width, annotate_inline=lab_algo)\n- ax.set_title(args.title)\n- tmp_fig = "./tmp.svg"\n- # Galaxy specific shenanigans\n- plt.savefig(tmp_fig)\n- plt.close()\n- with open("tmp.svg", "rb") as img:\n- for line in img:\n- args.out_img.write(line)\n' |
| b |
| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/linear_genome_plot.xml --- a/cpt_linear_genome_plot/linear_genome_plot.xml Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,289 +0,0 @@\n-<tool id="edu.tamu.cpt.genome_viz.linear_genome_plot" name="Linear Genome Plot" version="1.0">\n- <description>Linear Genome Plot</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="requirements">\n- </expand>\n- <command detect_errors="aggressive"><![CDATA[\n-python $__tool_directory__/linear_genome_plot.py\n-$input_file\n---plot_width $plot_width\n---common_features_excluded "$common_features_excluded"\n---features_excluded "$features_excluded"\n---common_ignore_feature_labels "$common_ignore_feature_labels"\n---ignored_feature_labels "$ignored_feature_labels"\n---common_ignore_product_labels "$common_ignore_product_labels"\n---ignore_labeling "$ignore_labeling"\n---feature_label_order "$feature_label_order"\n---title "$title"\n-$label_algo\n-$label_box\n-#if $selectregion.custom_region:\n- --sz $selectregion.start_zoom\n- --ez $selectregion.end_zoom\n-#end if\n-#if $multiline.multi_line:\n- --multiline\n- --nucl_per_line $multiline.nucl_per_line\n-#end if\n-#for $feature_color in $feature_colors:\n- #if $feature_color.feature_color_selector.feature_color_options == "add_colors":\n- --feature_id #for $feat_id in $feature_color.feature_color_selector.feature_id:\n- "${feat_id}" #end for\n- --feature_id_color #for $feat_col in $feature_color.feature_color_selector.feature_id_color:\n- "${feat_col}" #end for\n- #end if\n-#end for\n-#for $gene_color in $gene_colors:\n- #if $gene_color.gene_color_selector.gene_color_options == "add_colors":\n- --gene_id #for $gene_id in $gene_color.gene_color_selector.gene_id:\n- "${gene_id}" #end for\n- --gene_id_color #for $gene_col in $gene_color.gene_color_selector.gene_id_color:\n- "${gene_col}" #end for\n- #end if\n-#end for\n---file_stats $file_stats\n---out_img $out_img\n- ]]></command>\n- <inputs>\n- <param label="Annotated Genome File (Gbk)" name="input_file" type="data" format="genbank" />\n- <param label="Plot Width" name="plot_width" type="integer" value="10" help="Width of the plot. Increase for larger genomes." />\n- <param label="Box Label" name="label_box" type="boolean" checked="true" help="Select \'no\' to have no label box around feature labels" truevalue="--label_box" falsevalue="" />\n- <conditional name="selectregion">\n- <param label="Select Custom Region" name="custom_region" type="boolean" checked="false" help="Plot a specific region of the genome" />\n- <when value="true">\n- <param name="start_zoom" label="Start Zoom" type="integer" help="start zoom" optional="true"/>\n- <param name="end_zoom" label="End Zoom" type="integer" help="end zoom" optional="true"/>\n- </when>\n- <when value="false">\n- </when>\n- </conditional>\n- <conditional name="multiline">\n- <param label="Multi Line Plot" name="multi_line" type="boolean" checked="false" help="Breaks up the plot into multiple lines"/>\n- <when value="true">\n- <param name="nucl_per_line" label="Nucleotides Per Line" type="integer" optional="true" />\n- </when>\n- <when value="false">\n- </when>\n- </conditional>\n- <param argument="common_features_excluded" label="Common Feature(s) to EXCLUDE" type="select" multiple="true" help="Common Features to be excluded from the plot">\n- <option value="source" selected="true">source</option>\n- <option value="gene" selected="true">gene</option>\n- <option value="CDS">CDS</option>\n- <option value="RBS">RBS</option>\n- <option value="misc_feature">misc_feature</option>\n- <option value="misc_difference">misc_difference</option>\n- </param>\n- <param label="Extra Feature(s) to EXCLUDE" name="features_excluded" type="text" optional="true" help="Feature(s) to exclude from plot (example: variation'..b' features that are excluded. **"Extra Feature(s) to EXCLUDE"** is where you can pass one, or multiple, feature(s) to be excluded from the plot. Separate by commas with NO spaces.\n-\n-* Feature(s) label(s) to EXCLUDE :: The **"Common Feature(s) label(s) to EXCLUDE from labeling"** select menu has frequent labels from features that are excluded. Input specific features that you do not want to include in the **"Extra Feature(s) label(s) to EXCLUDE"**. Use this when you still want to plot the feature but not label it. A good sample case is if you are zoomed into a specific region and looking at overlapping genes but do not want to label all of the RBS sites. \n-\n-* Products(s) names label(s) to EXCLUDE :: The **"Common Product names to EXCLUDE from labeling"** select menu has frequent product names that are excluded. Input specific names that you do not want to include in the **"Extra Product(s) name label(s) to EXCLUDE"**. Any product with this name will NOT be labeled. It must be spelt, spaced, and capitalized exactly as it is within the file to be caught. However, if you wish to exclude labels with common patterns, say JX0101.orf01, you could pass "JX" to the input box and it will skip all names containing JX. Realize that passing something like protein will also eliminate labels such as DNA binding protein. Of note, if you choose to label by locus_tags, and want to skip over each, for example, hypothetical protein; the script will still pass their label and not label them.\n-\n-* Name ordering :: In case you want to customize the selection method of labeling genes by a specific feature, use this argument. "product" will use the product names from within the file. If you want to use product, and if there is no name, use locus_tag as the next name, pass the following: product,locus_tag.\n-\n-* Label algorithm dictates label placement :: DNA-features (the orginal python package) has a very nice spacing algorithm for deciding how to space and where to put the label. Selecting no will force ALL features to placed outside of their gene box. If more tuning is desired, a custom pixel control can be implemented as an argument (not currently implemented) to allow more user control for label placement within gene boxes.\n-\n-* Select Custom Region :: If you would like to zoom in and look at a specific region of select a start and end site to zoom in on. Values are based on Nucleotides.\n-\n-* Multiline :: Permits plotting of the genome across multiple lines. Select the amount of nucleotides per line you would like in the **"Nucleotides Per Line"** field. Smaller widths (which are recommended for multiline plots) and larger nucleotides per line will have faster compute times. This can also be combined with the custom region parameters.\n-\n-* Feature Colors :: Customizing Feature colors based on their exact name as listed in the file (check the output stats file for spelling).\n-\n-* Product Name Colors :: Customizing Product colors based on their exact name as listed in the file (check the output stats file for spelling). **NOW**, in addition to the exact name, general words can be used to grab similiarly named features. For example, if the genome has a two component spanin system (i-spanin + o-spanin), using "spanin" would change the color for both the i-spanin and o-spanin.\n-\n-**Output**\n-\n-* file_stats will output the different product names as well as the count of each respective feature\n-* svg output\n-\n-**Output Example**\n-\n-Using the zoom function and custom colors for various product names\n-\n-.. image:: $PATH_TO_IMAGES/sample.png\n-\n- ]]></help>\n- <citations>\n- <citation type="doi">https://doi.org/10.1101/2020.01.09.900589</citation>\n- <citation type="bibtex">\n- @unpublished{galaxyTools,\n- author = {C. Ross},\n- title = {CPT Galaxy Tools},\n- year = {2020-},\n- note = {https://github.com/tamu-cpt/galaxy-tools/}\n- }\n- </citation>\n- </citations>\n-</tool>\n' |
| b |
| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/macros.xml --- a/cpt_linear_genome_plot/macros.xml Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,19 +0,0 @@ -<?xml version="1.0"?> -<macros> - <xml name="requirements"> - <requirements> - <requirement type="package" version="3.8.13">python</requirement> - <requirement type="package" version="1.77">biopython</requirement> - <requirement type="package" version="1.2.2">cpt_gffparser</requirement> - <requirement type="package" version="1.0.5">pandas</requirement> - <requirement type="package" version="3.3.2">matplotlib</requirement> - <!-- <requirement type="package" version="3.0.1">dna-features-viewer</requirement> --> - <yield/> - </requirements> - <version_command> - <![CDATA[ - cd $__tool_directory__ && git rev-parse HEAD - ]]> - </version_command> - </xml> -</macros> |
| b |
| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/test-data/Mu50-profile.xml.xml --- a/cpt_linear_genome_plot/test-data/Mu50-profile.xml.xml Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<BRIG blastOptions="" legendPosition="upper-right"> - <cgview_settings arrowheadLength="medium" backboneColor="black" backboneRadius="600" backboneThickness="medium" backgroundColor="white" borderColor="black" featureSlotSpacing="medium" featureThickness="30" giveFeaturePositions="false" globalLabel="true" height="2500" isLinear="false" labelFont="SansSerif,plain,25" labelLineLength="medium" labelLineThickness="medium" labelPlacementQuality="best" labelsToKeep="1000" longTickColor="black" minimumFeatureLength="medium" moveInnerLabelsToOuter="true" origin="12" rulerFont="SansSerif,plain,35" rulerFontColor="black" rulerPadding="40" rulerUnits="bases" shortTickColor="black" shortTickThickness="medium" showBorder="true" showShading="true" showWarning="false" tickDensity="0.2333" tickThickness="medium" titleFont="SansSerif,plain,45" titleFontColor="black" useColoredLabelBackgrounds="false" useInnerLabels="true" warningFont="Default,plain,35" warningFontColor="black" width="2500" zeroTickColor="black" tickLength="medium" /> - <brig_settings Ring1="102,0,102" Ring2="0,102,102" Ring3="0,102,0" Ring4="0,0,153" Ring5="102,102,0" Ring6="0,153,0" Ring7="204,51,0" Ring8="0,102,102" Ring9="0,153,102" Ring10="204,0,51" defaultUpper="70" defaultLower="50" defaultMinimum="50" genbankFiles="gbk" fastaFiles="fna,faa,fas,fasta,fa" emblFiles="embl" blastLocation="" divider="3" multiplier="3" memory="1500" defaultSpacer="0" /> - <special value="GC Content" /> - <special value="GC Skew" /> -</BRIG> - |
| b |
| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/test-data/Mu50.sam --- a/cpt_linear_genome_plot/test-data/Mu50.sam Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,50001 +0,0 @@\n-@SQ\tSN:S.aureusMu50-plasmid-AP003367.gbk\tLN:25107\n-r1.1\t4\t*\t0\t0\t*\t*\t0\t0\tGTTACCTCTTGCTCTAGTCTGATTCTAAACCTTTTTTTAGTTCTTTCGCTTAATAAGTTACCTCTAATTCAGCAAAACGCTACTCGATCATTGTAAAAAACATCTTTCCCATTGGGTCTTTTGTATTGATATTCATATCAATAATTTGTAATTCAATACTTATTATTTTCTAACCATTGGGCTAAATCTATCAGTTGCTTAGTAGTCCTGCCTAATCTATCTAGCTTGAAATAACTAAAGTGTCGCCTTCACGTAAATAATCTAAACTATTTATCTAGTTC\t*\n-r2.1\t4\t*\t0\t0\t*\t*\t0\t0\tTAAAAAAGAAAGTCTTTCCGTTTTTCTTAATAGTTATTAGGTTATTTCCGTATTGATCTGTTATAGAGCCATACACGGTATTATTGTCTTTATTTTTTATTCAATATTACTTTTAATTTTTTGTATTTGCTCATTGTATTGTTCTTGATTTTCTTTACTTTTAACTAAATAACACAAAGTTTTTAGCATCATTTTCAGATAAAGTTTCTTCTTTATTAGTATAACTTTTTAGCAATACTATTGTAGTCACTTATGTCTGTACTAATTTTTCAAATTCTTTAACGTTGTCCTTTAGCATTATTCAAACTGATTAAATAG\t*\n-r3.1\t4\t*\t0\t0\t*\t*\t0\t0\tGGTACGAAGATATATTAAATTGATTTTTGAATTTTTGAAAAAAGAAAGAAATAGCTAATGCAGTTACTTTTAGACCCTCATAAAAATAATCCAAGAGACAATAAGGGCATACCAAAAAATCTGGGTTTTAGAATTATTGAAGTATTGCCAGAACATGAATTACACGAGGGCAAAAAAGAAGATTGTTATTTAATGGAATATAGATATGATGATAATGCCACAAATGTTAAGGCAATGAAAATATTTAACTTGAGCATTACTTTGATAATTTCAAAGTAGATAG\t*\n-r4.1\t4\t*\t0\t0\t*\t*\t0\t0\tTAATCATCTAAATTAGTTAAGTTATAATCAAATTCAGAATCATACTAGTACTTATAATATGTGGTGTTTGATATTTTTTCGTTAGAATCGTCTAAATCATAAACTGGTTGAGTATACACTTCGTTATAGAAATTATTTTCTACTAGACGTAAACTTACCTACTATCGCTTTTTATTAGTACATATCTCTTTGATCATTCATTTGTTTATCACTTGCTGGCACAAAATAAAATTCAGAATTTAGTTCATAATCGGTGTTGTTCAAAAATTTCCTCGGGGTGTAA\t*\n-r5.1\t4\t*\t0\t0\t*\t*\t0\t0\tTATAAATGTTTTCTTTAAACCAAAGCTAATTTACCACATTGGGTTAAGTTTCTTATTATTAAAGAAGAACTTTGTATGATTTCAACTGCTTACTATCTTCTCATTTGGTTATTTCTCTCTTGTTTCTTCTTCTTTTTCTAGATGATTAATATTGTTTTGCTTTTCAGTTTCGTTCGCATAGTACATAAGAAAGTCACTAGCATTTATCGTTGGTAAATTAATGTGATTAGTTTGTTCATTTTCATGTTCAATACGATTGTCATGTATCATTTCTATCTACG\t*\n-r6.1\t4\t*\t0\t0\t*\t*\t0\t0\tAGAATAATTGTATAACACAATACAGCCATTTAAATTTCGCAAGATTTTTTGTTGTAATATGTAAAAAAAATAGATTATAATCCTTATAGACCGATCGCACGGTCTATAAGGATTGGAGGGGAACTTAAATGATTTCATTTTTTACAAAAACTACTGATATGATGACATCAAAAAAAAGATGGACTGCACTAGTAGTATTAGCTGTTAGTTTGTTTGTTGTTACAATAGGATATGACAATATTAATTATGGCTTTACCGGAATTAGTAAGAGAGTTAGAGCCTTC\t*\n-r7.1\t4\t*\t0\t0\t*\t*\t0\t0\tAAATGAGAGAATAATTTTCTAAATTCATTACGCTTTTGGGTATCGAAAAATCACTAAGATGTATATCGAGTAATTTTTTCAAAAAAAACATCAATTTTGCTCTTGTGCTCTTTGAGCCAAACGTCGCAAACTTTTCCAACTTCTCTATTAGATATTACTTTAATAAGGTTTGGGTCTATATATTGAAGAGTGTCTTCTTCAATAGAAATATTTAAATAATCAGTTGATTAGCATCATGATTGAATTTGGTACATACTAGTGTCACTCATA\t*\n-r8.1\t4\t*\t0\t0\t*\t*\t0\t0\tTCATGTAACTTAAAAAATAGATGAAAGTTGCTACTTAGTGCTCCTAAAAATATAGTTATAGTTAAGTTCTACATCAAATATTTTAAAAATATCTGCTCTATTCATCAGTTAATCACTCCTTTCAAGGTTTATTAATACTAATAAATTATTAGATATAGGTATATCATATTATTAATTTAAGAAAATTGTCTTTATAATTTTACTTAATAATAAAAAAGTAGAACCATTTAAATTAATGGTTCTACTTTTTTAACTAGTTACTAATTTTAAAAATAAACGTAATCTACAATATCTAAAAATATATGTTTAGTAC\t*\n-r9.1\t4\t*\t0\t0\t*\t*\t0\t0\tTATTGGTTATGCTCGTGTATCTACCAGAGATCAAAGTTTAGATTTACAAATAGACGCTTTTGAGTAATTTTCGGTTGTGAGAAAATATTTAGCGAAAAACGTTAGTGGGCGTAAAGTAAATAGAACTGAACTAGATAAATGTTTAGATTATTTACTGAAGGCGACACTTTAGTTATTTTACAAGCGTAGATAGATTAGGCAGGACTACTAAGCAACTGATAGATTTAGCCCAATGGTTAGAAATAATAATTATTGAATTACAAATTATTGATATGAATATCAA\t*\n-r10.1\t4\t*\t0\t0\t*\t*\t0\t0\tAAACTCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGCGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATACTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATAGCCAAGTCGCTTAATTGGTAGCCGTTCTTATGGACCTACATGATAGAA\t*\n-r11.1\t4\t*\t0\t0\t*\t*\t0\t0\tTACTTTGAAATTATCTAAAGTAATGCTCAATTAAATATTTTCATTGCCTTAACGATTTGTGGTGATTATCATCATATCTATATTCCTACGTTAAATAACAATCTTCTTTTTTGCCCTCGTGTAATTCATGTTCTGGCAAATACTTCAATTAATTCTAAAACCAGATTTTTGGTATGCCTTATTGCTCTTGGATTATTTTTATGAGGGTCTAAAATAACTGCATTAGCATTTCTTTTCTTTTTTCAAAAATTCAAAAATCAATTTAATATATCTTGTACCAATTCCTTTAC\t*\n-r12.1\t4\t*\t0\t0\t*\t*\t0\t0\tCAGATATTATTCCATGGGTTGTAATAGTATTAGCTAATTTACCATATAGTGATATTTGTTAAACGTAAGTTTATCGAAGTTCTGATCCAATGTTAGACGTAAGACTTTTTAAAAAGAGATCATTTTCAGCTGGTACAATTGCTGCATTTAATGACAATGTTTGCAATGGCATCTGTTTTGTTATTAGCTTCACAATCGGTTACAGGTTGTGGAAGAACTTTCTCCTTTTAAAGCTGGCTTATACCTATTACCTATGGCAATAGGAGA\t*\n-r13.1\t4\t*\t0\t0\t*\t*\t0\t0\tAGCTTCTAATTCACAACTTTTTCTTTATAAATTGCACTATTTTTTGGCTTGTGGATTTACTTTTGAGCCTTTTGGTATTTCTGAACATAAACATTTTTAATACCTTTTAAATCATTTCTTGTAGATATTAACTGATACCAAACTCGTGCATATTCAATTTCTTTCGAGTTTAAAAATTATTTAAGTAACTTTTATT'..b'GAATTTTGAACAACACCGATTATGAACTAAATTCTGAATTTTATTATGTGCCAGCAAGTGATAAACTAAATGAATGATCAAAGAGATATGACTAATAAAAGACATAGTAGGTAATTTAGTCTATAGAAATAATTTCTATAACGAAGTGTATACTCGAACCAGTTTAGTGATTTAGACGATTCTAACG\t*\n-r49989.1\t4\t*\t0\t0\t*\t*\t0\t0\tAATGAATGTAAGGCCTCAACTTCTATTAACTACGCCATATCTCTGATAAATGTTTTCGTAAATACTTATTTCTGATCGCCCAACTAACCTAAACTGAATAAATGCTGTAATATCAGTGTTGTATACCACTATAAGAAGGGCTATCATTCTCTGGAAATTGTTGTATATGAATATAAAATTCATTTTTAGGGGAATATGTTTATCATTTTATTAGAGAAGTTACGACTAAACACATCTGTTTTATTAGTTAAAAGCCATACCAATAAAATGATTTCTAG\t*\n-r49990.1\t4\t*\t0\t0\t*\t*\t0\t0\tATGATGAGTGCATTCGTGAACTTGAAGCTAATTTATTAAGTGAACGAACTAAAAAAGGTTTAGGAAAGCTGCAAGAGCAAGAGGGAGAAAAGGTGGAAGACCTTCACTACCAGATCATAAGAAAAGAGAGATCAAATTCGTTATATGATGAACAAAAGCTGTCTGGTGAAGAAATTGCTGAACAAACAGGAGTGAGTCGTTACTACTGTATATTAGGATTATTAAAGAGTCTAAGAAAAATATAAAGTACTAAATTAAAGTTTTAATATACCCTTTAATTG\t*\n-r49991.1\t4\t*\t0\t0\t*\t*\t0\t0\tAAGAGGCGTAATATACGCCTCCTTAAAACAATATAATGTGTTTTGTATCTCTATAGTTGTTTCTTTCCGGCAGTATTAATTTTTATATCTGCGCCGACAACGCCGATTCTAGTTCGTGCAGTATTAATTTTTATATCTGCGCCACAACGCCGATTCTAGTTCGTGTAGTATTAATTTTTATATCGTGACGCCACAACGCCGATTCTTTTCTTCTTATATTATATCAATACCTGTCATGTTATGCAATGTTTAGGATTACTTTTTAAACTCTCGGAAAA\t*\n-r49992.1\t4\t*\t0\t0\t*\t*\t0\t0\tCGATAATTGGTCCAAAAACAGCACCTATCATGAAGCGATTGACATACTAGCGTAATGCAGTGGCCCTTTTTTAGGTTTTCAAAAATTACTCTTATCATTGAAAAGAGTAGTTGGCGATTATTAAAGCACCTGAATACCTAAGTAAAAATCGAATAGCTATTACGAACTCGTGCACTTTCTGCGAAAAAATATAGCTAATGAAACGAGGCCAAATAAAGCAAATCCAGTTAAAAATGCTTTTTTTCTTCCCCATTTTATCAGCAAAGGCACTCAA\t*\n-r49993.1\t4\t*\t0\t0\t*\t*\t0\t0\tATGTCCAATTTTTGTTTCCAAATTATTTTTCTCCTTAACTTTAAGACTATATTTAAACTCAATTTTTTCTATCGATATTTATGAACATTAGTATTTTTTTATGCGAAATACCTGTGAACAATCGCATAATTCAAAGGTTTTTCTATAATTATACACGTTTTAAAATACATTGTGATAATACATAGAATGTACCTTATCTAAGTATATAAATGTTTTCTTTAAACCAAAGCTAATTACCACATTGGGTTAAGTTTCTTATTAATTAAAGAATGAACTTTGTATGATTCAACTGCGTTACTA\t*\n-r49994.1\t4\t*\t0\t0\t*\t*\t0\t0\tTTTCACTTTTTTTGAATTAATCGTACGCTTTAAAACGCTTAAGAACATTAACAATTTCAAATTCCATATCTTCTAATAAATAATATGCATCAATAGAATTGTTGAAGGATGTTTTGGCTTTTAATAACACAGATTAATAAGTTAATTTCAGAGTACAGAAAAGTTACTTAAATAACTTGAATACTTTGTGGTAGTTCTTCAAGTAATTGAAATTTTAAAGCTTCATCATTGAATTTGAATAGTAGTGTATTTGAATGATTTGTATGATTACTAGAATATGTTAATTTCTA\t*\n-r49995.1\t4\t*\t0\t0\t*\t*\t0\t0\tCATTCATTTCTCTTTTGAATATTATTTCTATCTATAATCTAACTCGTCTTCGGTATAAAAACATTGTAACTTGGCATAACATTGTTTAACTGGTTCTGTTGCAAAGTTGAATTTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATAATAAACAATTTAACAAGGATGTTATCACTGTAGCGGTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGGGAACGTGGTGTCAACG\t*\n-r49996.1\t4\t*\t0\t0\t*\t*\t0\t0\tTTATATCTTCTAATTTGTTCATTTTTCTAGTCCGTAATAAGTAACGGGTTGGTACTCGACTACCCTCTTTTTCACAGCGTTTTCTTTCATTTTAGTTTCTAATCTATATTCTTCTCTTGTAAGTGGAATTTCGGCAATTTTTTCTAAACCTTCGCGCTTCAAAAGAACGACTATCATATCGTCTTAAACTTTGTTCGACGTTCTGAGTATTGATTTAATTTTAATTCCCAATGCTTACGAACTTACTTTGAAATCAAAGTCGGCAAATCGTTCTTGTTTTCTAACTTTATTAACCATTTTTATTTAAAATCGCATTGCC\t*\n-r49997.1\t4\t*\t0\t0\t*\t*\t0\t0\tAAATTAAGCATCATGCTAGCAGTTTAAGCGAACACTGACATGATAAATTAGTGGGTTGCTATACTTTTTTACTTTGCAACAGAACCAAACTAAAAGATAAAATAACATCTTGGCTTGATAAAGATAACAACTAAAAACGAATAATATAGGAGGGGTTTTTTGGGGAACTTTAGATTTTGATCACGAAGGATACAGAAAACTATTACCATTAAAAGATTTCAAACATTTTACTAAAACATAGCGACAGCAAGACTAGAAATCATTTTATTGGTAGTGGCTTTTAATAATAAAACAGA\t*\n-r49998.1\t4\t*\t0\t0\t*\t*\t0\t0\tCATTTATTCAGTTTAGGTTAGTTGGGCGTCAGAAAATAAGTATTTAGAAAACATTATCAGAGATTATGGCGTATTAATAGAAGTTGAGGACCTTAACATTCATTTAAAAAAGGTATGGGGGCAATGCTTGTAAGTCAATTGGAAAAGTTATCAGATAAACTGTTTATACCTATATATCTTTATGATACTAATTTAAAAGATGAATTATATTATCAAGACTTAGGATTCTTTGATACTACTAAAAAAGGGAATCATGGAGAACCACTTTTAGTATATAAACCTAAAAATCTAG\t*\n-r49999.1\t4\t*\t0\t0\t*\t*\t0\t0\tCATATTACGAACAAAAAAATCTTCGCGAAATTTAAATGGCTGTATTGTGTTATACAATTATTCTTTTGAATTTTTTGTGCTATCATTGATAGTACTTAATACTCATTAAAGGCGTGATGAACTTGAAAGATAAAAATACGTAGGTGTCGCAAAGGGAATTATTTATAAAAAATGGATATAATGCCACTACTACTGGAGAAATTGTTAAATTATCAGAAAGTAGTAAAGGGAATCTTTATTATCACTTTAAAACAAAAGAAAACTATTTTTTAGAAATTTTAAATATAGAAGAATCTAAATGG\t*\n-r50000.1\t4\t*\t0\t0\t*\t*\t0\t0\tTGCAAGGCTGAACTAACAATGGTGGCATTAGATAGTGATGAACTTGATTCATTACTTTATATGCTAGTTACATGGAACGTTATGCTATCTTTTGAACTAATGATAAAAAAAGACGCCTAATTTTAGGCGCCTTTTTAACTAATCTACTAACTAACTTATTATATCTAATTTTACTTGCTAACTTAGCTACTGTTTTATTGTCGTAGGGTTTAATATAGACTCGTTTCATATTCTCCTCTATTGCTTTTTTTGTTATCTTATTCATTTGACTATAATCGAC\t*\n' |
| b |
| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/test-data/mga.fa --- a/cpt_linear_genome_plot/test-data/mga.fa Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2300 +0,0 @@\n->01\n-TACTACTATTACTACTACTAAGTACCTTTGTTATGTACTACTATTACTACTACTATTACT\n-ACTACTATTACTATTACTACTACTATTACTACTACTATTACTACTACTATTACTACTACT\n-ATTACTACTACTACTAAGTACCTGGGAATTCTTTTACCTCTCTCACTCAGCCTATTACTT\n-ATTACCGACTTCCCTAACTACTTATTCTATAGTTATAATATTCATTTATTATACAATACT\n-TAAACTATAGTATTCTACTGTTAATCTATGCTGAAGCGGTCTTAATCTATGGTTATTATA\n-TAATAATCTTATATAATGGTACATTAATCTAGTATATTACATTAGAATCATTCTAATCTA\n-GGATTTTAATCTTTAGACCCTAGGAAAAGTGGTACTAAAATATAAAACCCTATAGGTATG\n-GGATTCTTATTTTTAAAATTACTAAAAAGTATTAGGTTTTCCCTAGGGCAAAGTTTTAAT\n-GTACTTAAAATAGTAAGTAGCTACTTATCATTTAGGGTTCTATAATTGAGAATATTGAGA\n-GATAATCCGCTTCAATTGTAATTAATTGTTGACAACTATGAAGCGGGTATGCTATAATTA\n-GGTATAGTCAAATTTAGGAGATGAAATAGATGATTGATATATACTTAGGAGAAGGTTATA\n-ATAAAGAATACTTGTCTAAAGCACTCAGATTAATCAATGACCATGCTCCTAGGGAGTTAA\n-GTTATGATTTTAATAATGTAGAAGCGGATGTTAATATTCACACAATGTTATATGTTAAAC\n-CTGAAGATAGATTTATATATAAGGATATATCCTATTACTTCCCGGGTGATTTAATTATTT\n-GTATAGTTGATGATGATGCTATTGTATACCACCAAGGTGAGCAGATTTCAGGTATTAGTA\n-TTTTAAGAATACTAGAAGAGATATTTTAAGGAGGATAAGTAATCATGATAGGAATAACAA\n-TATTAATTACGATAATGAGTATATCAACTATCTCTATGTATATTTATTTTTTAGTAGACT\n-TGATTCAGTCAATCAGATATAATAGTTTTGATAAGGTAATTAACGTCATAACATTTGTAC\n-TTATGACAGTTATAATAGCATCAGGTATTTTAGCTATACTTGGAATATAGAGCTCATTTA\n-AGAAGCGGTTAAGTAGTTAGAGGGGATTTGTCCTAAAATAGTATACCGCTTCTATATGGA\n-AGGCTGAGAGGTCTTAGAATTGAAAGGAGAGATATAATGATTCATATATTTGTAAAAGAG\n-GATTATAATAAAGAAACATTAAGGAGTTTACTTGAGTATATTAATGATACTGTAGGTAGG\n-GAATTAACTTATGGTATTAATACAGACTATGATAAGGATGTCGTGATTGAAACCGATGAC\n-CCTATAGATGAGGAGGATACAATTGAGTTATCAGGTACAAACATGTTCAAGGATGACTTA\n-TGTATTCTTATAGAAGAGCTATACTGTAAGGCATTTGTTAATGGTGAACCTGTTATTATA\n-CGTAAGTATGTAGAGGAGATGTTATAATGATTATAATATTTTTAACTGAAAAATATGATG\n-CCAAGGCTTTAAAGAAAGTATTAGAACATATTGATAATTGTAGTAGTAGAGGTCTTAGCT\n-ATTTAATGGGAAAAGGAGAAGCGGATGTATGTATAGAGAAAAATGTATTTAGAGAAAGAG\n-ATGATGTAAGGATTAACTCAAACATTATTGATGAAGGTAAACTTTGTATACTAATAAATA\n-GACATGGTTTAGAATGTAGCTACTATAGAGGTATATCATGTAATATTGGTTCCTTCGTAA\n-AGGAGAGATTATAATGATAGAGATATACCTTAGTGAAAATTATGATAAGAATTTACTAAA\n-AGCAGAATTAAAATGGATTAAAGAGACCGCTTCAAGAGAACTAACTTATGATGTTAATAG\n-AAGTCCAGGATTGGATGTTTATGTTAATCCCTATAGGTGTACTAAAGACGAAGTTGAAGA\n-ATGGAGTACACTTCCTCCATTTGAAGATGATATACTTGTATTTATAGCGGAGACGTGGAT\n-ACATGAATATCTTAAGGGTGAATCAATAGGTGTAGATAGTATGGAAGAGTATGTAAAGGA\n-GATGTAACTAATGTTTAAGGTATATTATACAGTCTACCATAGAGGTAGTATGAAAACTAT\n-TAAGGATAAGCTAGATAGAAGTAGTTTAATATACTTCTTGTATGATACTTGGTATAAAGA\n-TATTAGTAACGTATTCCCTAATCACTATAATAAAGAGTTTGGGAGTAAGAGTGATGATAT\n-AGATATAGATAAACTTATTGAAGCGGTTAATGAGGAAGGTATATTACTTATCAATAGAGG\n-TAATTATGTTACAATAAGAGAATGGTAGGATAGGATAAACTTAGGATAGAAAATAATTTA\n-GGATGAGTTACAATAGGATAGGATAGGATAGGGGGTTAAGTTAGGATGGATACTTTAACA\n-TACACTATTATTCATAAAGAATCTGATAGGGTAATAGCTAGCGGTTTAAATGAGACAGAA\n-ACTATGAACTTAGTTCAAAGGATGATAAATACTAATCTAGTTACTGATATATCATTAGAT\n-GATTATAAACGCAGACCACATGGAAAGATAGATGTAGTCAATTTACTAGTAGATATTAGA\n-AGACAAGGCGTATTTGATTTCAATCACATTTGGCACGTAGGATAGGAGGGATAGGATGAT\n-AGTTATATATACAGATGTTTCTAAGGATTATTTAAAAGACGAGTTCTTACCTTGGCTTAA\n-TGAAAGGGATAGATACTTAGAATACTATAAAGATGAATTACCTGAGGATATAGATTCCTC\n-TTATATTGTATCAGTTGTATACTGTAAGGATATGGAAGGTCTATTAGAAAGAAAAGACAT\n-TGTTCTTGATAATAGTTATAATGAACCTGTAGCTTTATTAGGTGTTCCTGAGTTTTTTGG\n-TAATTATAGTAATTATTTCTATTATAGAGGAGAAAGTATTAGTAAACATGACCTAGGAGA\n-AATTGTTAGGTTAAAAGCTTGGCAACGTATGGGTGGGGATTGACTAAGTAGCTCTCCCTA\n-ATTTCACTAAGTAGCTCCCTAGGAATTGCCTAAGTAGCTCGGTATGATTTTACCCTAAGT\n-AGCTCCCTCTGTTTTCTACTAGTTTATTTTAACCGCTTCAGGTGTCTATATATATATAGA\n-CGGTTGGAATAATATCAGACCGCAAAAATAAATACACTAGGATATTATTCCTAGTGTATT\n-ATATAATTTTTTTATAGAATATTTATAACATTGTATTCAAATTCATTTACTTCATGTTGT\n-GATTTAATTAAATTTTTAATTAATCCGTTTTGTGTTTTATACTCTTTTATTAGTTTTTCA\n-TTTTCTATAATTAAATTATTAAATTCTTCTTTTGTTGTTTCCTCATCTACATAAAATTTA\n-CTTTCATATATTTCATAATATTTTTTATCTGTTCCGCCATCTAAATCATCTGATATTTGA\n-TAATTTTTGAATATAATTTCTTTTGTTTCTAATTCATTTACTAATAATTGTGATTTTGCA\n-TATTGTAATACATCTTCATTGTCCCACATTGGAATATAGTTTATTTTCATTTAAATCAAA\n-TCCTTTTCTTATAATTTTTTTATATAATATTTGTAGAAGCGGTTGGGGTTTGTCCCTTGC\n-CTTACTACACTTTATATATTACAGTATAGTTATTCAGAAGTCAATACTTTTGAGTAACTT\n-TTTTTAAATTCTTTTTTCTTCTATATAATAGTAGTTTTTAGCCCTAAAAATGTTTTTAAA\n-AGAATTTGCATTTTCTTATTGACTTTATTATCATATGGTAGTAATATAAAGGTACAGCAA\n-GGGAAC'..b'ACTTTTGGGGT\n-AATATGACTAAAACTTTACCTAGATTAAAGGATATTATTATGGAACGTAATGGTAAAGTA\n-GTAATCAGACCTGATAGTGGAGACCCTGTTAAAATTATTTGCGGAGACCCTGATGCAGAC\n-ACTGAATATGAACGTAAAGGTGCAGTAGAAGTGCTTTGGGATACATTTGGAGGTACTGAA\n-ACTGAAAAAGGGTACAAAGTATTAGATGAACATGTAGGATTAATTTATGGAGACTCTATT\n-AACTATGAACGTGCTCAACAAATTTGTGAAGGATTAAAAGAAAAAGGTTTTGCAAGTATT\n-AATGTTGTATTAGGTGTAGGTAGTTTCTCTTACCAATTTAATACTCGTGATACCCACGGG\n-TTTGCAATCAAAGCAACGTATGCTAAGATTAAAAATGAAGAAAAACTTATCTATAAAAAT\n-CCTAAAACAGATAGTGGTAAACGTTCACATAAAGGTCGAGTAGCTGTATATAAAGACGGT\n-TCATGGGAAGATAACTTAACCTTACATCAATGGCTAAACAAACAAAATGTTAATCAATTA\n-GAAAGAGTATTTGAAGATGGTAAACTTTATAGAGACCAGTCGTTAAGTGAAATTAGAGAA\n-ATAATTAAAAATAATTAATAAATATTTAAACTCCCTATTGACAAAGGGAGTTTTTTATTA\n-TATAGTAGGGCTATAGTAAATAAAGGAGTGAAAGAAATGATTTATAAAATATCAAAACAT\n-AATTACTATAGTAGATTTGAGCATTCCACTTATCCTCCTGATGAGGGGTTTGCGTATGTA\n-GATTATGTAGATGTGATTCTTATTGGTGTAGATAATCCTAGGAAAAGAAAGATTATTACC\n-TTAAAAGTAAATGAGTTCAACCCGGATGACTACAGAGTAGGTCATAAGTACAATATTATA\n-AAAATACTATGGTTTGAAAAATGGGAATGGTTAAAGCCATAAGTAAAAGGAGAGAAATAA\n-AATGATTATAGATAAATTAAATGGAGTTAAATTAGAAATAGGTGGGCATGTCGTATCATT\n-TAGTGTAAGAAAGTTTAATACAATTAATGGTGAGAGACAATTAATAGACTACCATCATAT\n-TAAAAGAAATAGACAACAGTACTTTAGAACTACTGAAGAATTTTATAATGAATATAAAGA\n-AATTAAGCCTGACAAAAATGAAATAGATGAAATGTTTGAATCTCTAGGTTATGTAGATAC\n-TGAGTTAGATGATGTAGTAAGAAACCAGGAAAAGGTTACTGAAATATTAGGAGTTAGTGA\n-ACAATATTTAAATCAGTTATCTTATAAAGCTATAGAGGAGTATGTAGATAAAGTAGTTAC\n-ACTTGAAATTAAAGAGTTGAAAGGAGAGAAATAGCATGAATAATAACTGGGAAAAAGAAG\n-GAGTTAACTATTGGGAAAACGAAGACTGTCCTAGGGAATACTTAGAGAAAGCATTCATTG\n-ACCTGGTAGAATATGTTGAAGGAGTTACAGTACCACCTAAAGATGTTAAGCAGTTAAGAG\n-AAGATAAACTTAGAGAAGATATTGGGTTTTATGAGTACGTAGCTGATAAATAAATTAGTA\n-TCTACCTATTGACTTAGGTAGGTATCTATTATATAATAGTATACAAGGAGATGAAAATAT\n-GAAAAAGTTAATAGTATTACTTACAATTACTATTTCTCTATTACTAGGGGGTTGCTCTCC\n-TGATAACCATGAAGGTAAAGTAGTAGGAGTAGGTGAATACAGAGAACCAACTACTTATAT\n-AAAATCAGGTAGCGTTACTGTACCAGTCATTGGTGAAATGAAATACTATGTAGATTTAGA\n-GACAGATAAAGGAGAAGACCGTGTATATCTTAATAAAGAGGTCTATCATAAGTTTGATAA\n-AGGTGATGATTTCTCTAATGTAGGTGAGAAAGTGTATAAGAATGATGAATTAATATATAA\n-AGGAGACTAACTATGTATTTAAATGATTATGTAGGTAAATTTATAAAGGAAGATAACTAT\n-TATGGATATCAATCTACAGACTTAGTATCTAATTATGTTCAACGATTAACTCTAGGTAGG\n-TACAAAACTAAGTTAAATGCTAATAAAATGAAATACGAAAGATTACCTAGTTCTTGGAAA\n-ATAATTAAAGCCAAAGATTTGTTAAGAACAGATGATTATAGAGAAGGAGATATATTTGTA\n-TCAGAAAGAATCTCCGTATTCGGTTTTAATGGTATTATTGTATATAACCATGATTTTAAC\n-AATGTAACTGTTATTACTCAAAATAGAGATGGTAAAGCTACTAATCCTGTAGAGGAGCAT\n-TTATATCCAAAGAAAGATATTGATTATATTATTAGACCTATCGAGAGGGACTACAGGGAA\n-TACTTTAAAAAATCAGATTCAAAAGAAAAAGTTACTCTTTCGAAGCAAGAATATAAAAAA\n-TTATTAGAGGCTTATAATAAAATGAAGGAAGTGTTTAAGTAATATGAATAGTACAAAATT\n-AGTAGAGTACTTTACAAATAAACAAGGTAAATCTCTAATATTACCTGATGAAAATAAAGT\n-TGAGTTATATAGAGTTGATGTAACACCTTATACTATGAGACTTAATTTCACTTACAATAC\n-AGAAGTTGTAGCTATAGATATTGATAAGTTACACTCAGATTCTATAGAAATGCATATACC\n-ACAAGGTCTTTATATAACAACTGTTGTTAAAATTACTAGTACGCAGAGTATTAGTTCAGT\n-TCTTCATAAGGTATTAGAGGAATGGGTAAGACAAGTACAAAATGATGGTATATTCGGATT\n-CGTATGGGAGTAATTATAATGATAAGTATAGAACATGATTATACAATAAGAACTGTAGAT\n-AATAGAAAATATACTTATTATAGTAAATACGAATCACTAGTTACTTTGTATGAAAATATT\n-ATGAGTAAAGATTGTATTGAAGTAACTAAATATGGGAAAGATAAAAAAGTTATTATTGAT\n-ACTAGACATATTGTATCTATTGAACGATGGTAAATAATAAGGAGGAGTAAACTATTATGA\n-TAAATGCAGGGCATGCTAAGTACCTATCAGAAATTTATGAAGATGATGTACATTATGAAA\n-CTATAGATAGTATTGTAGAAGATATACTAGATAATATTAATGATGGTATTATTGAAGAAG\n-CTATGAAAGGTAATACAAGTTATCAATATGTTCTTAGAGACTTAAGAGTAGATAATGAAG\n-TAGAATATAGAGTTATAGAAGAACTTACTAACCAAGGATATAGTGTAAACCACATTAGTA\n-ATGATATAGAGTACCCTTCTATATCTACAAATAATTTAGCAGGGTTAGATTACTTAAATA\n-TTAAATGGTAAGGGAGGGAATTAATATGATAAATAAATATAAAAAGTTATGGGATGAAAT\n-AACTCAACAAATTGTTAATGTAGAAATTATTAACTTTAAAAATGAAACAGTAACAATAGA\n-ATCTACAGATGATTCAGGATTATCAGAGATAAGAGGTTTTGAAGAAGTAGAGTTTATAGA\n-TTACTATGGATAAGATGTTTAAAGTATATAATTTATAAGGAGGAAACATATGGACTTGTT\n-TGCAAAAATAATTATTATGTCTATAGGAGTTGTTCCCTTGTTAACTATTATTGTTGCACA\n-GCTAATTACAGATTACCATGATAATCATTAAGTATTATAGTAATAGGAAGGACAATATTT\n-AGAGTGAGAGTATGTTGACTAATGAGGAAGATATAGAATGAGAACCTAACCAAGTAAAAC\n-TAAGTACCTTTGTTATGTACTACTATTACTACTACTACTATTACTACTACTATTACTACT\n-ACTACTACTACTACTATTACTATTACTACTACTATTACTACTACTAAGTACCTTTGTTAT\n-GTACTACTATTACTA\n-\n' |
| b |
| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/test-data/mu_reanno.gb --- a/cpt_linear_genome_plot/test-data/mu_reanno.gb Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1877 +0,0 @@\n-LOCUS Exported 36717 bp ds-DNA linear PHG 03-JUN-2020\n-DEFINITION Enterobacteria phage Mu, complete genome.\n-ACCESSION NC_000929\n-VERSION .\n-KEYWORDS .\n-SOURCE Escherichia phage Mu\n- ORGANISM Escherichia phage Mu\n-REFERENCE 1 (bases 1 to 36717)\n- AUTHORS Morgan GJ, Hatfull GF, Casjens S, Hendrix RW.\n- TITLE Bacteriophage Mu genome sequence: analysis and comparison with \n- Mu-like prophages in Haemophilus, Neisseria and Deinococcus\n- JOURNAL J. Mol. Biol. 317 (3), 337-359 (2002)\n- PUBMED 11922669\n-REFERENCE 2 (bases 1 to 36717)\n- TITLE Direct Submission\n- JOURNAL Submitted (05-MAY-2009) National Center for Biotechnology \n- Information, NIH, Bethesda, MD 20894, USA\n-REFERENCE 3 (bases 1 to 36717)\n- AUTHORS Morgan G, Hatfull G, Hendrix R.\n- TITLE Direct Submission\n- JOURNAL Submitted (13-AUG-1998) Pittsburgh Bacteriophage Institute and \n- Department of Biological Sciences, University of Pittsburgh, \n- Pittsburgh, PA 15260, USA\n-REFERENCE 4 (bases 1 to 36717)\n- AUTHORS .\n- TITLE Direct Submission\n- JOURNAL Exported Wednesday, Jun 3, 2020 from SnapGene 5.1.3\n- https://www.snapgene.com\n-COMMENT SGRef: number: 1; type: "Journal Article"; journalName: "J. Mol.\n- Biol."; date: "2002"; volume: "317"; issue: "3"; pages: "337-359"\n-COMMENT SGRef: number: 2; type: "Journal Article"; journalName: "Submitted\n- (05-MAY-2009) National Center for Biotechnology Information, NIH,\n- Bethesda, MD 20894, USA"\n-COMMENT SGRef: number: 3; type: "Journal Article"; journalName: "Submitted\n- (13-AUG-1998) Pittsburgh Bacteriophage Institute and Department of\n- Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260,\n- USA"\n-COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final \n- NCBI review. The reference sequence was derived from AF083977. \n- COMPLETENESS: full length.\n-FEATURES Location/Qualifiers\n- source 1..36717\n- /organism="Escherichia phage Mu"\n- /host="Escherichia coli"\n- /mol_type="genomic DNA"\n- /label=G(+) form\n- /note="G(+) form"\n- /db_xref="taxon:2681603"\n- gene complement(339..942)\n- /locus_tag="Mup01"\n- /label=Mup01\n- /db_xref="GeneID:2636266"\n- CDS complement(339..929)\n- /codon_start=1\n- /transl_table=11\n- /locus_tag="Mup01"\n- /product="repressor protein c"\n- /label=Mup01\n- /note="Mup01 or immunity repressor or MuR for repressor of\n- replication or Rep c; see PMIDs 16154589 and 9546656,\n- 11135677 for structure; contains InterPro domain IPR003314\n- Mu-type HTH domain also found in Mu transposase (Mup03 or\n- A)"\n- /db_xref="GeneID:2636266"\n- /protein_id="NP_050605.1"\n- /translation="MAADGMPGSVAGVHYRANVQGWTKQKKEGVKGGKAVEYDVMSMPT\n- KEREQVIAHLGLSTPDTGAQANEKQDSSELINKLTTTLINMIEELEPDEARKALKLLSK\n- GGLLALMPLVFNEQKLYSFIGFSQQSIQTLMMLDALPEEKRKEILSKYGIHEQESVVVP\n- SQEPQEVKKAV"\n- RBS complement(938..942)\n- /locus_tag="Mup01"\n- gene 1085..1326\n- /locus_tag="Mup02"\n- /label=Mup02\n- /db_xref="GeneID:2636289"\n- RBS 1085..1090\n- /locus_tag="Mup02"\n- CDS 1099..1326\n- /codon_start=1\n- /transl_table=11\n- '..b'3601 agcatccact ctgttaattt ttgtttattc tcgtcggaaa tgatgcccag ccgtagctgt\n- 33661 gagtcccata gctgtgtttt atccctgacg agctgtagca ggctttgctt ttcattttcc\n- 33721 gcttgttgcc tctgctcttc ctcggtataa gttcgcttta tcactacacc atctttgaac\n- 33781 atccatttac ccgaaatatc agcccggcga tttgctgtaa tatcaggaac ctcaacgacg\n- 33841 tttgcgcctt ctggattaat tgctgaaaca tccttttcaa tacaaataat aacgccgttg\n- 33901 tggtcataga ccattttcaa cgtatcaggc tgaaagttct tttgttcctc ataccagttt\n- 33961 ttcccatcct ctgtataaag ccatttgatg ttaaattgtt tcgttagctg gtattgctct\n- 34021 tttgttttag ggttgccagc agtaatattt tttaagtgca tcataattaa atactccccg\n- 34081 cgttatacca cgttccatta atgcaatact gaattggcct tgcctgagtt gtatcaatta\n- 34141 attcatcacg gtttccgtta actgaacccg taacgacata acctgacctg tcagaccagc\n- 34201 cgggaccatt ccatgtctga acagatgaca gaccgccaag acgaatacct gtaataaacc\n- 34261 ttgagttaca ttctgcctgc gtatatgcac caacatctcc cgctgatggc ttacgtgttg\n- 34321 tggtgtaaat ttctgaccag tcagcttcga atccgtaacc atcacgcgct gaacgataaa\n- 34381 aaataccgcc gttcctgtaa ttcacacgga actgtacggc agggcaactc cccgtattca\n- 34441 tattgaagtg gaggattaat gtcgatgcgc caccaatatt tgcgttatag accccgctat\n- 34501 tccagttcca gccaacagct ttatcatttc cgacagtgct tcctgtttgt cctaaagcaa\n- 34561 atgcaggctg ctggtttttc gtgttgtagt ctcgtcgcca gccaggagca taagcatcac\n- 34621 catgattaat ataagtgaat tgagcgttag tgattccgcc gccgctggac gtactcggcg\n- 34681 tagtaacgcg tatggtcatt gcgccgcgag tgccaataac ttccaccaca gcacctgcaa\n- 34741 gacaaatatt tccgcaacct gtatctgtaa tgaccttatt gtttgcataa gcccatgagc\n- 34801 ctttgcacat ccagtaagga tggttaaatg ccccctgact ctccagccac gaaataaatt\n- 34861 gtgcggttgt ccagacctga ctatcgccac caatattcag ccatgcgcta tatgcgcgac\n- 34921 aggccccaat atttttggtg aaggtatctt ttcctggaat atctgcgccg ttctggtttt\n- 34981 gctgtaatgc gccagaagcc tgatttaccg tttcctgtaa accgaggttt tggataatgg\n- 35041 tcgattttgg cacgcatggc atgattggcg cttttaaaca ggagatccag agtgctgatt\n- 35101 ggctatgtaa gggtatcaac aaatgaccag aatacagacc tgcaacgaaa cgctcttgtt\n- 35161 tgtgcaggat gtgaacaaat atttgaagat aaattaagcg gaacaaggac agaccgaccg\n- 35221 ggattaaaac gcgctttaaa gcgccttcaa aaaggtgaca cactggttgt ctggaaactg\n- 35281 gatcgcctcg ggcgaagcat gaaacatttg atttctctcg taggggaatt acgagagcga\n- 35341 gggattaatt ttcgcagtct tactgacagt attgatacgt catctccaat ggggcgtttt\n- 35401 ttcttccacg ttatgggtgc cctggctgaa atggaacgag aactaattat cgagcgaacg\n- 35461 atggctggac ttgctgccgc cagaaataaa ggccgtattg gtgggcgacc acctaaacta\n- 35521 accaaagcgg aatgggagca ggccgggcgt ttattagcac aaggaatccc ccgcaagcag\n- 35581 gttgcattga tctacgatgt ggccctgtca actctgtata aaaaacaccc cgcgaaacga\n- 35641 gcgcatatag aaaacgacga tcgaatcaat taaatcgatc ggtaatacag atcgattatg\n- 35701 ccccaataac cacactcaac ccatgatgtt ttttaagata gtggcgaatt gatgcaaagg\n- 35761 aggtgagatg aaatcaattc gctgtaaaaa ctgcaacaaa ctgttattta aggcggattc\n- 35821 ctttgatcac attgaaatca ggtgtccgcg ttgcaaacgt cacatcataa tgctgaatgc\n- 35881 ctgcgagcat cccacggaga aacattgtgg gaaaagagaa aaaatcacgc attctgacga\n- 35941 aaccgtgcgt tattgagtat gaaggccaga ttgttggcta tggttcaaag gagctgcgcg\n- 36001 ttgaaaccat atcctgctgg ctggcccgca caattattca gacaaagcac tattcccgcc\n- 36061 gttttgtgaa taactcttac cttcacctgg gggtattcag cggacgcgat ctggttggcg\n- 36121 ttctccagtg gggatatgcc cttaacccca actcaggtcg tcgtgtcgtg cttgaaacgg\n- 36181 ataaccgggg ctatatggag ttgaaccgca tgtggctaca cgacgacatg ccccgcaact\n- 36241 ctgaatcacg ggccatcagc tacgcgctga aagttatcag attactgtat ccgtcagtgg\n- 36301 agtgggttca gtcctttgca gatgaacgct gcggacgcgc aggcgttgtg tatcaggcgt\n- 36361 cgaattttga ttttattggc agtcatgaaa gtacgttcta cgagctggat ggtgagtggt\n- 36421 atcacgagat aacgatgaac gcgattaagc gaggtggaca acgaggcgtg tatttacggg\n- 36481 ctaataaaga gcgtgccgtg gtacacaaat ttaatcagta tcgctacatc agattcctga\n- 36541 acaaacgagc aaggaagcgg ctaaatacca aactattcaa ggttcagcca taccctaagt\n- 36601 gatccccatg taatgaataa aaagcagtaa ttaatacatc tgtttcattt gaagcgcgaa\n- 36661 agctaaagtt ttcgcattta tcgtgaaacg ctttcgcgtt tttcgtgcgc cgcttca\n-//\n' |
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| diff -r 621754dd31f8 -r e923c686ead9 cpt_linear_genome_plot/test-data/out_img.svg --- a/cpt_linear_genome_plot/test-data/out_img.svg Fri Jun 17 12:59:24 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/BiopythonTranslator/BiopythonTranslator.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/BiopythonTranslator/BiopythonTranslator.py Mon Jun 05 02:45:31 2023 +0000 |
| [ |
| @@ -0,0 +1,130 @@ +from .BiopythonTranslatorBase import BiopythonTranslatorBase + + +class BiopythonTranslator(BiopythonTranslatorBase): + """A translator from SeqRecords to dna_features_viewer GraphicRecord. + + This can be subclassed to create custom "themes" (see the example + ``custom_biopython_translator.py`` in the docs). + + This class is meant to be customized by subclassing and changing the + methods (``compute_feature_label``, etc.) and/or the attributes + (``default_feature_color`` etc). + + Attributes + ---------- + + default_feature_color = "#7245dc" + graphic_record_parameters + Dictionnary containing keyword arguments that will be passed to the + (Circular)GraphicRecord constructor + + ignored_features_types + A list or tuple of strings indicating all the feature types that should + always be ignored (i.e. not included in the graphic record) by the + translator + + label_fields + This list of strings provides the order in which the different + attributes of a Genbank feature will be considered, when automatically + determining the feature label. For instance if the list is + ["label", "source", "locus_tag"] and a feature has no label but has a + "source", the "source" will be displayed in the plots. + + Parameters + ---------- + + features_filters + List of filters (some_biopython_feature) => True/False. + Only features passing all the filters are kept. + This only works if you haven't redefined ``compute_filtered_features`` + + features_properties + A function (feature)=> properties_dict + + """ + + default_feature_color = "#7245dc" + ignored_features_types = () + label_fields = [ + "label", + "name", + "gene", + "product", + "source", + "locus_tag", + "note", + ] + + def __init__(self, features_filters=(), features_properties=None): + self.features_filters = features_filters + self.features_properties = features_properties + + def compute_feature_color(self, feature): + """Compute a color for this feature. + + If the feature has a ``color`` qualifier it will be used. Otherwise, + the classe's ``default_feature_color`` is used. + + To change the behaviour, create a subclass of ``BiopythonTranslator`` + and overwrite this method. + """ + if "color" in feature.qualifiers: + color = feature.qualifiers["color"] + if isinstance(color[0], str): + return "".join(feature.qualifiers["color"]) + else: + return color + else: + return self.default_feature_color + + def compute_feature_fontdict(self, feature): + """Compute a font dict for this feature.""" + return None + + def compute_feature_box_linewidth(self, feature): + """Compute a box_linewidth for this feature.""" + return 0.3 + + def compute_feature_box_color(self, feature): + """Compute a box_color for this feature.""" + return "auto" + + def compute_feature_label_link_color(self, feature): + """Compute the color of the line linking the label to its feature.""" + return "black" + + def compute_filtered_features(self, features): + """Return the list of features minus the ignored ones. + + By the method keeps any feature whose type is not in + ignored_features_types and for which all filter(f) pass + """ + return [ + f + for f in features + if all([fl(f) for fl in self.features_filters]) + and f.type not in self.ignored_features_types + ] + + def compute_feature_label(self, feature): + """Compute the label of the feature.""" + label = feature.type + for key in self.label_fields: + if key in feature.qualifiers and len(feature.qualifiers[key]): + label = feature.qualifiers[key] + break + if isinstance(label, list): + label = "|".join(label) + return label + + def compute_feature_linewidth(self, feature): + """Compute the edge width of the feature's arrow/rectangle.""" + return 1.0 + + def compute_feature_legend_text(self, feature): + return None + + def compute_feature_html(self, feature): + """Gets the 'label' of the feature.""" + return self.compute_feature_label(feature) |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/BiopythonTranslator/BiopythonTranslatorBase.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/BiopythonTranslator/BiopythonTranslatorBase.py Mon Jun 05 02:45:31 2023 +0000 |
| [ |
| @@ -0,0 +1,120 @@ +from ..biotools import load_record +from ..GraphicRecord import GraphicRecord +from ..CircularGraphicRecord import CircularGraphicRecord +from ..GraphicFeature import GraphicFeature + + +class BiopythonTranslatorBase: + """Base class for all BiopythonTranslators. + + This class needs to be complemented with methods compute_feature_label, + compute_features_color, etc. to be usable. See BiopythonTranslator for + an example of minimal working subclass. + + Parameters + ---------- + + features_filters + List of filters (some_biopython_feature) => True/False. + Only features passing all the filters are kept. + This only works if you haven't redefined ``compute_filtered_features`` + + features_properties + A function (feature)=> properties_dict + + """ + + graphic_record_parameters = {} + + def __init__(self, features_filters=(), features_properties=None): + self.features_filters = features_filters + self.features_properties = features_properties + + def translate_feature(self, feature): + """Translate a Biopython feature into a Dna Features Viewer feature.""" + properties = dict( + label=self.compute_feature_label(feature), + color=self.compute_feature_color(feature), + html=self.compute_feature_html(feature), + fontdict=self.compute_feature_fontdict(feature), + box_linewidth=self.compute_feature_box_linewidth(feature), + box_color=self.compute_feature_box_color(feature), + linewidth=self.compute_feature_linewidth(feature), + label_link_color=self.compute_feature_label_link_color(feature), + legend_text=self.compute_feature_legend_text(feature), + ) + if self.features_properties is not None: + other_properties = self.features_properties + if hasattr(other_properties, "__call__"): + other_properties = other_properties(feature) + properties.update(other_properties) + + return GraphicFeature( + start=feature.location.start, + end=feature.location.end, + strand=feature.location.strand, + **properties + ) + + def translate_record(self, record, record_class=None): + """Create a new GraphicRecord from a BioPython Record object. + + Parameters + ---------- + + record + A BioPython Record object or the path to a Genbank or a GFF file. + + record_class + The graphic record class to use, e.g. GraphicRecord (default) or + CircularGraphicRecord. Strings 'circular' and 'linear' can also be + provided. + """ + classes = { + "linear": GraphicRecord, + "circular": CircularGraphicRecord, + None: GraphicRecord, + } + if record_class in classes: + record_class = classes[record_class] + + if isinstance(record, str) or hasattr(record, "read"): + record = load_record(record) + filtered_features = self.compute_filtered_features(record.features) + return record_class( + sequence_length=len(record), + sequence=str(record.seq), + features=[ + self.translate_feature(feature) + for feature in filtered_features + if feature.location is not None + ], + **self.graphic_record_parameters + ) + + @classmethod + def quick_class_plot(cls, record, figure_width=12, **kwargs): + """Allows super quick and dirty plotting of Biopython records. + + This is really meant for use in a Jupyter/Ipython notebook with + the "%matplotlib inline" setting. + + >>> from dna_features_viewer import BiopythonTranslator + >>> BiopythonTranslator.quick_plot(my_record) + """ + graphic_record = cls().translate_record(record) + ax, _ = graphic_record.plot(figure_width=figure_width, **kwargs) + return ax + + def quick_plot(self, record, figure_width=12, **kwargs): + """Allows super quick and dirty plotting of Biopython records. + + This is really meant for use in a Jupyter/Ipython notebook with + the "%matplotlib inline" setting. + + >>> from dna_features_viewer import BiopythonTranslator + >>> BiopythonTranslator.quick_plot(my_record) + """ + graphic_record = self.translate_record(record) + ax, _ = graphic_record.plot(figure_width=figure_width, **kwargs) + return ax |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/BiopythonTranslator/BlackBoxlessLabelTranslator.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/BiopythonTranslator/BlackBoxlessLabelTranslator.py Mon Jun 05 02:45:31 2023 +0000 |
| b |
| @@ -0,0 +1,14 @@ +from .BiopythonTranslator import BiopythonTranslator + + +class BlackBoxlessLabelTranslator(BiopythonTranslator): + """Translates Biopython records into GraphicRecords where annotations + appear black on a white background with no box. Which can be cleaner.""" + + def compute_feature_box_linewidth(self, feature): + """Return 0 as this translator doesn't show a box.""" + return 0 + + def compute_feature_box_color(self, feature): + """Return white.""" + return "white" |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/BiopythonTranslator/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/BiopythonTranslator/__init__.py Mon Jun 05 02:45:31 2023 +0000 |
| [ |
| @@ -0,0 +1,4 @@ +from .BiopythonTranslator import BiopythonTranslator +from .BlackBoxlessLabelTranslator import BlackBoxlessLabelTranslator + +__all__ = ["BiopythonTranslator", "BlackBoxlessLabelTranslator"] |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/CircularGraphicRecord/ArrowWedge.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/CircularGraphicRecord/ArrowWedge.py Mon Jun 05 02:45:31 2023 +0000 |
| [ |
| @@ -0,0 +1,98 @@ +"""Implements the missing Matplotlib ArrowWedge patch class. + +This is a plain arrow curved alongside a protion of circle, like you would +expect a circular genetic feature to look. +""" +import numpy as np +import matplotlib.patches as mpatches + + +class ArrowWedge(mpatches.Wedge): + """Matplotlib patch shaped as a tick fraction of circle with a pointy end. + + This is the patch used by CircularGraphicRecord to draw features. + + Parameters + ---------- + + center + Center of the circle around which the arrow-wedge is drawn. + + radius + Radius of the circle around which the arrow-wedge is drawn. + + theta1 + Start angle of the wedge + + theta2 + End angle of the wedge + + width + Width or thickness of the arrow-wedge. + + direction + Determines whether the pointy end points in direct sense (+1) or + indirect sense (-1) or no sense at all (0) + """ + + def __init__(self, center, radius, theta1, theta2, width, direction=+1, **kwargs): + + self.direction = direction + self.radius = radius + mpatches.Wedge.__init__(self, center, radius, theta1, theta2, width, **kwargs) + self._recompute_path() + + def _recompute_path(self): + """Recompute the full path forming the "tick" arrowed wedge + + This method overwrites "mpatches.Wedge._recompute_path" in the + super-class. + """ + + if self.direction not in [-1, +1]: + return mpatches.Wedge._recompute_path(self) + + theta1, theta2 = self.theta1, self.theta2 + arrow_angle = min(5, abs(theta2 - theta1) / 2) + normalized_arrow_width = self.width / 2.0 / self.radius + if self.direction == +1: + angle_start_arrow = theta1 + arrow_angle + arc = mpatches.Path.arc(angle_start_arrow, theta2) + outer_arc = arc.vertices[::-1] * (1 + normalized_arrow_width) + inner_arc = arc.vertices * (1 - normalized_arrow_width) + arrow_vertices = [ + outer_arc[-1], + np.array([np.cos(np.deg2rad(theta1)), np.sin(np.deg2rad(theta1))]), + inner_arc[0], + ] + else: + angle_start_arrow = theta2 - arrow_angle + arc = mpatches.Path.arc(theta1, angle_start_arrow) + outer_arc = arc.vertices * (self.radius + self.width / 2.0) / self.radius + inner_arc = ( + arc.vertices[::-1] * (self.radius - self.width / 2.0) / self.radius + ) + arrow_vertices = [ + outer_arc[-1], + np.array([np.cos(np.deg2rad(theta2)), np.sin(np.deg2rad(theta2))]), + inner_arc[0], + ] + p = np.vstack([outer_arc, arrow_vertices, inner_arc]) + + path_vertices = np.vstack([p, inner_arc[-1, :], (0, 0)]) + + path_codes = np.hstack( + [ + arc.codes, + 4 * [mpatches.Path.LINETO], + arc.codes[1:], + mpatches.Path.LINETO, + mpatches.Path.CLOSEPOLY, + ] + ) + path_codes[len(arc.codes)] = mpatches.Path.LINETO + + # Shift and scale the wedge to the final location. + path_vertices *= self.r + path_vertices += np.asarray(self.center) + self._path = mpatches.Path(path_vertices, path_codes) |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/CircularGraphicRecord/CircularGraphicRecord.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/CircularGraphicRecord/CircularGraphicRecord.py Mon Jun 05 02:45:31 2023 +0000 |
| [ |
| @@ -0,0 +1,162 @@ +"""Implements the CircularGraphicRecord class. +""" + +import matplotlib.patches as mpatches +import numpy as np + +from ..GraphicRecord import GraphicRecord +from .ArrowWedge import ArrowWedge + + +class CircularGraphicRecord(GraphicRecord): + """Set of Genetic Features of a same DNA sequence, to be plotted together. + + Parameters + ---------- + + sequence_length + Length of the DNA sequence, in number of nucleotides + + features + list of GraphicalFeature objects. + + top_position + The index in the sequence that will end up at the top of the circle + + feature_level_height + Width in inches of one "level" for feature arrows. + + annotation_height + Width in inches of one "level" for feature annotations. + + labels_spacing + Distance in basepairs to keep between labels to avoid "quasi-collisions" + + **kw + Other keyword arguments - do not use, these parameters are allowed for + making it easier to use GraphicRecord and CircularGraphicRecord + interchangeably. + + """ + + default_elevate_outline_annotations = True + min_y_height_of_text_line = 0.1 + + def __init__( + self, + sequence_length, + features, + top_position=0, + feature_level_height=0.2, + annotation_height="auto", + labels_spacing=12, + **kw + ): + + self.radius = 1.0 + self.sequence_length = sequence_length + self.features = features + self.top_position = top_position + self.feature_level_height = feature_level_height + self.annotation_height = annotation_height + self.labels_spacing = labels_spacing + + def initialize_ax(self, ax, draw_line, with_ruler): + """Initialize the ax with a circular line, sets limits, aspect etc.""" + + if draw_line: + circle = mpatches.Circle( + (0, -self.radius), self.radius, facecolor="none", edgecolor="k" + ) + ax.add_patch(circle) + ax.axis("off") + if with_ruler: + # only display the xaxis ticks + ax.set_frame_on(False) + ax.yaxis.set_visible(False) + ax.xaxis.tick_bottom() + else: + # don't display anything + ax.axis("off") + + ax.set_xlim(-1.1 * self.radius, 1.1 * self.radius) + ax.set_ylim(-self.radius, 3 * self.radius) + ax.set_aspect("equal") + + def finalize_ax( + self, + ax, + features_levels, + annotations_max_level, + auto_figure_height=False, + ideal_yspan=None, + annotations_are_elevated=True, + ): + """Final display range and figure dimension tweakings.""" + annotation_height = self.determine_annotation_height(annotations_max_level) + ymin = -2 * self.radius - self.feature_level_height * (features_levels + 1) + ymax = self.feature_level_height * (features_levels + 1) + annotation_height * ( + annotations_max_level + 1 + ) + if ideal_yspan is not None: + ymax = max(annotation_height * ideal_yspan + ymin, ymax) + xmin = -self.radius - self.feature_level_height * (features_levels + 1) + xmax = -xmin + ax.set_xlim(xmin, xmax) + ax.set_ylim(ymin, ymax) + ratio = 1.0 * (ymax - ymin) / (xmax - xmin) + + if auto_figure_height: + figure_width = ax.figure.get_size_inches()[0] + ax.figure.set_size_inches(figure_width, figure_width * ratio) + + def plot_feature(self, ax, feature, level): + """Plot an ArrowWedge representing the feature at the giben height + level. + + + """ + a_start = self.position_to_angle(feature.start) + a_end = self.position_to_angle(feature.end) + a_start, a_end = sorted([a_start, a_end]) + r = self.radius + level * self.feature_level_height + patch = ArrowWedge( + center=(0, -self.radius), + radius=r, + theta1=a_start, + theta2=a_end, + width=0.7 * self.feature_level_height, + direction=feature.strand, + edgecolor=feature.linecolor, + linewidth=feature.linewidth, + facecolor=feature.color, + zorder=1, + ) + ax.add_patch(patch) + + def position_to_angle(self, position): + """Convert a sequence position into an angle in the figure.""" + a = 360.0 * (position - self.top_position) / self.sequence_length + return 90 - a + + def coordinates_in_plot(self, position, level): + """Convert a sequence position and height level to (x, y) coordinates.""" + r = self.radius + level * self.feature_level_height + angle = self.position_to_angle(position) + rad_angle = np.deg2rad(angle) + return np.array([r * np.cos(rad_angle), r * np.sin(rad_angle) - self.radius]) + + def determine_annotation_height(self, max_annotations_level): + """Auto-select the annotations height. + + Annotation height is 0.2 at most, or else whatever will make + the figure a 5*radius tall rectangle where the circular plasmid + occupies the bottom-2 5th and the annotations occupy the top-3 5th. + """ + return min(0.25, 3.0 * self.radius / (1.0 + max_annotations_level)) + + def compute_padding(self, ax): + """""" + ax_width = ax.get_window_extent(ax.figure.canvas.get_renderer()).width + xmin, xmax = ax.get_xlim() + return 3 * self.labels_spacing * (xmax - xmin) / (1.0 * ax_width) |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/CircularGraphicRecord/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/CircularGraphicRecord/__init__.py Mon Jun 05 02:45:31 2023 +0000 |
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| @@ -0,0 +1,3 @@ +from .CircularGraphicRecord import CircularGraphicRecord + +__all__ = ["CircularGraphicRecord"] |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/GraphicFeature.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/GraphicFeature.py Mon Jun 05 02:45:31 2023 +0000 |
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| @@ -0,0 +1,160 @@ +from copy import deepcopy + + +class GraphicFeature: + """Genetic Feature to be plotted. + + Parameters + ---------- + + start, end + Coordinates of the feature in the final sequence. + + strand + Directionality of the feature. can be +1/-1/0 for direct sense, + anti-sense, or no directionality. + + label + Short descriptive text associated and plotted with the feature + + color + Color of the feature, any Matplotlib-compatible format is accepted, + such as "white", "w", "#ffffff", (1,1,1), etc. + + linecolor + Color of the feature's border, any Matplotlib-compatible format is + accepted, such as "white", "w", "#ffffff", (1,1,1), etc. + + linewidth + Width of the line (=edge) surrounding the graphic feature, in pixels. + + thickness + Vertical span of the feature + + box_color + Color of the label box. Set to None for no box around the label. + Leave to "auto" for a box color that is a lightened version of the + feature's color. + + data + Any other keyword is kept into the feature.data[] dictionary. + + fontdict + A Matplotlib fontdict for the font to be used in the label, e.g. + ``size=11``, ``weight='bold'``, ``family='Helvetica'``, etc. + + open_left, open_right + Set to True if this feature does not end on the right or left because it + is a cropped version of a bigger feature. + + box_linewidth + Width of the line delimiting the text box when the annotation is outside + the graphic feature. Set to 0 for no box borders + + box_color + Background color of the annotation's text box. If left to "auto" the + color will be a lighter version of the feature's color. + + label_link_color + Color of the line linking the text annotation to its respective graphic + feature. Set to auto for the line to automatically be a darker version + of the feature's color. + """ + + feature_type = "feature" + + def __init__( + self, + start=None, + end=None, + strand=None, + label=None, + color="#000080", + thickness=14, + linewidth=1.0, + linecolor="#000000", + fontdict=None, + html=None, + open_left=False, + open_right=False, + box_linewidth=1, + box_color="auto", + legend_text=None, + label_link_color="black", + **data + ): + self.start = start + self.end = end + self.strand = strand + self.label = label + self.color = color + self.linecolor = linecolor + self.data = data + self.thickness = thickness + self.linewidth = linewidth + self.box_linewidth = box_linewidth + self.box_color = box_color + self.label_link_color = label_link_color + self.fontdict = dict([("fontsize", 11)] + list((fontdict or {}).items())) + self.html = html + self.open_left = open_left + self.open_right = open_right + self.legend_text = legend_text + + def split_in_two(self, x_coord=0): + """Return two features by cutting this feature at x_coord.""" + copy1 = deepcopy(self) + copy2 = deepcopy(self) + copy1.end = x_coord + copy2.start = x_coord + 1 + return copy1, copy2 + + def crop(self, window): + """Return a the fragment of the feature that is in the window. + + If there is no overlap between the feature location and the window, + None is returned. + """ + s, e = window + if (s > self.end) or (e < self.start): + return None + copy = deepcopy(self) + if s > self.start: + copy.start = s + copy.open_left = True + if e < self.end: + copy.end = e + copy.open_right = True + return copy + + def overlaps_with(self, other): + """Return whether the feature's location overlaps with feature `other`""" + loc1, loc2 = (self.start, self.end), (other.start, other.end) + loc1, loc2 = sorted(loc1), sorted(loc2) + loc1, loc2 = sorted([loc1, loc2], key=lambda loc: loc[0]) + return loc1[1] > loc2[0] + + @property + def length(self): + """Return the length of the feature (end-start)""" + return abs(self.end - self.start) + + @property + def x_center(self): + """Return the x-center of the feature, (start+end)/2""" + return 0.5 * (self.start + self.end - 1) + + @staticmethod + def from_biopython_feature(feature, **props): + """Create a GraphicalFeature from a Biopython.Feature object.""" + return GraphicFeature( + start=feature.location.start, + end=feature.location.end, + strand=feature.location.strand, + **props + ) + + def __repr__(self): + return ("GF(%(label)s, %(start)d-%(end)d " % self.__dict__) + ( + ")" if self.strand is None else "(%d))" % self.strand + ) |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/GraphicRecord/BokehPlottableMixin.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/GraphicRecord/BokehPlottableMixin.py Mon Jun 05 02:45:31 2023 +0000 |
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| @@ -0,0 +1,174 @@ +try: + from bokeh.plotting import figure, ColumnDataSource + from bokeh.models import Range1d, HoverTool + + BOKEH_AVAILABLE = True +except ImportError: + BOKEH_AVAILABLE = False + +try: + import pandas as pd + + PANDAS_AVAILABLE = True +except ImportError: + PANDAS_AVAILABLE = False + +import matplotlib.pyplot as plt + + +class BokehPlottableMixin: + def bokeh_feature_patch( + self, + start, + end, + strand, + figure_width=5, + width=0.4, + level=0, + arrow_width_inches=0.05, + **kwargs + ): + """Return a dict with points coordinates of a Bokeh Feature arrow. + + Parameters + ---------- + + start, end, strand + + """ + hw = width / 2.0 + x1, x2 = (start, end) if (strand >= 0) else (end, start) + bp_per_width = figure_width / self.sequence_length + delta = arrow_width_inches / bp_per_width + if strand >= 0: + head_base = max(x1, x2 - delta) + else: + head_base = min(x1, x2 + delta) + result = dict( + xs=[x1, x1, head_base, x2, head_base, x1], + ys=[e + level for e in [-hw, hw, hw, 0, -hw, -hw]], + ) + result.update(kwargs) + return result + + def plot_with_bokeh(self, figure_width=5, figure_height="auto", tools="auto"): + """Plot the graphic record using Bokeh. + + Examples + -------- + + >>> + + + """ + if not BOKEH_AVAILABLE: + raise ImportError("``plot_with_bokeh`` requires Bokeh installed.") + if not PANDAS_AVAILABLE: + raise ImportError("``plot_with_bokeh`` requires Pandas installed.") + + # Set up default tools + if tools == "auto": + tools = [HoverTool(tooltips="@hover_html"), "xpan,xwheel_zoom,reset,tap"] + + # FIRST PLOT WITH MATPLOTLIB AND GATHER INFOS ON THE PLOT + ax, (features_levels, plot_data) = self.plot(figure_width=figure_width) + width, height = [int(100 * e) for e in ax.figure.get_size_inches()] + plt.close(ax.figure) + if figure_height == "auto": + height = int(0.5 * height) + else: + height = 100 * figure_height + height = max(height, 185) # Minimal height to see all icons + + max_y = max( + [data["annotation_y"] for f, data in plot_data.items()] + + list(features_levels.values()) + ) + + # BUILD THE PLOT () + plot = figure( + plot_width=width, + plot_height=height, + tools=tools, + x_range=Range1d(0, self.sequence_length), + y_range=Range1d(-1, max_y + 1), + ) + plot.patches( + xs="xs", + ys="ys", + color="color", + line_color="#000000", + source=ColumnDataSource( + pd.DataFrame.from_records( + [ + self.bokeh_feature_patch( + feature.start, + feature.end, + feature.strand, + figure_width=figure_width, + level=level, + color=feature.color, + label=feature.label, + hover_html=( + feature.html + if feature.html is not None + else feature.label + ), + ) + for feature, level in features_levels.items() + ] + ) + ), + ) + + if plot_data != {}: + plot.text( + x="x", + y="y", + text="text", + text_align="center", + text_font_size="12px", + text_font="arial", + text_font_style="normal", + source=ColumnDataSource( + pd.DataFrame.from_records( + [ + dict( + x=feature.x_center, + y=pdata["annotation_y"], + text=feature.label, + color=feature.color, + ) + for feature, pdata in plot_data.items() + ] + ) + ), + ) + plot.segment( + x0="x0", + x1="x1", + y0="y0", + y1="y1", + line_width=0.5, + color="#000000", + source=ColumnDataSource( + pd.DataFrame.from_records( + [ + dict( + x0=feature.x_center, + x1=feature.x_center, + y0=pdata["annotation_y"], + y1=pdata["feature_y"], + ) + for feature, pdata in plot_data.items() + ] + ) + ), + ) + + plot.yaxis.visible = False + plot.outline_line_color = None + plot.grid.grid_line_color = None + plot.toolbar.logo = None + + return plot |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/GraphicRecord/GraphicRecord.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/GraphicRecord/GraphicRecord.py Mon Jun 05 02:45:31 2023 +0000 |
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| @@ -0,0 +1,198 @@ +from ..biotools import find_narrowest_text_wrap + +from Bio.Seq import Seq +from Bio.SeqRecord import SeqRecord +from Bio.SeqFeature import FeatureLocation, SeqFeature +from Bio.Alphabet import DNAAlphabet + +from .MatplotlibPlottableMixin import MatplotlibPlottableMixin +from .BokehPlottableMixin import BokehPlottableMixin + + +class GraphicRecord(MatplotlibPlottableMixin, BokehPlottableMixin): + """Set of Genetic Features of a same DNA sequence, to be plotted together. + + Parameters + ---------- + + sequence_length + Length of the DNA sequence, in number of nucleotides + + features + list of GraphicalFeature objects. + + feature_level_height + Width in inches of one "level" for feature arrows. + + annotation_height + Width in inches of one "level" for feature annotations. + + first_index + Indicates the first index to plot in case the sequence is actually a + subsequence of a larger one. For instance, if the Graphic record + represents the segment (400, 420) of a sequence, we will have + ``first_index=400`` and ``sequence_length=20``. + + plots_indexing + Indicates which standard to use to show nucleotide indices in the plots. + If 'biopython', the standard python indexing is used (starting at 0). + If 'genbank', the indexing follows the Genbank standard (starting at 1). + + labels_spacing + Number of pixels that will "pad" every labels to force some horizontal + space between two labels or between a label and the borders of a feature. + + ticks_resolution + Leave to "auto" for an auto-selected number of ticks on the ruler, or set + to e.g. 50 for a tick every 50 nucleotide. + + Attributes + ---------- + + default_font_family + Default font to use for a feature that doesn't declare a font. + + default_ruler_color + Default ruler color to use when no color is given at plot() time. + + default_box_color + Default box color for non-inline annotations. If set to None, no + boxes will be drawn unless the features declare a box_color. + If "auto", a color (clearer version of the feature's color) will be + computed, for all features also declaring their box_color as "auto". + + default_elevate_outline_annotations + Value to use for elevate_outline_annotations when no specific value is + given at ``graphic_record.plot(...)`` time. Set to true to have all + text annotations appears above all features, or false else. + """ + + default_font_family = None + default_ruler_color = "grey" + default_box_color = "auto" + min_y_height_of_text_line = 0.5 + + def __init__( + self, + sequence_length=None, + sequence=None, + features=(), + feature_level_height=1, + first_index=0, + plots_indexing="biopython", + labels_spacing=8, + ticks_resolution="auto", + ): + if sequence_length is None: + sequence_length = len(sequence) + self.features = features + self.sequence_length = sequence_length + self.feature_level_height = feature_level_height + self.sequence = sequence + self.first_index = first_index + self.plots_indexing = plots_indexing + self.labels_spacing = labels_spacing + self.ticks_resolution = ticks_resolution + + @property + def last_index(self): + return self.first_index + self.sequence_length + + @property + def span(self): + """Return the display span (start, end) accounting for first_index.""" + return self.first_index, self.last_index + + def to_biopython_record(self, sequence): + """ + Example + ------- + from Bio import SeqIO + gr_record = GraphicRecord(features=features, sequence_length=len(seq), + sequence=seq) + bio_record = gr_record.to_biopython_record() + with open("example.gb", "w+") as f: + SeqIO.write(record, f, "genbank") + """ + features = [ + SeqFeature( + FeatureLocation(f.start, f.end, f.strand), + type=f.feature_type, + qualifiers={"label": f.label}, + ) + for f in self.features + ] + if not isinstance(sequence, Seq): + sequence = Seq(sequence, alphabet=DNAAlphabet()) + return SeqRecord(seq=sequence, features=features) + + def crop(self, window): + start, end = window + first_index = self.first_index + if (start < first_index) or (end > self.last_index): + raise ValueError("out-of-bound cropping") + new_features = [] + for f in self.features: + cropped_feature = f.crop(window) + if cropped_feature is not None: # = has ovelap with the window + new_features.append(cropped_feature) + + return GraphicRecord( + sequence=self.sequence[start - first_index : end - first_index] + if self.sequence is not None + else None, + sequence_length=end - start, + features=new_features, + feature_level_height=self.feature_level_height, + first_index=start, + plots_indexing=self.plots_indexing, + labels_spacing=self.labels_spacing, + ticks_resolution=self.ticks_resolution, + ) + + def determine_annotation_height(self, levels): + """By default the ideal annotation level height is the same as the + feature_level_height.""" + # TODO: Improve me! ideally, annotation width would be linked to the + # height of one line of text, so dependent on font size and ax + # height/span. + return self.feature_level_height + + def coordinates_in_plot(self, x, level): + """Convert a sequence position and height level into a (x, y) position.""" + return (x, level * self.feature_level_height) + + def split_overflowing_features_circularly(self): + """Split the features that overflow over the edge for circular + constructs (inplace).""" + new_features = [] + for f in self.features: + if f.start < 0 < f.end: + f1, f2 = f.split_in_two(-1) + f1.start, f1.end = ( + f1.start + self.sequence_length, + f1.end + self.sequence_length, + ) + new_features += [f1, f2] + elif f.start < self.sequence_length < f.end: + f1, f2 = f.split_in_two(self.sequence_length - 1) + f2.start, f2.end = ( + f2.start - self.sequence_length, + f2.end - self.sequence_length, + ) + new_features += [f1, f2] + else: + new_features.append(f) + self.features = new_features + + def _format_label(self, label, max_label_length=50, max_line_length=40): + if len(label) > max_label_length: + label = label[: max_label_length - 1] + "…" + if len(label) > max_line_length: + label = find_narrowest_text_wrap(label, max_line_length) + return label + + def compute_padding(self, ax): + ax_width = ax.get_window_extent(ax.figure.canvas.get_renderer()).width + xmin, xmax = ax.get_xlim() + return self.labels_spacing * (xmax - xmin) / (1.0 * ax_width) |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/GraphicRecord/MatplotlibPlottableMixin.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/GraphicRecord/MatplotlibPlottableMixin.py Mon Jun 05 02:45:31 2023 +0000 |
| [ |
| b'@@ -0,0 +1,630 @@\n+"""Useful functions for the library"""\n+\n+import colorsys\n+\n+import matplotlib.pyplot as plt\n+import matplotlib.patches as mpatches\n+from matplotlib.patches import Patch\n+import matplotlib.ticker as ticker\n+\n+from ..compute_features_levels import compute_features_levels\n+from ..GraphicFeature import GraphicFeature\n+from matplotlib.colors import colorConverter\n+from .MultilinePlottableMixin import MultilinePlottableMixin\n+from .SequenceAndTranslationMixin import SequenceAndTranslationMixin\n+\n+\n+class MatplotlibPlottableMixin(MultilinePlottableMixin, SequenceAndTranslationMixin):\n+ """Class mixin for matplotlib-related methods."""\n+\n+ default_elevate_outline_annotations = False\n+ default_strand_in_label_threshold = None\n+\n+ def initialize_ax(self, ax, draw_line, with_ruler, ruler_color=None):\n+ """Initialize the ax: remove axis, draw a horizontal line, etc.\n+\n+ Parameters\n+ ----------\n+\n+ draw_line\n+ True/False to draw the horizontal line or not.\n+\n+ with_ruler\n+ True/False to draw the indices indicators along the line.\n+\n+ """\n+ ruler_color = ruler_color or self.default_ruler_color\n+ start, end = self.span\n+ plot_start, plot_end = start - 0.8, end - 0.2\n+ if draw_line:\n+ ax.plot([plot_start, plot_end], [0, 0], zorder=-1000, c="k")\n+\n+ if with_ruler: # only display the xaxis ticks\n+ ax.set_frame_on(False)\n+ ax.yaxis.set_visible(False)\n+ ax.xaxis.tick_bottom()\n+ if ruler_color is not None:\n+ ax.tick_params(axis="x", colors=ruler_color)\n+ else: # don\'t display anything\n+ ax.axis("off")\n+\n+ ax.set_xlim(plot_start, plot_end)\n+ if self.first_index != 0:\n+ ax.ticklabel_format(useOffset=False, style="plain")\n+ fmt = lambda x, p: "{:,}".format(int(x))\n+ ax.xaxis.set_major_formatter(ticker.FuncFormatter(fmt))\n+ if self.ticks_resolution == "auto":\n+ ax.xaxis.set_major_locator(ticker.MaxNLocator(integer=True))\n+ else:\n+ locator = ticker.MultipleLocator(self.ticks_resolution)\n+ ax.xaxis.set_major_locator(locator)\n+\n+ def finalize_ax(\n+ self,\n+ ax,\n+ features_levels,\n+ annotations_max_level,\n+ auto_figure_height=False,\n+ ideal_yspan=None,\n+ annotations_are_elevated=True,\n+ ):\n+ """Prettify the figure with some last changes.\n+\n+ Changes include redefining y-bounds and figure height.\n+\n+ Parameters\n+ ==========\n+ ax\n+ ax on which the record was plotted\n+\n+ features_levels\n+\n+ annotations_max_level\n+ Number indicating to the method the maximum height for an\n+ annotation, so the method can set ymax accordingly\n+\n+ auto_figure_height\n+ If true, the figure\'height will be automatically re-set to a nice\n+ value (counting ~0.4inch per level in the figure).\n+\n+ ideal_yspan\n+ if provided, can help the method select a better ymax to make sure\n+ all constraints fit.\n+\n+ """\n+\n+ # Compute the "natural" ymax\n+ annotation_height = self.determine_annotation_height(None)\n+ features_ymax = self.feature_level_height * (features_levels + 1)\n+ annotations_ymax = annotation_height * annotations_max_level\n+ if annotations_are_elevated:\n+ ymax = features_ymax + annotations_ymax\n+ else:\n+ ymax = max(features_ymax, annotations_ymax) + 1\n+ ymin = min(ax.get_ylim()[0], -0.5)\n+\n+ # ymax could be even bigger if a "ideal_yspan" has been set.\n+ if (ideal_yspan is not None) and not (auto_figure_height):\n+ ymax = max(ideal_yspan + ymin, ymax)\n+ ax.set_ylim(ymin, ymax)\n+ if auto_figure_height:\n+ figure_width = ax.figure.get_size_inches()[0]\n+ ax.figure.set_size_inch'..b' = self.coordinates_in_plot(\n+ feature.data["feature"].x_center, feature.data["feature_level"]\n+ )\n+\n+ # PLOT THE LABEL-TO-FEATURE LINK\n+ link_color = feature.label_link_color\n+ if link_color == "auto":\n+ link_color = change_luminosity(feature.color, luminosity=0.2)\n+ ax.plot([x, fx], [new_y, fy], c=link_color, lw=0.5, zorder=-10)\n+ labels_data[feature.data["feature"]] = dict(\n+ feature_y=fy, annotation_y=new_y\n+ )\n+\n+ if plot_sequence:\n+ self.plot_sequence(ax, **(sequence_params or {}))\n+\n+ self.finalize_ax(\n+ ax=ax,\n+ features_levels=max([1] + list(features_levels.values())),\n+ annotations_max_level=max_annotations_level,\n+ auto_figure_height=auto_figure_height,\n+ ideal_yspan=ideal_yspan,\n+ annotations_are_elevated=elevate_outline_annotations,\n+ )\n+ return ax, (features_levels, labels_data)\n+\n+ def plot_legend(\n+ self, ax, allow_ambiguity=False, include_edge=True, **legend_kwargs\n+ ):\n+ handles = []\n+ features_parameters = {}\n+ for feature in self.features:\n+ text = feature.legend_text\n+ if text is None:\n+ continue\n+ parameters = dict(\n+ label=text,\n+ facecolor=feature.color,\n+ edgecolor="black",\n+ )\n+ if include_edge:\n+ parameters.update(\n+ dict(\n+ linewidth=feature.linewidth,\n+ edgecolor=feature.linecolor,\n+ )\n+ )\n+ if text in features_parameters:\n+ previous_parameters = features_parameters[text]\n+ if (not allow_ambiguity) and any(\n+ [parameters[k] != previous_parameters[k] for k in parameters]\n+ ):\n+ raise ValueError("Cannot generate an unambiguous legend as two")\n+ continue\n+ features_parameters[text] = parameters\n+ handles.append(Patch(**parameters))\n+ ax.legend(handles=handles, **legend_kwargs)\n+\n+\n+def change_luminosity(color, luminosity=None, min_luminosity=None, factor=None):\n+ """Return a version of the color with different luminosity.\n+\n+ Parameters\n+ ----------\n+ color\n+ A color in any Matplotlib-compatible format such as "white", "w",\n+ (1,1,1), "#ffffff", etc.\n+ luminosity\n+ A float in 0-1. If provided, the returned color has this level of\n+ luminosity.\n+ factor\n+ Only used if `luminosity` is not set. Positive factors increase\n+ luminosity and negative factors decrease it. More precisely, the\n+ luminosity of the new color is L^(-factor), where L is the current\n+ luminosity, between 0 and 1.\n+ """\n+ r, g, b = colorConverter.to_rgb(color)\n+ h, l, s = colorsys.rgb_to_hls(r, g, b)\n+ new_l = l\n+ if luminosity is not None:\n+ new_l = luminosity\n+ if factor is not None:\n+ new_l = l ** (-factor)\n+ if min_luminosity is not None:\n+ new_l = max(new_l, min_luminosity)\n+\n+ return colorsys.hls_to_rgb(h, new_l, s)\n+\n+\n+def get_text_box(text, margin=0):\n+ """Return the coordinates of a Matplotlib Text.\n+\n+ `text` is a Matplotlib text obtained with ax.text().\n+ This returns `(x1,y1, x2, y2)` where (x1,y1) is the lower left corner\n+ and (x2, y2) is the upper right corner of the text, in data coordinates.\n+ If a margin m is supplied, the returned result is (x1-m, y1-m, x2+m, y2+m)\n+ """\n+ renderer = text.axes.figure.canvas.get_renderer()\n+ bbox = text.get_window_extent(renderer) # bounding box\n+ __x1, y1, __x2, y2 = bbox.get_points().flatten()\n+ bbox = bbox.transformed(text.axes.transData.inverted())\n+ x1, __y1, x2, __y2 = bbox.get_points().flatten()\n+ return [x1, y1, x2, y2]\n' |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/GraphicRecord/MultilinePlottableMixin.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/GraphicRecord/MultilinePlottableMixin.py Mon Jun 05 02:45:31 2023 +0000 |
| [ |
| @@ -0,0 +1,153 @@ +import matplotlib.pyplot as plt +from matplotlib.backends.backend_pdf import PdfPages +import numpy + + +class MultilinePlottableMixin: + def plot_on_multiple_lines( + self, + n_lines=None, + nucl_per_line=None, + plot_sequence=False, + figure_width="auto", + **plot_params + ): + """Plot the features on different lines (one Matplotlib ax per line) + + Parameters + ---------- + + n_lines + Number of lines on which the record will be plotted. A number of + nucleotides per line can be provided instead (see below). + + nucl_per_line + Number of nucleotides to be represented on every line (determines + the number of lines ``n_lines``). + + plot_sequence + Whether to plot the nucleotide sequence on each line + + figure_width + Width of the figure in inches. Leave to auto for a width of either 10 + (if not sequence is plotted) or 0.15*nucl_per_line inches + (if a sequence is plotted). + + **plot_params + Parameters from ``graphic_record.plot()`` to be used in the plotting + of the individual lines. This includes ``draw_line``, ``with_ruler``, + ``annotate_inline``, ``plot_sequence``, + ``evelate_outline_annotations``, ``strand_in_label_pixel_threshold`` + + Returns + ------- + + figure, axes + The matplotlib figure and axes generated. + """ + + if n_lines is None: + n_lines = int(numpy.ceil(self.sequence_length / nucl_per_line)) + else: + nucl_per_line = self.sequence_length // n_lines + 1 + + if figure_width == "auto": + if plot_sequence: + figure_width = 0.15 * nucl_per_line + else: + figure_width = 10 + + figures_heights = [] + + def plot_line(line_index, ax=None): + first, last = self.first_index, self.last_index + line_start = first + line_index * nucl_per_line + line_virtual_end = first + (line_index + 1) * nucl_per_line + line_end = min(last, line_virtual_end) + line_record = self.crop((line_start, line_end)) + line_ax, _ = line_record.plot( + figure_width=figure_width, + x_lim=(line_start, line_virtual_end), + ax=ax, + plot_sequence=plot_sequence, + **plot_params + ) + return line_ax + + for line_index in range(n_lines): + line_ax = plot_line(line_index) + figures_heights.append(line_ax.figure.get_figheight()) + plt.close(line_ax.figure) + fig, axes = plt.subplots( + n_lines, + 1, + gridspec_kw={"height_ratios": figures_heights}, + figsize=(figure_width, 0.9 * sum(figures_heights)), + ) + if n_lines == 1: + axes = [axes] + for line_index, ax in enumerate(axes): + plot_line(line_index, ax=ax) + fig.tight_layout() + return fig, axes + + def plot_on_multiple_pages( + self, + pdf_target, + n_lines=None, + nucl_per_line=None, + lines_per_page=5, + figure_width="auto", + **plot_params + ): + """Plot the features on different lines on different pages of a PDF. + + This function returns None + + Parameters + ---------- + + pdf_target + Either a path to a PDF, or a file(-like) handle. + + n_lines + Number of lines on which the record will be plotted. A number of + nucleotides per line can be provided instead (see below). + + nucl_per_line + Number of nucleotides to be represented on every line (determines + the number of lines ``n_lines``). + + lines_per_page + Number of lines on each page + + plot_sequence + Whether to plot the nucleotide sequence on each line + + figure_width + Width of the figure in inches. Leave to auto for a width of either 10 + (if not sequence is plotted) or 0.15*nucl_per_line inches + (if a sequence is plotted). + + **plot_params + Parameters from ``graphic_record.plot()`` to be used in the plotting + of the individual lines. This includes ``draw_line``, ``with_ruler``, + ``annotate_inline``, ``plot_sequence``, + ``evelate_outline_annotations``, ``strand_in_label_pixel_threshold`` + """ + nucl_per_page = nucl_per_line * lines_per_page + number_of_pages = int(numpy.ceil(self.sequence_length / nucl_per_page)) + with PdfPages(pdf_target) as pdf: + for page_index in range(number_of_pages): + first, last = self.first_index, self.last_index + page_start = first + page_index * nucl_per_page + page_end = first + (page_index + 1) * nucl_per_page + page_end = min(last, page_end) + page_record = self.crop((page_start, page_end)) + fig, axes = page_record.plot_on_multiple_lines( + nucl_per_line=nucl_per_line, + figure_width=figure_width, + **plot_params + ) + pdf.savefig(fig) + plt.close(fig) |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/GraphicRecord/SequenceAndTranslationMixin.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/GraphicRecord/SequenceAndTranslationMixin.py Mon Jun 05 02:45:31 2023 +0000 |
| [ |
| @@ -0,0 +1,143 @@ +from ..biotools import extract_graphical_translation + + +class SequenceAndTranslationMixin: + def plot_sequence( + self, ax, location=None, y_offset=1, fontdict=None, guides_intensity=0 + ): + """Plot a sequence of nucleotides at the bottom of the plot. + + Parameters + ---------- + + ax + Which axes the translation should be plotted to + + location + location of the segment to translate, either (start, end) or + (start, end, strand) + + y_offset + Number of text levels under the plot's base line where to draw the + nucleotides. Should be 1 if the nucleotide sequence is to be plotted + directly under the main line. + + fontdict + Matplotlib fontdict for the text, e.g. + ``{'size': 11, 'weight':'bold'}`` + + background + tuple (color1, color2) of alternate colors to plot behind each + nucleotide position to guide vision. Leave to None for no background. + + guides_intensity + Intensity of the vertical guides marking the different nucleotides + (0 = no guides) + """ + if self.sequence is None: + raise ValueError("No sequence in the graphic record") + if location is None: + location = self.span + location_start, location_end = location + fontdict = dict(size=11) + fontdict.update(fontdict or {}) + for i, nucleotide in enumerate(self.sequence): + index = i + location_start + if location_start <= index <= location_end: + ax.text( + index, + -0.7 * self.feature_level_height * y_offset, + nucleotide, + ha="center", + va="center", + fontdict=fontdict, + ) + if guides_intensity: + color = (0, 0, 0, guides_intensity) + for i in range(location_start, location_end + 1): + ax.axvline(i - 0.5, linewidth=0.1, color=color, zorder=-10000) + ymin = ax.get_ylim()[0] + if ymin < -500: + ymin = 0 + ax.set_ylim(bottom=min(ymin, -y_offset * self.feature_level_height)) + + def plot_translation( + self, + ax, + location=None, + y_offset=2, + fontdict=None, + guides_intensity=0.5, + translation=None, + long_form_translation=True, + ): + """Plot a sequence of amino-acids at the bottom of the plot. + + Parameters + ---------- + + ax + Which axes the translation should be plotted to + + location + location of the segment to translate (start, end) + + y_offset + Number of text levels under the plot's base line where to draw the + amino acid names. Should be 2 if the nucleotide sequence is also + plotted at level 1. + + fontdict + Matplotlib fontdict for the text, e.g. + ``{'size': 11, 'weight':'bold'}`` + + background + tuple (color1, color2) of alternate colors to plot behind each + amino acid position to guide vision. Leave to None for no background. + + translation + Sequence of amino acids either as a string ``'MAKG...'`` or as a list + ``['Met', 'Ala', ...]`` + + + """ + start, end = location[0], location[1] + strand = location[2] if (len(location) == 3) else 1 + s, e = self.span + start = max(start, s + ((start - s) % 3)) + end = min(end, e - ((end - e) % 3)) + if translation is None: + new_loc = start - self.first_index, end - self.first_index, strand + translation = extract_graphical_translation( + self.sequence, + location=new_loc, + long_form=long_form_translation, + ) + texts = [ + ((start + 3 * i, start + 3 * (i + 1)), aa) + for i, aa in enumerate(translation) + ] + + y = -0.7 * y_offset * self.feature_level_height + ymin = ax.get_ylim()[0] + ax.set_ylim(bottom=min(ymin, -y_offset * self.feature_level_height)) + fontdict = fontdict or {} + guides_color = (0, 0, 0, guides_intensity) + for i, ((start, end), text) in enumerate(texts): + ax.text( + 0.5 * (start + end - 1), + y, + text, + ha="center", + va="center", + fontdict=fontdict, + ) + if guides_intensity: + ax.axvline( + start - 0.5, + linewidth=0.1, + color=guides_color, + zorder=-10000, + ) + if guides_intensity: + ax.axvline(end - 0.5, linewidth=0.1, color=guides_color, zorder=-10000) |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/GraphicRecord/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/GraphicRecord/__init__.py Mon Jun 05 02:45:31 2023 +0000 |
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| @@ -0,0 +1,3 @@ +from .GraphicRecord import GraphicRecord + +__all__ = ["GraphicRecord"] |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/README.md Mon Jun 05 02:45:31 2023 +0000 |
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| @@ -0,0 +1,13 @@ +# Code organization + +This document walks you trough the Geneblocks code. Please request changes if anything is unclear. + +- **GraphicFeature.py** implements a class for defining a *GraphicFeature*, which is an annotation (start, end, strand, label) with graphical properties (color, line width, font family...) + +- **GraphicRecord/** implements the *GraphicRecord* class, which can plot a set of *GraphicFeatures* using Matplotlib or Bokeh. To keep file sizes acceptable, many methods are implemented in separate files (*bokeh_plots.py*, *matplotlib_plots.py*) and added to *GraphicRecord* via class mixins. + +- **CircularGraphicRecord/** implements the *GraphicRecord* class, which inherits from *GraphicRecord* but draws features circularly using custom Matplotlib patches called "arrow-wedge" (defined in file *ArrowWedge.py*). + +- **compute_features_levels.py** implements the algorithm for deciding the levels on which the different features (and annotations) are drawn + +- **biotools.py** implements generic biology-related methods (reverse_complement, annotation of Biopython records, etc.) |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/__init__.py Mon Jun 05 02:45:31 2023 +0000 |
| [ |
| @@ -0,0 +1,22 @@ +""" dna_features_viewer/__init__.py """ + +from .GraphicRecord import GraphicRecord +from .CircularGraphicRecord import CircularGraphicRecord +from .GraphicFeature import GraphicFeature +from .BiopythonTranslator import ( + BiopythonTranslator, + BlackBoxlessLabelTranslator, +) +from .biotools import load_record, annotate_biopython_record + +from .version import __version__ + +__all__ = [ + "GraphicRecord", + "CircularGraphicRecord", + "GraphicFeature", + "BiopythonTranslator", + "BlackBoxlessLabelTranslator", + "annotate_biopython_record", + "__version__", +] |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/biotools.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/biotools.py Mon Jun 05 02:45:31 2023 +0000 |
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| @@ -0,0 +1,163 @@ +import textwrap +from Bio.Seq import Seq +from Bio.SeqFeature import SeqFeature, FeatureLocation +from Bio.PDB.Polypeptide import aa1, aa3 +from Bio import SeqIO + +try: + from BCBio import GFF +except ImportError: + + class GFF: + def parse(*a): + """Not available. Please install bcbio-gff.""" + raise ImportError("Please install the bcbio-gff library to parse GFF data") + + +def complement(dna_sequence): + """Return the complement of the DNA sequence. + + For instance ``complement("ATGCCG")`` returns ``"TACGGC"``. + + Uses BioPython for speed. + """ + return str(Seq(dna_sequence).complement()) + + +def reverse_complement(sequence): + """Return the reverse-complement of the DNA sequence. + + For instance ``complement("ATGCCG")`` returns ``"GCCGTA"``. + + Uses BioPython for speed. + """ + return complement(sequence)[::-1] + + +aa_short_to_long_form_dict = { + _aa1: _aa3[0] + _aa3[1:].lower() for (_aa1, _aa3) in zip(aa1 + "*", aa3 + ["*"]) +} + + +def translate(dna_sequence, long_form=False): + """Translate the DNA sequence into an amino-acids sequence MLKYQT... + + If long_form is true, a list of 3-letter amino acid representations + is returned instead (['Ala', 'Ser', ...]). + """ + result = str(Seq(dna_sequence).translate()) + if long_form: + result = [aa_short_to_long_form_dict[aa] for aa in result] + return result + + +def extract_graphical_translation(sequence, location, long_form=False): + """Return a string of the "graphical" translation of a sequence's subsegment. + + Here "graphical" means that the amino acid sequence is always given + left-to-right, as it will appear under the sequence in the plot. This matters + when the location is on the -1 strand. In this case, the amino-acids are + determined by (part of) the reverse-complement of the sequence, however + the sequence returned will be the mirror of the translated sequence, as + this is the left-to-right order in which the codons corresponding to the + amino-acids appear in the sequence. + + Parameters + ---------- + sequence + An "ATGC" string. + + location + Either (start, end) or (start, end, strand), with strand in (0, 1, -1). + + long_form + if True, a list of 3-letter amino acid representations is returned instead + (['Ala', 'Ser', ...]). + + """ + if len(location) == 3: + start, end, strand = location + else: + start, end = location + strand = 1 + subsequence = sequence[start:end] + if strand == -1: + subsequence = reverse_complement(subsequence) + translation = translate(subsequence, long_form=long_form) + if strand == -1: + translation = translation[::-1] + return translation + + +def load_record(path): + """Load a Genbank file""" + if isinstance(path, str): + # Input is a file path + if path.lower().endswith(".gff"): + return list(GFF.parse(path))[0] + else: + return SeqIO.read(path, "genbank") + else: + # Input is a file-like object + try: + return SeqIO.read(path, "genbank") + except: + path.seek(0) + return list(GFF.parse(path))[0] + + +def annotate_biopython_record( + seqrecord, location="full", feature_type="misc_feature", margin=0, **qualifiers +): + """Add a feature to a Biopython SeqRecord. + + Parameters + ---------- + + seqrecord + The biopython seqrecord to be annotated. + + location + Either (start, end) or (start, end, strand). (strand defaults to +1) + + feature_type + The type associated with the feature + + margin + Number of extra bases added on each side of the given location. + + qualifiers + Dictionnary that will be the Biopython feature's `qualifiers` attribute. + """ + if location == "full": + location = (margin, len(seqrecord) - margin) + + strand = location[2] if len(location) == 3 else 1 + seqrecord.features.append( + SeqFeature( + FeatureLocation(location[0], location[1], strand), + qualifiers=qualifiers, + type=feature_type, + ) + ) + + +def find_narrowest_text_wrap(text, max_line_length): + """Wrap the text into a multi-line text minimizing the longest line length. + + This is done by first wrapping the text using max_line_length, then + attempt new wraps by iteratively decreasing the line_length, as long as the + number of lines stays the same as with max_line_length. + """ + narrowest_wrap = textwrap.wrap(text, max_line_length) + narrowest_width = max([len(l) for l in narrowest_wrap]) + for line_length in range(max_line_length - 1, 0, -1): + wrap = textwrap.wrap(text, line_length) + if len(wrap) <= len(narrowest_wrap): + width = max([len(l) for l in wrap]) + if width < narrowest_width: + narrowest_wrap = wrap + narrowest_width = width + else: + break + return "\n".join(narrowest_wrap) |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/compute_features_levels.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/compute_features_levels.py Mon Jun 05 02:45:31 2023 +0000 |
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| @@ -0,0 +1,72 @@ +"""Implements the method used for deciding which feature goes to which level +when plotting.""" + +import itertools +import math + + +class Graph: + """Minimal implementation of non-directional graphs. + + Parameters + ---------- + + nodes + A list of objects. They must be hashable + edges + A list of the form [(n1,n2), (n3,n4)...] where (n1, n2) represents + an edge between nodes n1 and n2 + """ + + def __init__(self, nodes, edges): + self.nodes = nodes + self.neighbors = {n: [] for n in nodes} + for n1, n2 in edges: + self.neighbors[n1].append(n2) + self.neighbors[n2].append(n1) + + +def compute_features_levels(features): + """Compute the vertical levels on which the features should be displayed + in order to avoid collisions. + + `features` must be a list of `dna_features_viewer.GraphicFeature`. + + The method used is basically a graph coloring: + - The nodes of the graph are features and they will be colored with a level + - Two nodes are neighbors if and only if their features's locations overlap + - Levels are attributed to nodes iteratively starting with the nodes + corresponding to the largest features. + - A node receives the lowest level (starting at 0) that is not already + the level of one of its neighbors. + """ + edges = [ + (f1, f2) + for f1, f2 in itertools.combinations(features, 2) + if f1.overlaps_with(f2) + ] + graph = Graph(features, edges) + levels = {n: n.data.get("fixed_level", None) for n in graph.nodes} + + def collision(node, level): + """Return whether the node placed at base_level collides with its + neighbors in the graph.""" + line_factor = 0.5 + nlines = node.data.get("nlines", 1) + for neighbor in graph.neighbors[node]: + neighbor_level = levels[neighbor] + if neighbor_level is None: + continue + neighbor_lines = neighbor.data.get("nlines", 1) + min_distance = line_factor * (nlines + neighbor_lines) + if abs(level - neighbor_level) < min_distance: + return True + return False + + for node in sorted(graph.nodes, key=lambda f: -f.length): + if levels[node] is None: + level = 0 + while collision(node, level): + level += 0.5 + levels[node] = level + return levels |
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| diff -r 621754dd31f8 -r e923c686ead9 dna_features_viewer/version.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dna_features_viewer/version.py Mon Jun 05 02:45:31 2023 +0000 |
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| @@ -0,0 +1,1 @@ +__version__ = "3.0.1" |
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| diff -r 621754dd31f8 -r e923c686ead9 linear_genome_plot.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/linear_genome_plot.py Mon Jun 05 02:45:31 2023 +0000 |
| [ |
| b'@@ -0,0 +1,396 @@\n+#!/usr/bin/env python\n+from Bio import SeqIO\n+from dna_features_viewer import BiopythonTranslator, GraphicRecord\n+from matplotlib import rc_context\n+import matplotlib\n+import matplotlib.pyplot as plt\n+from itertools import cycle\n+import re\n+import sys\n+import argparse\n+\n+\n+class CPTTranslator(BiopythonTranslator):\n+ """\n+ This is a customized translator from the dna_features_viewer module to fit Galaxy\n+ """\n+\n+ global custom_feature_colors\n+ global box_status\n+ global label_fields\n+ global custom_name_colors\n+ global ignored_features_types\n+ global ignored_gene_labels\n+ global ignored_feature_labels\n+\n+ def compute_feature_color(self, feature):\n+ if feature.type == "CDS":\n+ if "product" in feature.qualifiers:\n+ color_specific = any(\n+ re.search(\n+ ("(\\\\b" + str(item) + "\\\\b)"), feature.qualifiers["product"][0]\n+ )\n+ for item in custom_name_colors.keys()\n+ ) or any(\n+ re.search((item), feature.qualifiers["product"][0])\n+ for item in custom_name_colors.keys()\n+ )\n+ if color_specific:\n+ try:\n+ return custom_name_colors[feature.qualifiers["product"][0]]\n+ except KeyError:\n+ for item in custom_name_colors.keys():\n+ if item in feature.qualifiers["product"][0]:\n+ custom_name_colors[\n+ feature.qualifiers["product"][0]\n+ ] = custom_name_colors[item]\n+ return custom_name_colors[\n+ feature.qualifiers["product"][0]\n+ ]\n+ # print(feature.qualifiers["product"][0])\n+ else:\n+ try:\n+ return custom_feature_colors[feature.type]\n+ except KeyError:\n+ return BiopythonTranslator.compute_feature_color(self, feature)\n+ else:\n+ if feature.type not in ignored_features_types:\n+ try:\n+ return custom_feature_colors[feature.type]\n+ except KeyError:\n+ return BiopythonTranslator.compute_feature_color(self, feature)\n+\n+ def compute_feature_label(self, feature): # remove the chop_blocks\n+ self.label_fields = label_fields\n+ if feature.type == "CDS":\n+ if "product" in feature.qualifiers:\n+ if ignored_gene_labels: # product name drop\n+ verify_chops = any(\n+ re.search(\n+ ("(\\\\b" + str(item) + "\\\\b)"),\n+ feature.qualifiers["product"][0],\n+ )\n+ for item in ignored_gene_labels\n+ ) or any(\n+ re.search((item), feature.qualifiers["product"][0])\n+ for item in ignored_gene_labels\n+ )\n+ if verify_chops:\n+ return None\n+ else:\n+ return BiopythonTranslator.compute_feature_label(self, feature)\n+ else:\n+ return BiopythonTranslator.compute_feature_label(self, feature)\n+ elif feature.type in ignored_feature_labels:\n+ return None\n+ else:\n+ return BiopythonTranslator.compute_feature_label(self, feature)\n+\n+ def compute_filtered_features(self, features):\n+ return [\n+ feature\n+ for feature in features\n+ if feature.type not in ignored_features_types\n+ ]\n+\n+ def compute_feature_legend_text(self, feature):\n+ return feature.type\n+\n+ def compute_feature_'..b'd:\n+ ignored_features_types = str.split(args.common_features_excluded, ",")\n+ if args.features_excluded:\n+ ignored_features_types += str.split(args.features_excluded, ",")\n+ elif args.features_excluded:\n+ ignored_features_types = str.split(args.features_excluded, ",")\n+ else:\n+ ignored_features_types = False\n+\n+ print(ignored_features_types)\n+\n+ ## product labels\n+ if args.common_ignore_product_labels:\n+ ignored_gene_labels = str.split(args.common_ignore_product_labels, ",")\n+ if args.ignore_labeling:\n+ ignored_gene_labels += str.split(args.ignore_labeling, ",")\n+ elif args.ignore_labeling:\n+ ignored_gene_labels = str.split(args.ignore_labeling, ",")\n+ else:\n+ ignored_gene_labels = False\n+\n+ print(ignored_gene_labels)\n+\n+ if args.feature_label_order != [""]:\n+ label_fields = str.split(args.feature_label_order, ",")\n+\n+ # if ignored_gene_labels == [\'\']:\n+ # ignored_gene_labels = False\n+\n+ ## Ignored Labeling\n+ if args.common_ignore_feature_labels:\n+ ignored_feature_labels = str.split(args.common_ignore_feature_labels, ",")\n+ if args.ignored_feature_labels:\n+ ignored_feature_labels += str.split(args.ignored_feature_labels, ",")\n+ elif args.ignored_feature_labels:\n+ ignored_feature_labels = str.split(args.ignored_feature_labels, ",")\n+ else:\n+ ignored_feature_labels = False\n+\n+ print(ignored_feature_labels)\n+ ## Print Statements for Debugging\n+ # print(custom_feature_colors)\n+ # print(custom_name_colors)\n+ # print(ignored_features_types)\n+ # print(ignored_gene_labels)\n+ # print(label_fields)\n+\n+ ## Part III ; PLOT\n+ # Housekeeping\n+ rc_context(\n+ {\n+ "font.family": ["monospace"],\n+ }\n+ ) # courier-like\n+ matplotlib.use("Agg") # I think this has to be used...\n+\n+ if args.label_algo:\n+ lab_algo = True\n+ else:\n+ lab_algo = False\n+\n+ translator = CPTTranslator()\n+ graphic_record = translator.translate_record(genome)\n+\n+ with open("tmp.svg", "wb") as img:\n+ img.truncate(0)\n+ img.close()\n+\n+ if (\n+ args.sz and not args.multiline\n+ ): # if user is wanting to look at a subset region of the genome\n+ zoom_start, zoom_end = args.sz, args.ez\n+ cropped = graphic_record.crop((zoom_start, zoom_end))\n+ ax, _ = cropped.plot(\n+ figure_width=args.plot_width, annotate_inline=lab_algo, figure_height=None\n+ )\n+ if args.translation_on:\n+ crop_seq = (args.st - 1, args.et)\n+ cropped.plot_translation(\n+ ax,\n+ location=crop_seq,\n+ fontdict={"size": 8, "weight": "bold"},\n+ y_offset=1,\n+ )\n+ ax.set_title(args.title)\n+ # Galaxy specific shenanigans\n+ tmp_fig = "./tmp.svg"\n+ plt.savefig(tmp_fig)\n+ plt.close()\n+ elif args.multiline:\n+ if args.sz:\n+ zoom_start, zoom_end = args.sz, args.ez\n+ else:\n+ zoom_start, zoom_end = 1, graphic_record.sequence_length\n+ cropped = graphic_record.crop((zoom_start, zoom_end))\n+ ax, _ = cropped.plot_on_multiple_lines(\n+ figure_width=args.plot_width,\n+ annotate_inline=lab_algo,\n+ figure_height=None,\n+ nucl_per_line=args.nucl_per_line,\n+ plot_sequence=False,\n+ )\n+ # ax.set_title(args.title)\n+ tmp_fig = "./tmp.svg"\n+ plt.savefig(tmp_fig)\n+ plt.close()\n+ else:\n+ ax, _ = graphic_record.plot(\n+ figure_width=args.plot_width, annotate_inline=lab_algo\n+ )\n+ ax.set_title(args.title)\n+ tmp_fig = "./tmp.svg"\n+ # Galaxy specific shenanigans\n+ plt.savefig(tmp_fig)\n+ plt.close()\n+ with open("tmp.svg", "rb") as img:\n+ for line in img:\n+ args.out_img.write(line)\n' |
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| diff -r 621754dd31f8 -r e923c686ead9 linear_genome_plot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/linear_genome_plot.xml Mon Jun 05 02:45:31 2023 +0000 |
| [ |
| b'@@ -0,0 +1,292 @@\n+<tool id="edu.tamu.cpt.genome_viz.linear_genome_plot" name="Linear Genome Plot" version="1.0">\n+ <description>Linear Genome Plot</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements">\n+ </expand>\n+ <command detect_errors="aggressive"><![CDATA[\n+python \'$__tool_directory__/linear_genome_plot.py\'\n+\'$input_file\'\n+--plot_width \'$plot_width\'\n+--common_features_excluded "$common_features_excluded"\n+--features_excluded "$features_excluded"\n+--common_ignore_feature_labels "$common_ignore_feature_labels"\n+--ignored_feature_labels "$ignored_feature_labels"\n+--common_ignore_product_labels "$common_ignore_product_labels"\n+--ignore_labeling "$ignore_labeling"\n+--feature_label_order "$feature_label_order"\n+--title "$title"\n+$label_algo\n+$label_box\n+#if $selectregion.custom_region:\n+ --sz \'$selectregion.start_zoom\'\n+ --ez \'$selectregion.end_zoom\'\n+#end if\n+#if $multiline.multi_line:\n+ --multiline\n+ --nucl_per_line \'$multiline.nucl_per_line\'\n+#end if\n+#for $feature_color in $feature_colors:\n+ #if $feature_color.feature_color_selector.feature_color_options == "add_colors":\n+ --feature_id #for $feat_id in $feature_color.feature_color_selector.feature_id:\n+ "${feat_id}" #end for\n+ --feature_id_color #for $feat_col in $feature_color.feature_color_selector.feature_id_color:\n+ "${feat_col}" #end for\n+ #end if\n+#end for\n+#for $gene_color in $gene_colors:\n+ #if $gene_color.gene_color_selector.gene_color_options == "add_colors":\n+ --gene_id #for $gene_id in $gene_color.gene_color_selector.gene_id:\n+ "${gene_id}" #end for\n+ --gene_id_color #for $gene_col in $gene_color.gene_color_selector.gene_id_color:\n+ "${gene_col}" #end for\n+ #end if\n+#end for\n+--file_stats \'$file_stats\'\n+--out_img \'$out_img\'\n+ ]]></command>\n+ <inputs>\n+ <param label="Annotated Genome File (Gbk)" name="input_file" type="data" format="genbank"/>\n+ <param label="Plot Width" name="plot_width" type="integer" value="10" help="Width of the plot. Increase for larger genomes."/>\n+ <param label="Box Label" name="label_box" type="boolean" checked="true" help="Select \'no\' to have no label box around feature labels" truevalue="--label_box" falsevalue=""/>\n+ <conditional name="selectregion">\n+ <param label="Select Custom Region" name="custom_region" type="boolean" checked="false" help="Plot a specific region of the genome"/>\n+ <when value="true">\n+ <param name="start_zoom" label="Start Zoom" type="integer" help="start zoom" optional="true"/>\n+ <param name="end_zoom" label="End Zoom" type="integer" help="end zoom" optional="true"/>\n+ </when>\n+ <when value="false">\n+ </when>\n+ </conditional>\n+ <conditional name="multiline">\n+ <param label="Multi Line Plot" name="multi_line" type="boolean" checked="false" help="Breaks up the plot into multiple lines"/>\n+ <when value="true">\n+ <param name="nucl_per_line" label="Nucleotides Per Line" type="integer" optional="true"/>\n+ </when>\n+ <when value="false">\n+ </when>\n+ </conditional>\n+ <param argument="common_features_excluded" label="Common Feature(s) to EXCLUDE" type="select" multiple="true" help="Common Features to be excluded from the plot">\n+ <option value="source" selected="true">source</option>\n+ <option value="gene" selected="true">gene</option>\n+ <option value="CDS">CDS</option>\n+ <option value="RBS">RBS</option>\n+ <option value="misc_feature">misc_feature</option>\n+ <option value="misc_difference">misc_difference</option>\n+ </param>\n+ <param label="Extra Feature(s) to EXCLUDE" name="features_excluded" type="text" optional="true" help="Feature(s) to exclude from plot (example'..b' features that are excluded. **"Extra Feature(s) to EXCLUDE"** is where you can pass one, or multiple, feature(s) to be excluded from the plot. Separate by commas with NO spaces.\n+\n+* Feature(s) label(s) to EXCLUDE :: The **"Common Feature(s) label(s) to EXCLUDE from labeling"** select menu has frequent labels from features that are excluded. Input specific features that you do not want to include in the **"Extra Feature(s) label(s) to EXCLUDE"**. Use this when you still want to plot the feature but not label it. A good sample case is if you are zoomed into a specific region and looking at overlapping genes but do not want to label all of the RBS sites. \n+\n+* Products(s) names label(s) to EXCLUDE :: The **"Common Product names to EXCLUDE from labeling"** select menu has frequent product names that are excluded. Input specific names that you do not want to include in the **"Extra Product(s) name label(s) to EXCLUDE"**. Any product with this name will NOT be labeled. It must be spelt, spaced, and capitalized exactly as it is within the file to be caught. However, if you wish to exclude labels with common patterns, say JX0101.orf01, you could pass "JX" to the input box and it will skip all names containing JX. Realize that passing something like protein will also eliminate labels such as DNA binding protein. Of note, if you choose to label by locus_tags, and want to skip over each, for example, hypothetical protein; the script will still pass their label and not label them.\n+\n+* Name ordering :: In case you want to customize the selection method of labeling genes by a specific feature, use this argument. "product" will use the product names from within the file. If you want to use product, and if there is no name, use locus_tag as the next name, pass the following: product,locus_tag.\n+\n+* Label algorithm dictates label placement :: DNA-features (the orginal python package) has a very nice spacing algorithm for deciding how to space and where to put the label. Selecting no will force ALL features to placed outside of their gene box. If more tuning is desired, a custom pixel control can be implemented as an argument (not currently implemented) to allow more user control for label placement within gene boxes.\n+\n+* Select Custom Region :: If you would like to zoom in and look at a specific region of select a start and end site to zoom in on. Values are based on Nucleotides.\n+\n+* Multiline :: Permits plotting of the genome across multiple lines. Select the amount of nucleotides per line you would like in the **"Nucleotides Per Line"** field. Smaller widths (which are recommended for multiline plots) and larger nucleotides per line will have faster compute times. This can also be combined with the custom region parameters.\n+\n+* Feature Colors :: Customizing Feature colors based on their exact name as listed in the file (check the output stats file for spelling).\n+\n+* Product Name Colors :: Customizing Product colors based on their exact name as listed in the file (check the output stats file for spelling). **NOW**, in addition to the exact name, general words can be used to grab similiarly named features. For example, if the genome has a two component spanin system (i-spanin + o-spanin), using "spanin" would change the color for both the i-spanin and o-spanin.\n+\n+**Output**\n+\n+* file_stats will output the different product names as well as the count of each respective feature\n+* svg output\n+\n+**Output Example**\n+\n+Using the zoom function and custom colors for various product names\n+\n+.. image:: $PATH_TO_IMAGES/sample.png\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">https://doi.org/10.1101/2020.01.09.900589</citation>\n+ <citation type="bibtex">\n+ @unpublished{galaxyTools,\n+ author = {C. Ross},\n+ title = {CPT Galaxy Tools},\n+ year = {2020-},\n+ note = {https://github.com/tamu-cpt/galaxy-tools/}\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 621754dd31f8 -r e923c686ead9 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jun 05 02:45:31 2023 +0000 |
| [ |
| @@ -0,0 +1,18 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.8.13">python</requirement> + <requirement type="package" version="1.77">biopython</requirement> + <requirement type="package" version="1.2.2">cpt_gffparser</requirement> + <requirement type="package" version="1.0.5">pandas</requirement> + <requirement type="package" version="3.3.2">matplotlib</requirement> + <!-- <requirement type="package" version="3.0.1">dna-features-viewer</requirement> --> + <yield/> + </requirements> + <version_command> + <![CDATA[ + cd '$__tool_directory__' && git rev-parse HEAD + ]]> + </version_command> + </xml> +</macros> |
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| diff -r 621754dd31f8 -r e923c686ead9 test-data/Mu50-profile.xml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mu50-profile.xml.xml Mon Jun 05 02:45:31 2023 +0000 |
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| @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<BRIG blastOptions="" legendPosition="upper-right"> + <cgview_settings arrowheadLength="medium" backboneColor="black" backboneRadius="600" backboneThickness="medium" backgroundColor="white" borderColor="black" featureSlotSpacing="medium" featureThickness="30" giveFeaturePositions="false" globalLabel="true" height="2500" isLinear="false" labelFont="SansSerif,plain,25" labelLineLength="medium" labelLineThickness="medium" labelPlacementQuality="best" labelsToKeep="1000" longTickColor="black" minimumFeatureLength="medium" moveInnerLabelsToOuter="true" origin="12" rulerFont="SansSerif,plain,35" rulerFontColor="black" rulerPadding="40" rulerUnits="bases" shortTickColor="black" shortTickThickness="medium" showBorder="true" showShading="true" showWarning="false" tickDensity="0.2333" tickThickness="medium" titleFont="SansSerif,plain,45" titleFontColor="black" useColoredLabelBackgrounds="false" useInnerLabels="true" warningFont="Default,plain,35" warningFontColor="black" width="2500" zeroTickColor="black" tickLength="medium" /> + <brig_settings Ring1="102,0,102" Ring2="0,102,102" Ring3="0,102,0" Ring4="0,0,153" Ring5="102,102,0" Ring6="0,153,0" Ring7="204,51,0" Ring8="0,102,102" Ring9="0,153,102" Ring10="204,0,51" defaultUpper="70" defaultLower="50" defaultMinimum="50" genbankFiles="gbk" fastaFiles="fna,faa,fas,fasta,fa" emblFiles="embl" blastLocation="" divider="3" multiplier="3" memory="1500" defaultSpacer="0" /> + <special value="GC Content" /> + <special value="GC Skew" /> +</BRIG> + |
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| diff -r 621754dd31f8 -r e923c686ead9 test-data/Mu50.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mu50.sam Mon Jun 05 02:45:31 2023 +0000 |
| b |
| b'@@ -0,0 +1,50001 @@\n+@SQ\tSN:S.aureusMu50-plasmid-AP003367.gbk\tLN:25107\n+r1.1\t4\t*\t0\t0\t*\t*\t0\t0\tGTTACCTCTTGCTCTAGTCTGATTCTAAACCTTTTTTTAGTTCTTTCGCTTAATAAGTTACCTCTAATTCAGCAAAACGCTACTCGATCATTGTAAAAAACATCTTTCCCATTGGGTCTTTTGTATTGATATTCATATCAATAATTTGTAATTCAATACTTATTATTTTCTAACCATTGGGCTAAATCTATCAGTTGCTTAGTAGTCCTGCCTAATCTATCTAGCTTGAAATAACTAAAGTGTCGCCTTCACGTAAATAATCTAAACTATTTATCTAGTTC\t*\n+r2.1\t4\t*\t0\t0\t*\t*\t0\t0\tTAAAAAAGAAAGTCTTTCCGTTTTTCTTAATAGTTATTAGGTTATTTCCGTATTGATCTGTTATAGAGCCATACACGGTATTATTGTCTTTATTTTTTATTCAATATTACTTTTAATTTTTTGTATTTGCTCATTGTATTGTTCTTGATTTTCTTTACTTTTAACTAAATAACACAAAGTTTTTAGCATCATTTTCAGATAAAGTTTCTTCTTTATTAGTATAACTTTTTAGCAATACTATTGTAGTCACTTATGTCTGTACTAATTTTTCAAATTCTTTAACGTTGTCCTTTAGCATTATTCAAACTGATTAAATAG\t*\n+r3.1\t4\t*\t0\t0\t*\t*\t0\t0\tGGTACGAAGATATATTAAATTGATTTTTGAATTTTTGAAAAAAGAAAGAAATAGCTAATGCAGTTACTTTTAGACCCTCATAAAAATAATCCAAGAGACAATAAGGGCATACCAAAAAATCTGGGTTTTAGAATTATTGAAGTATTGCCAGAACATGAATTACACGAGGGCAAAAAAGAAGATTGTTATTTAATGGAATATAGATATGATGATAATGCCACAAATGTTAAGGCAATGAAAATATTTAACTTGAGCATTACTTTGATAATTTCAAAGTAGATAG\t*\n+r4.1\t4\t*\t0\t0\t*\t*\t0\t0\tTAATCATCTAAATTAGTTAAGTTATAATCAAATTCAGAATCATACTAGTACTTATAATATGTGGTGTTTGATATTTTTTCGTTAGAATCGTCTAAATCATAAACTGGTTGAGTATACACTTCGTTATAGAAATTATTTTCTACTAGACGTAAACTTACCTACTATCGCTTTTTATTAGTACATATCTCTTTGATCATTCATTTGTTTATCACTTGCTGGCACAAAATAAAATTCAGAATTTAGTTCATAATCGGTGTTGTTCAAAAATTTCCTCGGGGTGTAA\t*\n+r5.1\t4\t*\t0\t0\t*\t*\t0\t0\tTATAAATGTTTTCTTTAAACCAAAGCTAATTTACCACATTGGGTTAAGTTTCTTATTATTAAAGAAGAACTTTGTATGATTTCAACTGCTTACTATCTTCTCATTTGGTTATTTCTCTCTTGTTTCTTCTTCTTTTTCTAGATGATTAATATTGTTTTGCTTTTCAGTTTCGTTCGCATAGTACATAAGAAAGTCACTAGCATTTATCGTTGGTAAATTAATGTGATTAGTTTGTTCATTTTCATGTTCAATACGATTGTCATGTATCATTTCTATCTACG\t*\n+r6.1\t4\t*\t0\t0\t*\t*\t0\t0\tAGAATAATTGTATAACACAATACAGCCATTTAAATTTCGCAAGATTTTTTGTTGTAATATGTAAAAAAAATAGATTATAATCCTTATAGACCGATCGCACGGTCTATAAGGATTGGAGGGGAACTTAAATGATTTCATTTTTTACAAAAACTACTGATATGATGACATCAAAAAAAAGATGGACTGCACTAGTAGTATTAGCTGTTAGTTTGTTTGTTGTTACAATAGGATATGACAATATTAATTATGGCTTTACCGGAATTAGTAAGAGAGTTAGAGCCTTC\t*\n+r7.1\t4\t*\t0\t0\t*\t*\t0\t0\tAAATGAGAGAATAATTTTCTAAATTCATTACGCTTTTGGGTATCGAAAAATCACTAAGATGTATATCGAGTAATTTTTTCAAAAAAAACATCAATTTTGCTCTTGTGCTCTTTGAGCCAAACGTCGCAAACTTTTCCAACTTCTCTATTAGATATTACTTTAATAAGGTTTGGGTCTATATATTGAAGAGTGTCTTCTTCAATAGAAATATTTAAATAATCAGTTGATTAGCATCATGATTGAATTTGGTACATACTAGTGTCACTCATA\t*\n+r8.1\t4\t*\t0\t0\t*\t*\t0\t0\tTCATGTAACTTAAAAAATAGATGAAAGTTGCTACTTAGTGCTCCTAAAAATATAGTTATAGTTAAGTTCTACATCAAATATTTTAAAAATATCTGCTCTATTCATCAGTTAATCACTCCTTTCAAGGTTTATTAATACTAATAAATTATTAGATATAGGTATATCATATTATTAATTTAAGAAAATTGTCTTTATAATTTTACTTAATAATAAAAAAGTAGAACCATTTAAATTAATGGTTCTACTTTTTTAACTAGTTACTAATTTTAAAAATAAACGTAATCTACAATATCTAAAAATATATGTTTAGTAC\t*\n+r9.1\t4\t*\t0\t0\t*\t*\t0\t0\tTATTGGTTATGCTCGTGTATCTACCAGAGATCAAAGTTTAGATTTACAAATAGACGCTTTTGAGTAATTTTCGGTTGTGAGAAAATATTTAGCGAAAAACGTTAGTGGGCGTAAAGTAAATAGAACTGAACTAGATAAATGTTTAGATTATTTACTGAAGGCGACACTTTAGTTATTTTACAAGCGTAGATAGATTAGGCAGGACTACTAAGCAACTGATAGATTTAGCCCAATGGTTAGAAATAATAATTATTGAATTACAAATTATTGATATGAATATCAA\t*\n+r10.1\t4\t*\t0\t0\t*\t*\t0\t0\tAAACTCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGCGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATACTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATAGCCAAGTCGCTTAATTGGTAGCCGTTCTTATGGACCTACATGATAGAA\t*\n+r11.1\t4\t*\t0\t0\t*\t*\t0\t0\tTACTTTGAAATTATCTAAAGTAATGCTCAATTAAATATTTTCATTGCCTTAACGATTTGTGGTGATTATCATCATATCTATATTCCTACGTTAAATAACAATCTTCTTTTTTGCCCTCGTGTAATTCATGTTCTGGCAAATACTTCAATTAATTCTAAAACCAGATTTTTGGTATGCCTTATTGCTCTTGGATTATTTTTATGAGGGTCTAAAATAACTGCATTAGCATTTCTTTTCTTTTTTCAAAAATTCAAAAATCAATTTAATATATCTTGTACCAATTCCTTTAC\t*\n+r12.1\t4\t*\t0\t0\t*\t*\t0\t0\tCAGATATTATTCCATGGGTTGTAATAGTATTAGCTAATTTACCATATAGTGATATTTGTTAAACGTAAGTTTATCGAAGTTCTGATCCAATGTTAGACGTAAGACTTTTTAAAAAGAGATCATTTTCAGCTGGTACAATTGCTGCATTTAATGACAATGTTTGCAATGGCATCTGTTTTGTTATTAGCTTCACAATCGGTTACAGGTTGTGGAAGAACTTTCTCCTTTTAAAGCTGGCTTATACCTATTACCTATGGCAATAGGAGA\t*\n+r13.1\t4\t*\t0\t0\t*\t*\t0\t0\tAGCTTCTAATTCACAACTTTTTCTTTATAAATTGCACTATTTTTTGGCTTGTGGATTTACTTTTGAGCCTTTTGGTATTTCTGAACATAAACATTTTTAATACCTTTTAAATCATTTCTTGTAGATATTAACTGATACCAAACTCGTGCATATTCAATTTCTTTCGAGTTTAAAAATTATTTAAGTAACTTTTATT'..b'GAATTTTGAACAACACCGATTATGAACTAAATTCTGAATTTTATTATGTGCCAGCAAGTGATAAACTAAATGAATGATCAAAGAGATATGACTAATAAAAGACATAGTAGGTAATTTAGTCTATAGAAATAATTTCTATAACGAAGTGTATACTCGAACCAGTTTAGTGATTTAGACGATTCTAACG\t*\n+r49989.1\t4\t*\t0\t0\t*\t*\t0\t0\tAATGAATGTAAGGCCTCAACTTCTATTAACTACGCCATATCTCTGATAAATGTTTTCGTAAATACTTATTTCTGATCGCCCAACTAACCTAAACTGAATAAATGCTGTAATATCAGTGTTGTATACCACTATAAGAAGGGCTATCATTCTCTGGAAATTGTTGTATATGAATATAAAATTCATTTTTAGGGGAATATGTTTATCATTTTATTAGAGAAGTTACGACTAAACACATCTGTTTTATTAGTTAAAAGCCATACCAATAAAATGATTTCTAG\t*\n+r49990.1\t4\t*\t0\t0\t*\t*\t0\t0\tATGATGAGTGCATTCGTGAACTTGAAGCTAATTTATTAAGTGAACGAACTAAAAAAGGTTTAGGAAAGCTGCAAGAGCAAGAGGGAGAAAAGGTGGAAGACCTTCACTACCAGATCATAAGAAAAGAGAGATCAAATTCGTTATATGATGAACAAAAGCTGTCTGGTGAAGAAATTGCTGAACAAACAGGAGTGAGTCGTTACTACTGTATATTAGGATTATTAAAGAGTCTAAGAAAAATATAAAGTACTAAATTAAAGTTTTAATATACCCTTTAATTG\t*\n+r49991.1\t4\t*\t0\t0\t*\t*\t0\t0\tAAGAGGCGTAATATACGCCTCCTTAAAACAATATAATGTGTTTTGTATCTCTATAGTTGTTTCTTTCCGGCAGTATTAATTTTTATATCTGCGCCGACAACGCCGATTCTAGTTCGTGCAGTATTAATTTTTATATCTGCGCCACAACGCCGATTCTAGTTCGTGTAGTATTAATTTTTATATCGTGACGCCACAACGCCGATTCTTTTCTTCTTATATTATATCAATACCTGTCATGTTATGCAATGTTTAGGATTACTTTTTAAACTCTCGGAAAA\t*\n+r49992.1\t4\t*\t0\t0\t*\t*\t0\t0\tCGATAATTGGTCCAAAAACAGCACCTATCATGAAGCGATTGACATACTAGCGTAATGCAGTGGCCCTTTTTTAGGTTTTCAAAAATTACTCTTATCATTGAAAAGAGTAGTTGGCGATTATTAAAGCACCTGAATACCTAAGTAAAAATCGAATAGCTATTACGAACTCGTGCACTTTCTGCGAAAAAATATAGCTAATGAAACGAGGCCAAATAAAGCAAATCCAGTTAAAAATGCTTTTTTTCTTCCCCATTTTATCAGCAAAGGCACTCAA\t*\n+r49993.1\t4\t*\t0\t0\t*\t*\t0\t0\tATGTCCAATTTTTGTTTCCAAATTATTTTTCTCCTTAACTTTAAGACTATATTTAAACTCAATTTTTTCTATCGATATTTATGAACATTAGTATTTTTTTATGCGAAATACCTGTGAACAATCGCATAATTCAAAGGTTTTTCTATAATTATACACGTTTTAAAATACATTGTGATAATACATAGAATGTACCTTATCTAAGTATATAAATGTTTTCTTTAAACCAAAGCTAATTACCACATTGGGTTAAGTTTCTTATTAATTAAAGAATGAACTTTGTATGATTCAACTGCGTTACTA\t*\n+r49994.1\t4\t*\t0\t0\t*\t*\t0\t0\tTTTCACTTTTTTTGAATTAATCGTACGCTTTAAAACGCTTAAGAACATTAACAATTTCAAATTCCATATCTTCTAATAAATAATATGCATCAATAGAATTGTTGAAGGATGTTTTGGCTTTTAATAACACAGATTAATAAGTTAATTTCAGAGTACAGAAAAGTTACTTAAATAACTTGAATACTTTGTGGTAGTTCTTCAAGTAATTGAAATTTTAAAGCTTCATCATTGAATTTGAATAGTAGTGTATTTGAATGATTTGTATGATTACTAGAATATGTTAATTTCTA\t*\n+r49995.1\t4\t*\t0\t0\t*\t*\t0\t0\tCATTCATTTCTCTTTTGAATATTATTTCTATCTATAATCTAACTCGTCTTCGGTATAAAAACATTGTAACTTGGCATAACATTGTTTAACTGGTTCTGTTGCAAAGTTGAATTTATAGTATAATTTTAACAAAAAGGAGTCTTCTGTATGAACTATTTCAGATAATAAACAATTTAACAAGGATGTTATCACTGTAGCGGTGGCTACTATCTAAGATATGCATTGAGTTATCGTGATATATCTGAAATATTAAGGGAACGTGGTGTCAACG\t*\n+r49996.1\t4\t*\t0\t0\t*\t*\t0\t0\tTTATATCTTCTAATTTGTTCATTTTTCTAGTCCGTAATAAGTAACGGGTTGGTACTCGACTACCCTCTTTTTCACAGCGTTTTCTTTCATTTTAGTTTCTAATCTATATTCTTCTCTTGTAAGTGGAATTTCGGCAATTTTTTCTAAACCTTCGCGCTTCAAAAGAACGACTATCATATCGTCTTAAACTTTGTTCGACGTTCTGAGTATTGATTTAATTTTAATTCCCAATGCTTACGAACTTACTTTGAAATCAAAGTCGGCAAATCGTTCTTGTTTTCTAACTTTATTAACCATTTTTATTTAAAATCGCATTGCC\t*\n+r49997.1\t4\t*\t0\t0\t*\t*\t0\t0\tAAATTAAGCATCATGCTAGCAGTTTAAGCGAACACTGACATGATAAATTAGTGGGTTGCTATACTTTTTTACTTTGCAACAGAACCAAACTAAAAGATAAAATAACATCTTGGCTTGATAAAGATAACAACTAAAAACGAATAATATAGGAGGGGTTTTTTGGGGAACTTTAGATTTTGATCACGAAGGATACAGAAAACTATTACCATTAAAAGATTTCAAACATTTTACTAAAACATAGCGACAGCAAGACTAGAAATCATTTTATTGGTAGTGGCTTTTAATAATAAAACAGA\t*\n+r49998.1\t4\t*\t0\t0\t*\t*\t0\t0\tCATTTATTCAGTTTAGGTTAGTTGGGCGTCAGAAAATAAGTATTTAGAAAACATTATCAGAGATTATGGCGTATTAATAGAAGTTGAGGACCTTAACATTCATTTAAAAAAGGTATGGGGGCAATGCTTGTAAGTCAATTGGAAAAGTTATCAGATAAACTGTTTATACCTATATATCTTTATGATACTAATTTAAAAGATGAATTATATTATCAAGACTTAGGATTCTTTGATACTACTAAAAAAGGGAATCATGGAGAACCACTTTTAGTATATAAACCTAAAAATCTAG\t*\n+r49999.1\t4\t*\t0\t0\t*\t*\t0\t0\tCATATTACGAACAAAAAAATCTTCGCGAAATTTAAATGGCTGTATTGTGTTATACAATTATTCTTTTGAATTTTTTGTGCTATCATTGATAGTACTTAATACTCATTAAAGGCGTGATGAACTTGAAAGATAAAAATACGTAGGTGTCGCAAAGGGAATTATTTATAAAAAATGGATATAATGCCACTACTACTGGAGAAATTGTTAAATTATCAGAAAGTAGTAAAGGGAATCTTTATTATCACTTTAAAACAAAAGAAAACTATTTTTTAGAAATTTTAAATATAGAAGAATCTAAATGG\t*\n+r50000.1\t4\t*\t0\t0\t*\t*\t0\t0\tTGCAAGGCTGAACTAACAATGGTGGCATTAGATAGTGATGAACTTGATTCATTACTTTATATGCTAGTTACATGGAACGTTATGCTATCTTTTGAACTAATGATAAAAAAAGACGCCTAATTTTAGGCGCCTTTTTAACTAATCTACTAACTAACTTATTATATCTAATTTTACTTGCTAACTTAGCTACTGTTTTATTGTCGTAGGGTTTAATATAGACTCGTTTCATATTCTCCTCTATTGCTTTTTTTGTTATCTTATTCATTTGACTATAATCGAC\t*\n' |
| b |
| diff -r 621754dd31f8 -r e923c686ead9 test-data/mga.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mga.fa Mon Jun 05 02:45:31 2023 +0000 |
| b |
| b'@@ -0,0 +1,2300 @@\n+>01\n+TACTACTATTACTACTACTAAGTACCTTTGTTATGTACTACTATTACTACTACTATTACT\n+ACTACTATTACTATTACTACTACTATTACTACTACTATTACTACTACTATTACTACTACT\n+ATTACTACTACTACTAAGTACCTGGGAATTCTTTTACCTCTCTCACTCAGCCTATTACTT\n+ATTACCGACTTCCCTAACTACTTATTCTATAGTTATAATATTCATTTATTATACAATACT\n+TAAACTATAGTATTCTACTGTTAATCTATGCTGAAGCGGTCTTAATCTATGGTTATTATA\n+TAATAATCTTATATAATGGTACATTAATCTAGTATATTACATTAGAATCATTCTAATCTA\n+GGATTTTAATCTTTAGACCCTAGGAAAAGTGGTACTAAAATATAAAACCCTATAGGTATG\n+GGATTCTTATTTTTAAAATTACTAAAAAGTATTAGGTTTTCCCTAGGGCAAAGTTTTAAT\n+GTACTTAAAATAGTAAGTAGCTACTTATCATTTAGGGTTCTATAATTGAGAATATTGAGA\n+GATAATCCGCTTCAATTGTAATTAATTGTTGACAACTATGAAGCGGGTATGCTATAATTA\n+GGTATAGTCAAATTTAGGAGATGAAATAGATGATTGATATATACTTAGGAGAAGGTTATA\n+ATAAAGAATACTTGTCTAAAGCACTCAGATTAATCAATGACCATGCTCCTAGGGAGTTAA\n+GTTATGATTTTAATAATGTAGAAGCGGATGTTAATATTCACACAATGTTATATGTTAAAC\n+CTGAAGATAGATTTATATATAAGGATATATCCTATTACTTCCCGGGTGATTTAATTATTT\n+GTATAGTTGATGATGATGCTATTGTATACCACCAAGGTGAGCAGATTTCAGGTATTAGTA\n+TTTTAAGAATACTAGAAGAGATATTTTAAGGAGGATAAGTAATCATGATAGGAATAACAA\n+TATTAATTACGATAATGAGTATATCAACTATCTCTATGTATATTTATTTTTTAGTAGACT\n+TGATTCAGTCAATCAGATATAATAGTTTTGATAAGGTAATTAACGTCATAACATTTGTAC\n+TTATGACAGTTATAATAGCATCAGGTATTTTAGCTATACTTGGAATATAGAGCTCATTTA\n+AGAAGCGGTTAAGTAGTTAGAGGGGATTTGTCCTAAAATAGTATACCGCTTCTATATGGA\n+AGGCTGAGAGGTCTTAGAATTGAAAGGAGAGATATAATGATTCATATATTTGTAAAAGAG\n+GATTATAATAAAGAAACATTAAGGAGTTTACTTGAGTATATTAATGATACTGTAGGTAGG\n+GAATTAACTTATGGTATTAATACAGACTATGATAAGGATGTCGTGATTGAAACCGATGAC\n+CCTATAGATGAGGAGGATACAATTGAGTTATCAGGTACAAACATGTTCAAGGATGACTTA\n+TGTATTCTTATAGAAGAGCTATACTGTAAGGCATTTGTTAATGGTGAACCTGTTATTATA\n+CGTAAGTATGTAGAGGAGATGTTATAATGATTATAATATTTTTAACTGAAAAATATGATG\n+CCAAGGCTTTAAAGAAAGTATTAGAACATATTGATAATTGTAGTAGTAGAGGTCTTAGCT\n+ATTTAATGGGAAAAGGAGAAGCGGATGTATGTATAGAGAAAAATGTATTTAGAGAAAGAG\n+ATGATGTAAGGATTAACTCAAACATTATTGATGAAGGTAAACTTTGTATACTAATAAATA\n+GACATGGTTTAGAATGTAGCTACTATAGAGGTATATCATGTAATATTGGTTCCTTCGTAA\n+AGGAGAGATTATAATGATAGAGATATACCTTAGTGAAAATTATGATAAGAATTTACTAAA\n+AGCAGAATTAAAATGGATTAAAGAGACCGCTTCAAGAGAACTAACTTATGATGTTAATAG\n+AAGTCCAGGATTGGATGTTTATGTTAATCCCTATAGGTGTACTAAAGACGAAGTTGAAGA\n+ATGGAGTACACTTCCTCCATTTGAAGATGATATACTTGTATTTATAGCGGAGACGTGGAT\n+ACATGAATATCTTAAGGGTGAATCAATAGGTGTAGATAGTATGGAAGAGTATGTAAAGGA\n+GATGTAACTAATGTTTAAGGTATATTATACAGTCTACCATAGAGGTAGTATGAAAACTAT\n+TAAGGATAAGCTAGATAGAAGTAGTTTAATATACTTCTTGTATGATACTTGGTATAAAGA\n+TATTAGTAACGTATTCCCTAATCACTATAATAAAGAGTTTGGGAGTAAGAGTGATGATAT\n+AGATATAGATAAACTTATTGAAGCGGTTAATGAGGAAGGTATATTACTTATCAATAGAGG\n+TAATTATGTTACAATAAGAGAATGGTAGGATAGGATAAACTTAGGATAGAAAATAATTTA\n+GGATGAGTTACAATAGGATAGGATAGGATAGGGGGTTAAGTTAGGATGGATACTTTAACA\n+TACACTATTATTCATAAAGAATCTGATAGGGTAATAGCTAGCGGTTTAAATGAGACAGAA\n+ACTATGAACTTAGTTCAAAGGATGATAAATACTAATCTAGTTACTGATATATCATTAGAT\n+GATTATAAACGCAGACCACATGGAAAGATAGATGTAGTCAATTTACTAGTAGATATTAGA\n+AGACAAGGCGTATTTGATTTCAATCACATTTGGCACGTAGGATAGGAGGGATAGGATGAT\n+AGTTATATATACAGATGTTTCTAAGGATTATTTAAAAGACGAGTTCTTACCTTGGCTTAA\n+TGAAAGGGATAGATACTTAGAATACTATAAAGATGAATTACCTGAGGATATAGATTCCTC\n+TTATATTGTATCAGTTGTATACTGTAAGGATATGGAAGGTCTATTAGAAAGAAAAGACAT\n+TGTTCTTGATAATAGTTATAATGAACCTGTAGCTTTATTAGGTGTTCCTGAGTTTTTTGG\n+TAATTATAGTAATTATTTCTATTATAGAGGAGAAAGTATTAGTAAACATGACCTAGGAGA\n+AATTGTTAGGTTAAAAGCTTGGCAACGTATGGGTGGGGATTGACTAAGTAGCTCTCCCTA\n+ATTTCACTAAGTAGCTCCCTAGGAATTGCCTAAGTAGCTCGGTATGATTTTACCCTAAGT\n+AGCTCCCTCTGTTTTCTACTAGTTTATTTTAACCGCTTCAGGTGTCTATATATATATAGA\n+CGGTTGGAATAATATCAGACCGCAAAAATAAATACACTAGGATATTATTCCTAGTGTATT\n+ATATAATTTTTTTATAGAATATTTATAACATTGTATTCAAATTCATTTACTTCATGTTGT\n+GATTTAATTAAATTTTTAATTAATCCGTTTTGTGTTTTATACTCTTTTATTAGTTTTTCA\n+TTTTCTATAATTAAATTATTAAATTCTTCTTTTGTTGTTTCCTCATCTACATAAAATTTA\n+CTTTCATATATTTCATAATATTTTTTATCTGTTCCGCCATCTAAATCATCTGATATTTGA\n+TAATTTTTGAATATAATTTCTTTTGTTTCTAATTCATTTACTAATAATTGTGATTTTGCA\n+TATTGTAATACATCTTCATTGTCCCACATTGGAATATAGTTTATTTTCATTTAAATCAAA\n+TCCTTTTCTTATAATTTTTTTATATAATATTTGTAGAAGCGGTTGGGGTTTGTCCCTTGC\n+CTTACTACACTTTATATATTACAGTATAGTTATTCAGAAGTCAATACTTTTGAGTAACTT\n+TTTTTAAATTCTTTTTTCTTCTATATAATAGTAGTTTTTAGCCCTAAAAATGTTTTTAAA\n+AGAATTTGCATTTTCTTATTGACTTTATTATCATATGGTAGTAATATAAAGGTACAGCAA\n+GGGAAC'..b'ACTTTTGGGGT\n+AATATGACTAAAACTTTACCTAGATTAAAGGATATTATTATGGAACGTAATGGTAAAGTA\n+GTAATCAGACCTGATAGTGGAGACCCTGTTAAAATTATTTGCGGAGACCCTGATGCAGAC\n+ACTGAATATGAACGTAAAGGTGCAGTAGAAGTGCTTTGGGATACATTTGGAGGTACTGAA\n+ACTGAAAAAGGGTACAAAGTATTAGATGAACATGTAGGATTAATTTATGGAGACTCTATT\n+AACTATGAACGTGCTCAACAAATTTGTGAAGGATTAAAAGAAAAAGGTTTTGCAAGTATT\n+AATGTTGTATTAGGTGTAGGTAGTTTCTCTTACCAATTTAATACTCGTGATACCCACGGG\n+TTTGCAATCAAAGCAACGTATGCTAAGATTAAAAATGAAGAAAAACTTATCTATAAAAAT\n+CCTAAAACAGATAGTGGTAAACGTTCACATAAAGGTCGAGTAGCTGTATATAAAGACGGT\n+TCATGGGAAGATAACTTAACCTTACATCAATGGCTAAACAAACAAAATGTTAATCAATTA\n+GAAAGAGTATTTGAAGATGGTAAACTTTATAGAGACCAGTCGTTAAGTGAAATTAGAGAA\n+ATAATTAAAAATAATTAATAAATATTTAAACTCCCTATTGACAAAGGGAGTTTTTTATTA\n+TATAGTAGGGCTATAGTAAATAAAGGAGTGAAAGAAATGATTTATAAAATATCAAAACAT\n+AATTACTATAGTAGATTTGAGCATTCCACTTATCCTCCTGATGAGGGGTTTGCGTATGTA\n+GATTATGTAGATGTGATTCTTATTGGTGTAGATAATCCTAGGAAAAGAAAGATTATTACC\n+TTAAAAGTAAATGAGTTCAACCCGGATGACTACAGAGTAGGTCATAAGTACAATATTATA\n+AAAATACTATGGTTTGAAAAATGGGAATGGTTAAAGCCATAAGTAAAAGGAGAGAAATAA\n+AATGATTATAGATAAATTAAATGGAGTTAAATTAGAAATAGGTGGGCATGTCGTATCATT\n+TAGTGTAAGAAAGTTTAATACAATTAATGGTGAGAGACAATTAATAGACTACCATCATAT\n+TAAAAGAAATAGACAACAGTACTTTAGAACTACTGAAGAATTTTATAATGAATATAAAGA\n+AATTAAGCCTGACAAAAATGAAATAGATGAAATGTTTGAATCTCTAGGTTATGTAGATAC\n+TGAGTTAGATGATGTAGTAAGAAACCAGGAAAAGGTTACTGAAATATTAGGAGTTAGTGA\n+ACAATATTTAAATCAGTTATCTTATAAAGCTATAGAGGAGTATGTAGATAAAGTAGTTAC\n+ACTTGAAATTAAAGAGTTGAAAGGAGAGAAATAGCATGAATAATAACTGGGAAAAAGAAG\n+GAGTTAACTATTGGGAAAACGAAGACTGTCCTAGGGAATACTTAGAGAAAGCATTCATTG\n+ACCTGGTAGAATATGTTGAAGGAGTTACAGTACCACCTAAAGATGTTAAGCAGTTAAGAG\n+AAGATAAACTTAGAGAAGATATTGGGTTTTATGAGTACGTAGCTGATAAATAAATTAGTA\n+TCTACCTATTGACTTAGGTAGGTATCTATTATATAATAGTATACAAGGAGATGAAAATAT\n+GAAAAAGTTAATAGTATTACTTACAATTACTATTTCTCTATTACTAGGGGGTTGCTCTCC\n+TGATAACCATGAAGGTAAAGTAGTAGGAGTAGGTGAATACAGAGAACCAACTACTTATAT\n+AAAATCAGGTAGCGTTACTGTACCAGTCATTGGTGAAATGAAATACTATGTAGATTTAGA\n+GACAGATAAAGGAGAAGACCGTGTATATCTTAATAAAGAGGTCTATCATAAGTTTGATAA\n+AGGTGATGATTTCTCTAATGTAGGTGAGAAAGTGTATAAGAATGATGAATTAATATATAA\n+AGGAGACTAACTATGTATTTAAATGATTATGTAGGTAAATTTATAAAGGAAGATAACTAT\n+TATGGATATCAATCTACAGACTTAGTATCTAATTATGTTCAACGATTAACTCTAGGTAGG\n+TACAAAACTAAGTTAAATGCTAATAAAATGAAATACGAAAGATTACCTAGTTCTTGGAAA\n+ATAATTAAAGCCAAAGATTTGTTAAGAACAGATGATTATAGAGAAGGAGATATATTTGTA\n+TCAGAAAGAATCTCCGTATTCGGTTTTAATGGTATTATTGTATATAACCATGATTTTAAC\n+AATGTAACTGTTATTACTCAAAATAGAGATGGTAAAGCTACTAATCCTGTAGAGGAGCAT\n+TTATATCCAAAGAAAGATATTGATTATATTATTAGACCTATCGAGAGGGACTACAGGGAA\n+TACTTTAAAAAATCAGATTCAAAAGAAAAAGTTACTCTTTCGAAGCAAGAATATAAAAAA\n+TTATTAGAGGCTTATAATAAAATGAAGGAAGTGTTTAAGTAATATGAATAGTACAAAATT\n+AGTAGAGTACTTTACAAATAAACAAGGTAAATCTCTAATATTACCTGATGAAAATAAAGT\n+TGAGTTATATAGAGTTGATGTAACACCTTATACTATGAGACTTAATTTCACTTACAATAC\n+AGAAGTTGTAGCTATAGATATTGATAAGTTACACTCAGATTCTATAGAAATGCATATACC\n+ACAAGGTCTTTATATAACAACTGTTGTTAAAATTACTAGTACGCAGAGTATTAGTTCAGT\n+TCTTCATAAGGTATTAGAGGAATGGGTAAGACAAGTACAAAATGATGGTATATTCGGATT\n+CGTATGGGAGTAATTATAATGATAAGTATAGAACATGATTATACAATAAGAACTGTAGAT\n+AATAGAAAATATACTTATTATAGTAAATACGAATCACTAGTTACTTTGTATGAAAATATT\n+ATGAGTAAAGATTGTATTGAAGTAACTAAATATGGGAAAGATAAAAAAGTTATTATTGAT\n+ACTAGACATATTGTATCTATTGAACGATGGTAAATAATAAGGAGGAGTAAACTATTATGA\n+TAAATGCAGGGCATGCTAAGTACCTATCAGAAATTTATGAAGATGATGTACATTATGAAA\n+CTATAGATAGTATTGTAGAAGATATACTAGATAATATTAATGATGGTATTATTGAAGAAG\n+CTATGAAAGGTAATACAAGTTATCAATATGTTCTTAGAGACTTAAGAGTAGATAATGAAG\n+TAGAATATAGAGTTATAGAAGAACTTACTAACCAAGGATATAGTGTAAACCACATTAGTA\n+ATGATATAGAGTACCCTTCTATATCTACAAATAATTTAGCAGGGTTAGATTACTTAAATA\n+TTAAATGGTAAGGGAGGGAATTAATATGATAAATAAATATAAAAAGTTATGGGATGAAAT\n+AACTCAACAAATTGTTAATGTAGAAATTATTAACTTTAAAAATGAAACAGTAACAATAGA\n+ATCTACAGATGATTCAGGATTATCAGAGATAAGAGGTTTTGAAGAAGTAGAGTTTATAGA\n+TTACTATGGATAAGATGTTTAAAGTATATAATTTATAAGGAGGAAACATATGGACTTGTT\n+TGCAAAAATAATTATTATGTCTATAGGAGTTGTTCCCTTGTTAACTATTATTGTTGCACA\n+GCTAATTACAGATTACCATGATAATCATTAAGTATTATAGTAATAGGAAGGACAATATTT\n+AGAGTGAGAGTATGTTGACTAATGAGGAAGATATAGAATGAGAACCTAACCAAGTAAAAC\n+TAAGTACCTTTGTTATGTACTACTATTACTACTACTACTATTACTACTACTATTACTACT\n+ACTACTACTACTACTATTACTATTACTACTACTATTACTACTACTAAGTACCTTTGTTAT\n+GTACTACTATTACTA\n+\n' |
| b |
| diff -r 621754dd31f8 -r e923c686ead9 test-data/mu_reanno.gb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mu_reanno.gb Mon Jun 05 02:45:31 2023 +0000 |
| b |
| b'@@ -0,0 +1,1877 @@\n+LOCUS Exported 36717 bp ds-DNA linear PHG 03-JUN-2020\n+DEFINITION Enterobacteria phage Mu, complete genome.\n+ACCESSION NC_000929\n+VERSION .\n+KEYWORDS .\n+SOURCE Escherichia phage Mu\n+ ORGANISM Escherichia phage Mu\n+REFERENCE 1 (bases 1 to 36717)\n+ AUTHORS Morgan GJ, Hatfull GF, Casjens S, Hendrix RW.\n+ TITLE Bacteriophage Mu genome sequence: analysis and comparison with \n+ Mu-like prophages in Haemophilus, Neisseria and Deinococcus\n+ JOURNAL J. Mol. Biol. 317 (3), 337-359 (2002)\n+ PUBMED 11922669\n+REFERENCE 2 (bases 1 to 36717)\n+ TITLE Direct Submission\n+ JOURNAL Submitted (05-MAY-2009) National Center for Biotechnology \n+ Information, NIH, Bethesda, MD 20894, USA\n+REFERENCE 3 (bases 1 to 36717)\n+ AUTHORS Morgan G, Hatfull G, Hendrix R.\n+ TITLE Direct Submission\n+ JOURNAL Submitted (13-AUG-1998) Pittsburgh Bacteriophage Institute and \n+ Department of Biological Sciences, University of Pittsburgh, \n+ Pittsburgh, PA 15260, USA\n+REFERENCE 4 (bases 1 to 36717)\n+ AUTHORS .\n+ TITLE Direct Submission\n+ JOURNAL Exported Wednesday, Jun 3, 2020 from SnapGene 5.1.3\n+ https://www.snapgene.com\n+COMMENT SGRef: number: 1; type: "Journal Article"; journalName: "J. Mol.\n+ Biol."; date: "2002"; volume: "317"; issue: "3"; pages: "337-359"\n+COMMENT SGRef: number: 2; type: "Journal Article"; journalName: "Submitted\n+ (05-MAY-2009) National Center for Biotechnology Information, NIH,\n+ Bethesda, MD 20894, USA"\n+COMMENT SGRef: number: 3; type: "Journal Article"; journalName: "Submitted\n+ (13-AUG-1998) Pittsburgh Bacteriophage Institute and Department of\n+ Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260,\n+ USA"\n+COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final \n+ NCBI review. The reference sequence was derived from AF083977. \n+ COMPLETENESS: full length.\n+FEATURES Location/Qualifiers\n+ source 1..36717\n+ /organism="Escherichia phage Mu"\n+ /host="Escherichia coli"\n+ /mol_type="genomic DNA"\n+ /label=G(+) form\n+ /note="G(+) form"\n+ /db_xref="taxon:2681603"\n+ gene complement(339..942)\n+ /locus_tag="Mup01"\n+ /label=Mup01\n+ /db_xref="GeneID:2636266"\n+ CDS complement(339..929)\n+ /codon_start=1\n+ /transl_table=11\n+ /locus_tag="Mup01"\n+ /product="repressor protein c"\n+ /label=Mup01\n+ /note="Mup01 or immunity repressor or MuR for repressor of\n+ replication or Rep c; see PMIDs 16154589 and 9546656,\n+ 11135677 for structure; contains InterPro domain IPR003314\n+ Mu-type HTH domain also found in Mu transposase (Mup03 or\n+ A)"\n+ /db_xref="GeneID:2636266"\n+ /protein_id="NP_050605.1"\n+ /translation="MAADGMPGSVAGVHYRANVQGWTKQKKEGVKGGKAVEYDVMSMPT\n+ KEREQVIAHLGLSTPDTGAQANEKQDSSELINKLTTTLINMIEELEPDEARKALKLLSK\n+ GGLLALMPLVFNEQKLYSFIGFSQQSIQTLMMLDALPEEKRKEILSKYGIHEQESVVVP\n+ SQEPQEVKKAV"\n+ RBS complement(938..942)\n+ /locus_tag="Mup01"\n+ gene 1085..1326\n+ /locus_tag="Mup02"\n+ /label=Mup02\n+ /db_xref="GeneID:2636289"\n+ RBS 1085..1090\n+ /locus_tag="Mup02"\n+ CDS 1099..1326\n+ /codon_start=1\n+ /transl_table=11\n+ '..b'3601 agcatccact ctgttaattt ttgtttattc tcgtcggaaa tgatgcccag ccgtagctgt\n+ 33661 gagtcccata gctgtgtttt atccctgacg agctgtagca ggctttgctt ttcattttcc\n+ 33721 gcttgttgcc tctgctcttc ctcggtataa gttcgcttta tcactacacc atctttgaac\n+ 33781 atccatttac ccgaaatatc agcccggcga tttgctgtaa tatcaggaac ctcaacgacg\n+ 33841 tttgcgcctt ctggattaat tgctgaaaca tccttttcaa tacaaataat aacgccgttg\n+ 33901 tggtcataga ccattttcaa cgtatcaggc tgaaagttct tttgttcctc ataccagttt\n+ 33961 ttcccatcct ctgtataaag ccatttgatg ttaaattgtt tcgttagctg gtattgctct\n+ 34021 tttgttttag ggttgccagc agtaatattt tttaagtgca tcataattaa atactccccg\n+ 34081 cgttatacca cgttccatta atgcaatact gaattggcct tgcctgagtt gtatcaatta\n+ 34141 attcatcacg gtttccgtta actgaacccg taacgacata acctgacctg tcagaccagc\n+ 34201 cgggaccatt ccatgtctga acagatgaca gaccgccaag acgaatacct gtaataaacc\n+ 34261 ttgagttaca ttctgcctgc gtatatgcac caacatctcc cgctgatggc ttacgtgttg\n+ 34321 tggtgtaaat ttctgaccag tcagcttcga atccgtaacc atcacgcgct gaacgataaa\n+ 34381 aaataccgcc gttcctgtaa ttcacacgga actgtacggc agggcaactc cccgtattca\n+ 34441 tattgaagtg gaggattaat gtcgatgcgc caccaatatt tgcgttatag accccgctat\n+ 34501 tccagttcca gccaacagct ttatcatttc cgacagtgct tcctgtttgt cctaaagcaa\n+ 34561 atgcaggctg ctggtttttc gtgttgtagt ctcgtcgcca gccaggagca taagcatcac\n+ 34621 catgattaat ataagtgaat tgagcgttag tgattccgcc gccgctggac gtactcggcg\n+ 34681 tagtaacgcg tatggtcatt gcgccgcgag tgccaataac ttccaccaca gcacctgcaa\n+ 34741 gacaaatatt tccgcaacct gtatctgtaa tgaccttatt gtttgcataa gcccatgagc\n+ 34801 ctttgcacat ccagtaagga tggttaaatg ccccctgact ctccagccac gaaataaatt\n+ 34861 gtgcggttgt ccagacctga ctatcgccac caatattcag ccatgcgcta tatgcgcgac\n+ 34921 aggccccaat atttttggtg aaggtatctt ttcctggaat atctgcgccg ttctggtttt\n+ 34981 gctgtaatgc gccagaagcc tgatttaccg tttcctgtaa accgaggttt tggataatgg\n+ 35041 tcgattttgg cacgcatggc atgattggcg cttttaaaca ggagatccag agtgctgatt\n+ 35101 ggctatgtaa gggtatcaac aaatgaccag aatacagacc tgcaacgaaa cgctcttgtt\n+ 35161 tgtgcaggat gtgaacaaat atttgaagat aaattaagcg gaacaaggac agaccgaccg\n+ 35221 ggattaaaac gcgctttaaa gcgccttcaa aaaggtgaca cactggttgt ctggaaactg\n+ 35281 gatcgcctcg ggcgaagcat gaaacatttg atttctctcg taggggaatt acgagagcga\n+ 35341 gggattaatt ttcgcagtct tactgacagt attgatacgt catctccaat ggggcgtttt\n+ 35401 ttcttccacg ttatgggtgc cctggctgaa atggaacgag aactaattat cgagcgaacg\n+ 35461 atggctggac ttgctgccgc cagaaataaa ggccgtattg gtgggcgacc acctaaacta\n+ 35521 accaaagcgg aatgggagca ggccgggcgt ttattagcac aaggaatccc ccgcaagcag\n+ 35581 gttgcattga tctacgatgt ggccctgtca actctgtata aaaaacaccc cgcgaaacga\n+ 35641 gcgcatatag aaaacgacga tcgaatcaat taaatcgatc ggtaatacag atcgattatg\n+ 35701 ccccaataac cacactcaac ccatgatgtt ttttaagata gtggcgaatt gatgcaaagg\n+ 35761 aggtgagatg aaatcaattc gctgtaaaaa ctgcaacaaa ctgttattta aggcggattc\n+ 35821 ctttgatcac attgaaatca ggtgtccgcg ttgcaaacgt cacatcataa tgctgaatgc\n+ 35881 ctgcgagcat cccacggaga aacattgtgg gaaaagagaa aaaatcacgc attctgacga\n+ 35941 aaccgtgcgt tattgagtat gaaggccaga ttgttggcta tggttcaaag gagctgcgcg\n+ 36001 ttgaaaccat atcctgctgg ctggcccgca caattattca gacaaagcac tattcccgcc\n+ 36061 gttttgtgaa taactcttac cttcacctgg gggtattcag cggacgcgat ctggttggcg\n+ 36121 ttctccagtg gggatatgcc cttaacccca actcaggtcg tcgtgtcgtg cttgaaacgg\n+ 36181 ataaccgggg ctatatggag ttgaaccgca tgtggctaca cgacgacatg ccccgcaact\n+ 36241 ctgaatcacg ggccatcagc tacgcgctga aagttatcag attactgtat ccgtcagtgg\n+ 36301 agtgggttca gtcctttgca gatgaacgct gcggacgcgc aggcgttgtg tatcaggcgt\n+ 36361 cgaattttga ttttattggc agtcatgaaa gtacgttcta cgagctggat ggtgagtggt\n+ 36421 atcacgagat aacgatgaac gcgattaagc gaggtggaca acgaggcgtg tatttacggg\n+ 36481 ctaataaaga gcgtgccgtg gtacacaaat ttaatcagta tcgctacatc agattcctga\n+ 36541 acaaacgagc aaggaagcgg ctaaatacca aactattcaa ggttcagcca taccctaagt\n+ 36601 gatccccatg taatgaataa aaagcagtaa ttaatacatc tgtttcattt gaagcgcgaa\n+ 36661 agctaaagtt ttcgcattta tcgtgaaacg ctttcgcgtt tttcgtgcgc cgcttca\n+//\n' |
| b |
| diff -r 621754dd31f8 -r e923c686ead9 test-data/out_img.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_img.svg Mon Jun 05 02:45:31 2023 +0000 |
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