DUf5MddlZddlmZddlZddlmZddlmZddlZddlZGddej Z Gdde Z dd Z d Zd ZGd de ZGddeZGddeZedkr~ ejdZejdZeedieZeeded eZejdSdS)N) defaultdict) collections)pyplotcTeZdZ d dZdZdZd Zd Zd Ze d Z dS)TrackNrdenseTc t|tjr"t|jtr||_n+tj||_||_||_||_ ||_ | | }| t|tjj|fd|i|dS)a Subclass of matplotlib's PolyCollection that can be added to an Axes. :param features: Can be an existing BedTool, or anything than can be used to create a BedTool (e.g., a filename or a generator of Interval objects) :param ybase: y-coord of the bottom edge of the track (in data coordinates) :param yheight: How high each feature will be, in data coordinates :param visibility: Mimics the settings in the UCSC Genome Browser: * "dense" is the default; overlapping features can be seen if you set alpha < 1. * "squish" prevents adjacent features from overlapping. This keeps `yheight` for all features, so if you have a lot of features piling up, the track will be a lot higher on the y-axis than `yheight`. :param stranded: If boolean and True, will draw arrrow-shaped features to indicate direction (where the point is 10% of the total gene length) If a dictionary, map strands to colors, e.g., {'+': 'r', '-': 'b'}. :param kwargs: Additional keyword args are passed to matplotlib.collections.PolyCollection. Notes: After creating a track, use the `ymax` attribute to get the max y-value used in the track -- useful if you've created a "squish" track but would like to stack another track on top, and need to calculate what the new Track's `ybase` should be. The returned PolyCollection will have the `features` attribute, which contains the BedTool it was created from -- so you can write callback functions for event handling, e.g.:: def callback(event): ''' prints the feature's line when clicked in the plot ''' coll = event.artist for i in event.ind: print coll.features[i] fig.canvas.mpl_connect('on_pick', callback) >>> a = pybedtools.example_bedtool('a.bed') >>> track = pybedtools.contrib.plotting.Track(a, alpha=0.5, picker=5) >>> import matplotlib.pyplot as plt >>> fig = plt.figure() >>> ax = fig.add_subplot(111) >>> ax.add_collection(track) #doctest: +ELLIPSIS >>> limits = ax.axis('tight') ) facecolorsvertsN) isinstance pybedtoolsBedToolfnstrfeaturessaveas _visibility_ybase_yheightstranded_check_stranded_dict_colorsupdatedictrPolyCollection__init__ _get_verts) selfrchromybaseyheight visibilityrkwargsr s X/var/www/html/software/conda/lib/python3.11/site-packages/pybedtools/contrib/plotting.pyrzTrack.__init__ sV h 2 3 3 B K9 9  B%DMM&.x88??AADM%     !!###\\^^  dj111222"+DTT8I8ITVTTTTTc|jrt|jtst|dz}|jdkr<|j|f|j||zf|j|z||zf|j||dzzf|j|z|fgS|jdkr<|j|f|j||zf|j|z ||zf|j||dzzf|j|z |fgS|j|f|j||zf|j||zf|j|fgS)N皙?-g?+)rr rlenstrandstopstart)rfeaturer!r"offsets r%_shapez Track._shapees5 = DM4!@!@ \\C'F~$$\5)\57?3]V+UW_=]EGcM$9:]V+U3 3&&]E*]EGO4\F*EGO<\57S=#89\F*E2 ]E " ]EGO , \57? + \5 !   r&cg}|jdkrR|jD]6}||||j|j7|j|jz|_|jdkrg}|j}|j|jz|_|jD]}d}t|D].\}}|j|kr|j||jzz}|j ||<n/|9|jt||jzz}||j |||||j|jt||jzz|_|S)Nr squish) rrappendr1rrymax enumerater.r-r+end)rr r/stackr!iss r%rzTrack._get_vertssp  w & &= O O T[[$+t}MMNNNN dm3DI  x ' 'EKE dm3DI= I I%e,,DAq}q(( $ a$-.? ?#*<a)= K#e**t}*DDELL--- T[[%GGHHHH c%jj4=&@@DI r&ct|jtsdSd|jvrtd|jzd|jvrtd|jzdS)NTr*z1stranded dict "%s" does not have required key "+"r)z1stranded dict "%s" does not have required key "-")r rr ValueErrorrs r%rzTrack._check_stranded_dictsv$-.. 4 dm # #FV  dm # #FV tr&c t|jtsdSg}|jD]V} ||j|j)#t $r!t d|jd|jdwxYw|S)Nzstrand color dict "z"" does not have a key for strand "")r rrrr4r,KeyError)rcolorsr/s r%rz Track._colorss$-.. 4}  G  dmGN;<<<<   h)-H   s %A+A:cR||j}|j|jfS)z; Needs `ax` to convert to transData coords ) get_datalim transDataxminxmax)raxbbs r% get_xlimszTrack.get_xlimss(  bl + +!!r&c6|j|j|jz dz zS)Ng@)rr5r=s r%midpointzTrack.midpoints{di$+5<<z&sort_binary_matrix..*s>>>!qAv>>>r&rN)axis)rshaperbargsortsum)mweights score_matinds r%rdrd$sp ?>uQ Q77"=>>>GG I *Y]]]** + +DDbD 1C Jr&cg}tt|ddD]}|d|zd|S)zQ Convenience function useful printing the results from binary_heatmap(). c|dS)NrrP)xs r%z binary_summary..:s adr&T)keyreversez%s : %s )sortedr^rar4join)dr:ris r%binary_summaryr5sa AtAGGIINNDIII%% d#$$$$ 99Q<<r&ceZdZddZddZdS)TrackCollectionrNr(c||_||_||_||_|jD]E\}}d|vrt d|jjzd|vrt d|jjzFdS)aZ Handles multiple tracks on the same figure. :param config: A list of tuples that configures tracks. Each tuple contains a filename, BedTool object, or other iterable of pybedtools.Interval objects and a dictionary of keyword args that will be used to create a corresponding Track object, e.g.:: [ ('a.bed', dict(color='r', alpha=0.5, label='a')), (BedTool('a.bed').intersect('b.bed'), dict(color='g', label='b')), ] In this dictionary, do not specify `ybase`, since that will be handled for you. Also do not specify `yheight` in these dictionaries -- `yheight` should be provided as a separate kwarg to so that the `padding` kwarg works correctly. :param figsize: Figure size tuple of (width, height), in inches. :param padding: Amount of padding to place in between tracks, as a fraction of `yheight` r!zLPlease do not specify "ybase"; this is handled automatically by the %s classr"zTPlease do not specify "yheight", this should be a separate arg to the %s constructorN)configrqr"paddingr< __class__rL)rrr"rqrrr$s r%rzTrackCollection.__init__@s>    $   Hf&   ?AEAXYF"" "$(N$;<#  r&cj|/tj|j}|d}g}g}d}d}|j|jz}|jdddD]\}} t|f|j|d| } | j|z}| | d| vr| | dn'| t||dz }| | j | ||||d |S) z If `ax` is None, create a new figure. Otherwise, plot on `ax`. Iterates through the configuration, plotting each BedTool-like object as a separate track. Nrprrrr)r"r!labelrtight)r}r~rqrr"rrrr5add_collectionr4rrK set_yticksset_yticklabelsr) rrGryticks yticklabelsr!r9rrr$ts r%rzTrackCollection.plotqsN :*T\222C%%B  ,-!% DDbD 1 & & HfhL ELLVLLAFW$E   a &  ""6'?3333""3q66***Q MM!* % % % % f ;'''  r&)rNr(r)rLrMrNrrrPr&r%rr?s=////b      r&rc8eZdZ dfd Zdfd ZxZS) BedToolsDemoNTc |i}|i}|i}||_||_||_d|D}|rX|D]U} t| dtst dt j|| d| d<Vtj |dd} t| |}t|dkr||ddfi|} n+t|dkr |di|} nt d| | |f| |_tt |j|g| Ri| dS) aT Class to handle BEDTools demos in a way that maintains flexibility. If the `config` list contains only one item, assume the method is one of the "-i" tools that only operate on one file. If the `config` list contains two items, then use the first as "-a" and the second as "-b". :param config: Either a list of (filename, options) tuples -- see docstring for TrackCollection for more info. :param method: Method of `BedTool` object to use, e.g., 'intersect' :param data_path: If not None, this path will be prepended to the files listed in `config` :param result_kwargs: Configuration for the results track. This isn't added to the config list because the results haven't been created yet... :param method_kwargs: Keyword argument that are passed to the method, e.g., `u=True` :param title_kwargs: Keyword args for plot title (the text itself will come from the command that was run; this is for things like font size) :param new_style: Edit commands so that they use the "new style" BEDTools calls ("bedtools intersect" rather than "intersectBed") :param subplots_adjust: Additional kwargs sent to the figure's subplots_adjust() method, e.g., `dict(top=0.7)` :param args: Addtional arguments sent to TrackCollection :param kwargs: Additional keyword arguments sent to TrackCollection Nc,g|]}t|SrP)r^rs r%rz)BedToolsDemo.__init__..s***a$q''***r&rz.s(AAAqrw//22AAAr&rP)rrrr_cmdsrrsettings _prog_namesrrr set_titlerrrr~)rrGcmdsrs r%rzBedToolsDemo.plots < & & + +B / /{ # > %1"'2B2B472K2KLM G  SXXAADAAABBXXdFWXXX   > %BI % = =(< = = = r&)NNNNTNr)rLrMrNrr __classcell__rs@r%rrs| ^D^D^D^D^D^D@          r&rceZdZfdZxZS)ConfiguredBedToolsDemoc ddl}|t|}ddg}|D]}||vrtd|z||d<||d<||t t |jdi|dS)a# Wrapper around BedToolsDemo class that reads in a YAML config file. Useful for using the same "style" configuration many times. Contents of `yaml_config` must be YAML versions of BedToolsDemo args and kwargs **except** `method` and `method_kwargs`. rNrrz*'%s' cannot be provided in the YAML configrP)yamlloadopenr<rrrr) r yaml_configrrr$rr disalloweddisrs r%rzConfiguredBedToolsDemo.__init__s  yyk**++0  U UCd{{ !MPS!STTT X -_ F4$d++4<rsK ######""""""$$$$$${={={={={=K &{={={=|AAAAAFAAAH&&&&0"RRRRRfRRRjlllll?lll^=====\===0 z , +,=>>I+ +B//I +R9    dff ! +TTD\\\Y    dff CHJJJJJ3r&