o Rŀg*{@s0dZddlmZddlmZddlmZddlmZddlmZddlmZddlm Z dd l m Z dd l m Z dd lmZdd lmZdd lmZddlmZeZGddde ZGdddeZGdddeZGdddeZd"ddZd"ddZGdddeZGdddeZGdd d eZ d!S)#aDraw representations of organism chromosomes with added information. These classes are meant to model the drawing of pictures of chromosomes. This can be useful for lots of things, including displaying markers on a chromosome (ie. for genetic mapping) and showing syteny between two chromosomes. The structure of these classes is intended to be a Composite, so that it will be easy to plug in and switch different parts without breaking the general drawing capabilities of the system. The relationship between classes is that everything derives from _ChromosomeComponent, which specifies the overall interface. The parts then are related so that an Organism contains Chromosomes, and these Chromosomes contain ChromosomeSegments. This representation differs from the canonical composite structure in that we don't really have 'leaf' nodes here -- all components can potentially hold sub-components. Most of the time the ChromosomeSegment class is what you'll want to customize for specific drawing tasks. For providing drawing capabilities, these classes use reportlab: http://www.reportlab.com This provides nice output in PDF, SVG and postscript. If you have reportlab's renderPM module installed you can also use PNG etc. )ArcPath)Drawing)Line)Rect)String)Wedge)Widget)colors)letter)inch) stringWidth)_write)_Colorsc@s0eZdZdZddZddZddZdd Zd S) _ChromosomeComponentzBase class specifying the interface for a component of the system. This class should not be instantiated directly, but should be used from derived classes. cCs g|_dS)zInitialize a chromosome component. Attributes: - _sub_components -- Any components which are contained under this parent component. This attribute should be accessed through the add() and remove() functions. N)_sub_componentsselfrP/var/www/html/myenv/lib/python3.10/site-packages/Bio/Graphics/BasicChromosome.py__init__=s z_ChromosomeComponent.__init__cCs(t|ts td||j|dS)z>Add a sub_component to the list of components under this item.z,Expected a _ChromosomeComponent object, got N) isinstancer TypeErrorrappendr componentrrraddHs z_ChromosomeComponent.addcCs4z |j|WdStytd|ddw)zRemove the specified component from the subcomponents. Raises a ValueError if the component is not registered as a sub_component. z Component z not found in sub_components.N)rremove ValueErrorrrrrrOs  z_ChromosomeComponent.removecCstd)zDraw the specified component.zSubclasses must implement.)AssertionErrorrrrrdraw\sz_ChromosomeComponent.drawN)__name__ __module__ __qualname____doc__rrrrrrrrr6s   rc@s2eZdZdZd ddZddZddZd d Zd S) OrganismaXTop level class for drawing chromosomes. This class holds information about an organism and all of its chromosomes, and provides the top level object which could be used for drawing a chromosome representation of an organism. Chromosomes should be added and removed from the Organism via the add and remove functions. pdfcCs&t|t|_d|_d|_||_dS)zInitialize the class.rN)rrr page_size title_size_legend_height output_format)rr*rrrrls  zOrganism.__init__c Cs|j\}}t||}|||||td}t|jdkr'|tt|j}n |jD](}|d||_|d||_|dt|_|j dt|_ | |||7}q+| ||j dt||durf|St |||jS)a Draw out the information for the Organism. Arguments: - output_file -- The name of a file specifying where the document should be saved, or a handle to be written to. The output format is set when creating the Organism object. Alternatively, output_file=None will return the drawing using the low-level ReportLab objects (for further processing, such as adding additional graphics, before writing). - title -- The output title of the produced document. ?r皙?ffffff?g?N)r'r _draw_titler lenrstart_x_positionend_x_positionstart_y_positionr)end_y_positionr _draw_legendr r*) r output_filetitlewidthheight cur_drawing cur_x_pos x_pos_change sub_componentrrrrzs$    z Organism.drawcCs6t|d|t|}d|_|j|_d|_||dS)z5Write out the title of the organism figure (PRIVATE).zHelvetica-BoldmiddleN)rr fontNamer(fontSize textAnchorr)rr:r7r8r9 title_stringrrrr/s zOrganism._draw_titlecCdS)zDraw a legend for the figure (PRIVATE). Subclasses should implement this (see also self._legend_height) to provide specialized legends. Nr)rr:start_yr8rrrr5zOrganism._draw_legendN)r%)r r!r"r#rrr/r5rrrrr$as  . r$c@s8eZdZdZddZddZddZdd Zd d Zd S) ChromosomezClass for drawing a chromosome of an organism. This organizes the drawing of a single organisms chromosome. This class can be instantiated directly, but the draw method makes the most sense to be called in the context of an organism. cCsVt|||_d|_d|_d|_d|_d|_d|_d|_ d|_ |j d|_ d|_ dS)aInitialize a Chromosome for drawing. Arguments: - chromosome_name - The label for the chromosome. Attributes: - start_x_position, end_x_position - The x positions on the page where the chromosome should be drawn. This allows multiple chromosomes to be drawn on a single page. - start_y_position, end_y_position - The y positions on the page where the chromosome should be contained. Configuration Attributes: - title_size - The size of the chromosome title. - scale_num - A number of scale the drawing by. This is useful if you want to draw multiple chromosomes of different sizes at the same scale. If this is not set, then the chromosome drawing will be scaled by the number of segments in the chromosome (so each chromosome will be the exact same final size). r&N?r+F) rr_namer1r2r3r4r( scale_num label_size chr_percentlabel_sep_percent _color_labels)rchromosome_namerrrrs   zChromosome.__init__cCsd}|jD]}||j7}q|S)z>Return the scaled size of all subcomponents of this component.r)rscale)r total_subr=rrrsubcomponent_sizes  zChromosome.subcomponent_sizec Cs|j|j|j|jfD] }|dksJdq |j}|jr'|jd|j|j}nt|jdkr;|jd|j|}n g}g}|jD]0}|j|}|j|_|j|_||_|||_g|_ g|_ | |||j 7}||j 7}||8}qC| |||| ||jdS)zDraw a chromosome on the specified template. Ideally, the x_position and y_*_position attributes should be set prior to drawing -- otherwise we're going to have some problems. rH Need to set drawing coordinates.r-rN)r1r2r3r4rLr0rrTrR _left_labels _right_labelsr _draw_labels _draw_labelrK) rr:position cur_y_pos y_pos_change left_labels right_labelsr=this_y_pos_changerrrrs@       zChromosome.drawcCsDd|j|j}|j}t|||}d|_|j|_d|_||dS)z*Draw a label for the chromosome (PRIVATE).r+zTimes-BoldItalicr?N) r1r2r4rr@r(rArBr)rr: label_name x_position y_position label_stringrrrrY%s zChromosome._draw_labelc Csz|jsdS|j}|j|j|j}|j|j|j}|jd|j|j|}g}|jD] } || j| jfq,t |} t |} ~|j } |||t || | | df|||||t || | | dffD]X\} }}}|D]O\}}}}}| t| ||||ddt||||d}d|_| |_|r||_|rt||j|j}| |kr|d }| t||d | || ||d | |qjqbdS) atLayout and draw sub-feature labels for the chromosome (PRIVATE). Tries to place each label at the same vertical position as the feature it applies to, but will adjust the positions to avoid or at least reduce label overlap. Draws the label text and a coloured line linking it to the location (i.e. feature) it applies to. Nr+endstartrJ) strokeColor strokeWidth)rB Helveticagg?)rf fillColor)rrPr2r1rNrOextendr3r4minmaxrM _place_labelsrrrr@rArir r)rr:r]r^ color_label segment_width label_sep segment_xy_limitsr=y_miny_maxhx1x2labelsanchory1y2color back_colornamercwrrrrX1sp         zChromosome._draw_labelsN) r r!r"r#rrTrrYrXrrrrrGs'5 rGc@s@eZdZdZddZddZddZdd Zd d Zd d Z dS)ChromosomeSegmentaRDraw a segment of a chromosome. This class provides the important configurable functionality of drawing a Chromosome. Each segment has some customization available here, or can be subclassed to define additional functionality. Most of the interesting drawing stuff is likely to happen at the ChromosomeSegment level. cCsDt|d|_d|_d|_d|_d|_d|_d|_d|_ d|_ dS)aInitialize a ChromosomeSegment. Attributes: - start_x_position, end_x_position - Defines the x range we have to draw things in. - start_y_position, end_y_position - Defines the y range we have to draw things in. Configuration Attributes: - scale - A scaling value for the component. By default this is set at 1 (ie -- has the same scale as everything else). Higher values give more size to the component, smaller values give less. - fill_color - A color to fill in the segment with. Colors are available in reportlab.lib.colors - label - A label to place on the chromosome segment. This should be a text string specifying what is to be included in the label. - label_size - The size of the label. - chr_percent - The percentage of area that the chromosome segment takes up. rHr.NrIrJ) rrr1r2r3r4rR fill_colorlabelrMrNrrrrrs  zChromosomeSegment.__init__cCsV|j|j|j|jfD] }|dksJdq ||||||||dS)ziDraw a chromosome segment. Before drawing, the range we are drawing in needs to be set. rHrUN)r1r2r3r4_draw_subcomponents _draw_segment_overdraw_subcomponentsrY)rr:rZrrrrs   zChromosomeSegment.drawcCrD)zDraw any subcomponents of the chromosome segment (PRIVATE). This should be overridden in derived classes if there are subcomponents to be drawn. Nrrr:rrrrrFz%ChromosomeSegment._draw_subcomponentsc Cs|j}|j|j|j}|j|j}|jd|j|j|}t|||||}t|||||||}|||||jdurYt||||}|j|_ d|_ ||dSdS)z.Draw the current chromosome segment (PRIVATE).r+N) r4r2r1rNr3rrrrrirf) rr: segment_yrosegment_heightrq right_line left_linefill_rectanglerrrrs*    zChromosomeSegment._draw_segmentcCrD)zDraw any subcomponents of the chromosome segment over the main part (PRIVATE). This should be overridden in derived classes if there are subcomponents to be drawn. NrrrrrrrFz)ChromosomeSegment._overdraw_subcomponentscCst|jdur8d|j|j|jd|j|j}|j|jd|j}t|||j}d|_|j|_ | |dSdS)zAdd a label to the chromosome segment (PRIVATE). The label will be applied to the right of the segment. This may be overlapped by any sub-feature labels on other segments! Nr+r,r>rh) rr1r2rNr3r4rr@rMrAr)rr:label_xlabel_yrcrrrrYs   zChromosomeSegment._draw_labelN) r r!r"r#rrrrrrYrrrrr|s$ rc s t|}|dkr |S|krtddd|dt|ks&t||kr4tdt|t||f||dkr\ddl}ddlm}|d |fd d t|DSd }rw|d}|ddD] } || krvd }nqj|r{|S|} d| | dd| dd| d| fD]} | fdd |Dfdd |D} tt| |krqst| | | dkrt | d|S| st| dkrt dSt| dkr#t| | | dkr#t dt | d|Sqt|t|} | |dkrK| |dfdd t|DSdt|dt||} | |dkrz| |dfdd t|DSfdd t|DS)aTry to layout label coordinates or other floats (PRIVATE). Originally written for the y-axis vertical positioning of labels on a chromosome diagram (where the minimum gap between y-axis coordinates is the label height), it could also potentially be used for x-axis placement, or indeed radial placement for circular chromosomes within GenomeDiagram. In essence this is an optimisation problem, balancing the desire to have each label as close as possible to its data point, but also to spread out the labels to avoid overlaps. This could be described with a cost function (modelling the label distance from the desired placement, and the inter- label separations as springs) and solved as a multi-variable minimization problem - perhaps with NumPy or SciPy. For now however, the implementation is a somewhat crude ad hoc algorithm. NOTE - This expects the input data to have been sorted! r.z Bad min/max fz and z&Data %f to %f out of bounds (%f to %f)rN)BiopythonWarningz Too many labels to avoid overlapcg|]}|qSrr.0i equal_stepminimumrr $z"_spring_layout..TFr+g@r>rJg?cs g|] }|dkr|qSr+rrxgapmidpointrrr3 cs g|] }|dkr|qSrrrrrrr4rcrrrrrlowrrrOrcrrrrrrrrVrcrrrrrrrrYr) r0rrkrlwarningsBiorwarnrange_spring_layout) desiredrmaximumrcountrrgoodprevnextspansplithighr)rrrrrrrsr   * rccsX|tdd|D|||}t||D]\}}|d|ft|ddVqdS)NcSsg|]}|dqSrr)rrowrrrrgsz!_place_labels..rr.)sortrziptuple) desired_etcrrrplacedoldr{rrrrmds  rmc@s(eZdZdZejdfddZddZdS)AnnotatedChromosomeSegmentzkAnnotated chromosome segment. This is like the ChromosomeSegment, but accepts a list of features. )generr~ locus_tagproductcCs2t|||_||_||_||_|jd|_dS)aInitialize. The features can either be SeqFeature objects, or tuples of values: start (int), end (int), strand (+1, -1, O or None), label (string), ReportLab color (string or object), and optional ReportLab fill color. Note we require 0 <= start <= end <= bp_length, and within the vertical space allocated to this segment lines will be places according to the start/end coordinates (starting from the top). Positive stand features are drawn on the right, negative on the left, otherwise all the way across. We recommend using consistent units for all the segment's scale values (e.g. their length in base pairs). When providing features as SeqFeature objects, the default color is used, unless the feature's qualifiers include an Artemis colour string (functionality also in GenomeDiagram). The caption also follows the GenomeDiagram approach and takes the first qualifier from the list or tuple specified in name_qualifiers. Note additional attribute label_sep_percent controls the percentage of area that the chromosome segment takes up, by default half of the chr_percent attribute (half of 25%, thus 12.5%) r+N)rr bp_lengthfeaturesdefault_feature_colorname_qualifiersrNrO)rrrrrrrrrss "z#AnnotatedChromosomeSegment.__init__c Cs4|j}|j|j|j}|j|j|j}|j|j}|jd|j|j|}g}g}|jD]} z?| jj} | jj } | jj } z t | j dd} Wn tyV|j} Ynw| }d}|jD]}|| j vrn| j |d}nq^Wn)ty| dd\} } } }} t | } t| dkrt | d}n| }Ynwd| kr| kr|jksJJ| dkr||d}|d }n| d kr|}|d }n|}|}||j}t||||| ||| | }||_| |_|||r|| krd}n|}|||| | ||f}| d kr|j|q/|j|q/dS) zDraw any annotated features on the chromosome segment (PRIVATE). Assumes _draw_segment already called to fill out the basic shape, and assmes that uses the same boundaries. r+r|rNr.g333333?g?rH)r4r2r1rNrOr3rlocationrerdstrand _color_trans translate qualifiers ExceptionrrAttributeErrorr0rrrirfrrVrrW)rr:rrorprrqr]r^rrerdrr|rr~ qualifierrr local_scalerr}valuerrrrs          (        z2AnnotatedChromosomeSegment._overdraw_subcomponentsN)r r!r"r#r bluerrrrrrrms   )rc@s"eZdZdZdddZddZdS) TelomereSegmenta)A segment that is located at the end of a linear chromosome. This is just like a regular segment, but it draws the end of a chromosome which is represented by a half circle. This just overrides the _draw_segment class of ChromosomeSegment to provide that specialized drawing. rcCst|||_dS)a8Initialize a segment at the end of a chromosome. See ChromosomeSegment for all of the attributes that can be customized in a TelomereSegments. Arguments: - inverted -- Whether or not the telomere should be inverted (ie. drawn on the bottom of a chromosome) N)rr _inverted)rinvertedrrrrs zTelomereSegment.__init__c Cs|j|j|j}|j|j}d|j|j}|d|}|jr(|j}d}d}n|j}d}d}t|||d|||} d| _|j| _ | | t } | |||d|||| | dS)zIDraw a half circle representing the end of a linear chromosome (PRIVATE).r+ihrr>N) r2r1rNr3r4rrrfrrirraddArc) rr:r8r9center_xstart_xcenter_y start_angle end_angle cap_wedgecap_arcrrrr s$   zTelomereSegment._draw_segmentNr)r r!r"r#rrrrrrrs  rc@seZdZdZddZdS) SpacerSegmentzA segment that is located at the end of a linear chromosome. Doesn't draw anything, just empty space which can be helpful for layout purposes (e.g. making room for feature labels). cCrD)zDraw nothing to the current diagram (dummy method). The segment spacer has no actual image in the diagram, so this method therefore does nothing, but is defined to match the expected API of the other segment objects. Nr)r cur_diagramrrrr-rFzSpacerSegment.drawN)r r!r"r#rrrrrr&s rNr)!r#reportlab.graphics.shapesrrrrrrreportlab.graphics.widgetbaser reportlab.libr reportlab.lib.pagesizesr reportlab.lib.unitsr reportlab.pdfbase.pdfmetricsr Bio.Graphicsr Bio.Graphics.GenomeDiagramrColorTranslatorrrr$rGrrrmrrrrrrrs6             +XD  f 5