o Rŀg@s.dZddlmZddlmZGdddZdS)zGraph module. Provides: - GraphData - Contains data from which a graph will be drawn, and information about its presentation For drawing capabilities, this module uses reportlab to draw and write the diagram: http://www.reportlab.com )sqrt)colorsc @seZdZdZddddejejdddf ddZddZdd Z d d Z d d Z ddZ ddZ ddZddZddZddZdS) GraphDataaGraph Data. Attributes: - id Unique identifier for the data - data Dictionary of describing the data, keyed by position - name String describing the data - style String ('bar', 'heat', 'line') describing how to draw the data - poscolor colors.Color for drawing high (some styles) or all values - negcolor colors.Color for drawing low values (some styles) - linewidth Int, thickness to draw the line in 'line' styles Nbarc Cs^|dur|}| dur | }||_i|_|dur||||_||_||_||_d|_||_dS)aInitialize. Arguments: - id Unique ID for the graph - data List of (position, value) tuples - name String describing the graph - style String describing the presentation style ('bar', 'line', 'heat') - color colors.Color describing the color to draw all or the 'high' (some styles) values (overridden by backwards compatible argument with UK spelling, colour). - altcolor colors.Color describing the color to draw the 'low' values (some styles only) (overridden by backwards compatible argument with UK spelling, colour). - center Value at which x-axis crosses y-axis. N) iddataset_datanamestyleposcolornegcolor linewidthcenter) selfrrr r coloraltcolorrcolour altcolourrU/var/www/html/myenv/lib/python3.10/site-packages/Bio/Graphics/GenomeDiagram/_Graph.py__init__,s  zGraphData.__init__cCs|D] \}}||j|<qdS)z/Add data as a list of (position, value) tuples.Nr)rrposvalrrrr \s  zGraphData.set_datacCs4g}|jD]}|j|}|||fq||S)z9Return data as a list of sorted (position, value) tuples.)rappendsort)rrxvalyvalrrrget_dataas   zGraphData.get_datacCs|\}}||j|<dS)zCAdd a single point to the set of data as a (position, value) tuple.Nr)rpointrrrrr add_pointjszGraphData.add_pointcCsHt|j}t|}|d||d||d|d|d|dfS)zCReturn (minimum, lowerQ, medianQ, upperQ, maximum) values as tuple.rr)sortedrvalueslen)rrdatalenrrr quartilesos  zGraphData.quartilescCst|j}|d|dfS)zReturn range of data as (start, end) tuple. Returns the range of the data, i.e. its start and end points on the genome as a (start, end) tuple. rr$)r%r)r positionsrrrrange{s zGraphData.rangecCst|j}t|t|S)z2Return the mean value for the data points (float).)listrr&sumr')rrrrrmeanszGraphData.meancCsHt|j}|}d}|D] }|||d7}qt|t|dS)z:Return the sample standard deviation for the data (float).gr)r,rr&r.rr')rrmruntotalentryrrrstdevs zGraphData.stdevcCs t|jS)z,Return the number of points in the data set.)r'r)rrrr__len__s zGraphData.__len__cCst|tr |j|St|tr?|j}|j}|jdur!|jdkr!tg}t|jD]}||kr<||kr<| ||j|fq(|St d)a@Return data value(s) at the given position. Given an integer representing position on the sequence returns a float - the data value at the passed position. If a slice, returns graph data from the region as a list or (position, value) tuples. Slices with step are not supported. Nr/zNeed an integer or a slice) isinstanceintrslicestartstopstep ValueErrorr%r TypeError)rindexlowhighoutlistrrrr __getitem__s  zGraphData.__getitem__cCsd|jd|jg}|dt|j|d||d|d|d||d|d |S) z*Return a string describing the graph data.z GraphData: z, ID: zNumber of points: %dzMean data value: z Sample SD: z.3fz,Minimum: %s 1Q: %s 2Q: %s 3Q: %s Maximum: %szSequence Range: %s..%s ) r rrr'rr.r3r)r+join)routstrrrr__str__s  zGraphData.__str__)__name__ __module__ __qualname____doc__r lightgreen darkseagreenrr rr!r)r+r.r3r4rArErrrrrs, 0     rN)rImathr reportlab.librrrrrrs