coolbox 0.3.8__py3-none-any.whl → 0.3.9__py3-none-any.whl

coolbox/core/track/ideogram.py

@@ -1,5 +1,5 @@
 import pandas as pd
-from matplotlib.collections import BrokenBarHCollection
+import matplotlib.pyplot as plt
 
 from coolbox.utilities import (
     get_logger, GenomeRange, file_to_intervaltree, hex2rgb,
@@ -24,7 +24,7 @@ class Ideogram(Track):
     color_scheme : dict, optional
         Color scheme of ideogram, default: Ideogram.DEFAULT_COLOR_SCHEME
 
-    show_name : bool, optional
+    show_band_name : bool, optional
         Show band name or not. default True.
 
     font_size : int, optional
@@ -55,7 +55,7 @@ class Ideogram(Track):
         properties_dict = {
             'file': file_,
             'color_scheme': Ideogram.DEFAULT_COLOR_SCHEME,
-            'show_name': True,
+            'show_band_name': True,
             'font_size': Ideogram.DEFAULT_FONT_SIZE,
             'border_color': '#000000',
             'border_width': Ideogram.DEFAULT_BORDER_WIDTH,
@@ -83,7 +83,7 @@ class Ideogram(Track):
             start, end = itv.begin, itv.end
             band_name, band_type = itv.data[:2]
             rows.append([gr.chrom, start, end, band_name, band_type])
-        fields = ['chrom', 'start', 'end', 'name', 'gieStain']
+        fields = ['chrom', 'start', 'end', 'band_name', 'band_type']
         return pd.DataFrame(rows, columns=fields)
 
     def plot(self, ax, gr: GenomeRange, **kwargs):
@@ -101,19 +101,28 @@ class Ideogram(Track):
                 self.properties['show_band_name'] != 'no'
                 and gr.length < 80_000_000
             ):
-                self.plot_text(band_name, start, end, band_color)
-        coll = BrokenBarHCollection(xranges, (0, band_height), facecolors=colors,
-                                    linewidths=self.properties['border_width'],
-                                    edgecolors=self.properties['border_color'])
+                self.plot_text(band_name, start, end, gr, band_color)
+        coll = plt.broken_barh(
+            xranges, (0, band_height), facecolors=colors,
+            linewidth=self.properties['border_width'],
+            edgecolor=self.properties['border_color'])
         ax.add_collection(coll)
         ax.set_ylim(-0.1, band_height + 0.1)
         ax.set_xlim(gr.start, gr.end)
         self.plot_label()
 
-    def plot_text(self, band_name, start, end, band_color):
+    def plot_text(self, band_name, start, end, gr, band_color):
         band_height = self.properties['height']
         x_pos = start + (end - start) * 0.15
+        if x_pos < gr.start:
+            x_pos = gr.start + 0.5 * (end - gr.start)
+            if (end - gr.start) < gr.length  * 0.10:
+                return
+        elif x_pos > gr.end:
+            x_pos = start + 0.5 * (gr.end - start)
+            if (gr.end - start) < gr.length * 0.10:
+                return
         y_pos = band_height / 2
         rgb = hex2rgb(band_color) if isinstance(band_color, str) else band_color
-        color = '#e2e2e2' if sum(rgb) < 100 else '#000000'
+        color = '#e2e2e2' if sum(rgb) < 200 else '#000000'
         self.ax.text(x_pos, y_pos, band_name, fontsize=self.properties['font_size'], color=color)

coolbox/core/track/pseudo.py

@@ -128,11 +128,15 @@ class XAxis(Track):
 
         ax.set_xlim(gr.start, gr.end)
         ticks = ax.get_xticks()
-        if ticks[-1] - ticks[1] <= 1e5:
+
+        if ticks[-1] - ticks[1] <= 1000:
+            labels = ["{:.0f}".format((x))
+                      for x in ticks]
+            labels[-2] += " bp"
+        elif ticks[-1] - ticks[1] <= 1e5:
             labels = ["{:,.0f}".format((x / 1e3))
                       for x in ticks]
             labels[-2] += " Kb"
-
         elif 1e5 < ticks[-1] - ticks[1] < 4e6:
             labels = ["{:,.0f}".format((x / 1e3))
                       for x in ticks]

coolbox/core/track/tad.py

@@ -0,0 +1,237 @@
+import numpy as np
+import pandas as pd
+
+from coolbox.utilities import (
+    get_logger
+)
+from coolbox.utilities.genome import GenomeRange
+from .bed.base import BedBase
+from .bed.fetch import FetchBed
+
+log = get_logger(__name__)
+
+
+class PlotTAD(object):
+    def __init__(self):
+        self.init_colormap()
+        self.cache_gr = None
+        self.cache_res = None
+
+    def fetch_plot_data(self, gr: GenomeRange, **kwargs):
+        if gr == self.cache_gr:
+            return self.cache_res
+        else:
+            self.cache_gr = gr
+            self.cache_res = self.fetch_data(gr, **kwargs)
+            return self.cache_res
+
+    def get_depth_ratio(self, gr=None):
+        if 'depth_ratio' not in self.properties:
+            return 1.0
+        dr = self.properties['depth_ratio']
+        if dr == 'full':
+            return 1.0
+        if dr == 'auto':
+            assert gr is not None
+            min_dr = 0.1
+            tads = self.fetch_plot_data(gr)
+            tads = tads[(tads['start'] >= gr.start) & (tads['end'] <= gr.end)]
+            if tads.shape[0] > 0:
+                dr = (tads['end'] - tads['start']).max() / (gr.end - gr.start)
+                return max(dr, min_dr)
+            else:
+                return min_dr
+        return dr
+
+    def get_track_height(self, frame_width, gr):
+        height = frame_width * 0.5
+        height *= self.get_depth_ratio(gr)
+        return height
+
+    def plot_tads(self, ax, gr: GenomeRange, tads: pd.DataFrame):
+        """
+        Plots the boundaries as triangles in the given ax.
+        """
+        self.set_colormap(tads)
+        depth = (gr.end - gr.start) / 2
+        ymax = (gr.end - gr.start)
+        if 'track' in self.__dict__:
+            from coolbox.core.track.hicmat import HicMatBase
+            assert isinstance(self.track, HicMatBase), f"The parent track should be instance of {HicMatBase}"
+
+            hicmat_tri_style = (HicMatBase.STYLE_WINDOW, HicMatBase.STYLE_TRIANGULAR)
+            hicmat_ma_style = (HicMatBase.STYLE_MATRIX,)
+
+            hictrack = self.track
+            hicmat_style = hictrack.properties['style']
+
+            # TODO Should we add plotting in BigWig, BedGraph, ABCCompartment, Arcs support?(The original codes supports)
+            for region in tads.itertuples():
+                if hicmat_style in hicmat_tri_style:
+                    self.plot_triangular(ax, gr, region, ymax, depth)
+                elif hicmat_style in hicmat_ma_style:
+                    self.plot_box(ax, gr, region)
+                else:
+                    raise ValueError(f"unsupported hicmat style {hicmat_style}")
+        else:
+            for region in tads.itertuples():
+                self.plot_triangular(ax, gr, region, ymax, depth)
+            dr = self.get_depth_ratio(gr)
+            if self.properties['orientation'] == 'inverted':
+                ax.set_ylim(depth * dr, 0)
+            else:
+                ax.set_ylim(0, depth * dr)
+            ax.set_xlim(gr.start, gr.end)
+
+        if len(tads) == 0:
+            log.debug("No regions found for Coverage {}.".format(self.properties['name']))
+
+    def plot_triangular(self, ax, gr, region, ymax, depth):
+        """
+              /\
+             /  \
+            /    \
+        _____________________
+           x1 x2 x3
+        """
+
+        from matplotlib.patches import Polygon
+        x1 = region.start
+        x2 = x1 + float(region.end - region.start) / 2
+        x3 = region.end
+        y1 = 0
+        y2 = (region.end - region.start)
+
+        y = (y2 / ymax) * depth
+
+        rgb, edgecolor = self.get_rgb_and_edge_color(region)
+
+        triangle = Polygon(np.array([[x1, y1], [x2, y], [x3, y1]]), closed=True,
+                           facecolor=rgb, edgecolor=edgecolor,
+                           alpha=self.properties['alpha'],
+                           linestyle=self.properties['border_style'],
+                           linewidth=self.properties['border_width'])
+        ax.add_artist(triangle)
+        self.plot_score(ax, gr, region, 'triangular', ymax, depth)
+
+    def plot_box(self, ax, gr, region):
+        from matplotlib.patches import Rectangle
+
+        x1 = region.start
+        x2 = region.end
+        x = y = x1
+        w = h = (x2 - x1)
+
+        rgb, edgecolor = self.get_rgb_and_edge_color(region)
+
+        fill = self.properties['border_only'] == 'no'
+
+        rec = Rectangle((x, y), w, h,
+                        fill=fill,
+                        facecolor=rgb,
+                        edgecolor=edgecolor,
+                        alpha=self.properties['alpha'],
+                        linestyle=self.properties['border_style'],
+                        linewidth=self.properties['border_width'])
+        ax.add_patch(rec)
+        self.plot_score(ax, gr, region, 'box')
+
+    def plot_score(self, ax, gr, region, style, ymax=None, depth=None):
+        properties = self.properties
+
+        if properties['show_score'] != 'yes':
+            return
+        bed = region
+        score = bed.score
+        if not isinstance(score, (float, int)):
+            # score is not number not plot
+            return
+        region_length = region.end - region.start
+        if region_length / gr.length < 0.05:
+            # region too small not plot score
+            return
+        font_size = properties['score_font_size']
+        if font_size == 'auto':
+            # inference the font size
+            from math import log2
+            base_size = 18
+            s_ = (region_length / gr.length) * 10
+            s_ = int(log2(s_))
+            font_size = base_size + s_
+        ratio = properties['score_height_ratio']
+        color = properties['score_font_color']
+        if style == 'box':
+            x1 = region.start
+            x2 = region.end
+            w = x2 - x1
+            x = x2 - w * ratio
+            y = x1 + w * ratio
+        else:  # triangular
+            x = region.begin + region_length * 0.4
+            y = (region_length / ymax) * depth * ratio
+        ax.text(x, y, "{0:.3f}".format(score), fontsize=font_size, color=color)
+
+
+class TAD(BedBase, PlotTAD, FetchBed):
+    """
+    Tad tack from bed file
+
+    Parameters
+    ----------
+    border_style: str, optional
+        Border style of tad. (Default: 'solid')
+
+    border_width: int, optional
+        Border width of tad. (Default: '2.0')
+
+    show_score : bool
+        Show bed score or not.
+        default False.
+
+    score_font_size : {'auto', int}
+        Score text font size.
+        default 'auto'
+
+    score_font_color : str
+        Score text color.
+        default '#000000'
+
+    score_height_ratio : float
+        (text tag height) / (TAD height). used for adjust the position of Score text.
+        default 0.5
+
+    border_only : bool
+        Only show border, default False
+
+    depth_ratio : {float, 'auto', 'full'}
+        Depth ratio of triangular, use 'full' for full depth, use 'auto' for calculate depth by current genome_range. default 'auto'.
+
+    orientation : {'normal', 'inverted'}
+        Invert y-axis or not, default 'normal'
+
+    """
+
+    DEFAULT_PROPERTIES = {
+        'alpha': 0.3,
+        'border_style': "--",
+        'border_width': 2.0,
+        "show_score": False,
+        "score_font_size": 'auto',
+        "score_font_color": "#000000",
+        "score_height_ratio": 0.4,
+        "border_only": False,
+        "depth_ratio": 'auto',
+        "orientation": 'inverted',
+    }
+
+    def __init__(self, file, **kwargs):
+        properties = TAD.DEFAULT_PROPERTIES.copy()
+        properties.update(kwargs)
+        super().__init__(file, **properties)
+        PlotTAD.__init__(self)
+
+    def plot(self, ax, gr: GenomeRange, **kwargs):
+        self.ax = ax
+        ov_intervals: pd.DataFrame = self.fetch_plot_data(gr, **kwargs)
+        self.plot_tads(ax, gr, ov_intervals)
+        self.plot_label()

coolbox/utilities/bed.py

@@ -170,7 +170,7 @@ class ReadBed(object):
         """
         fields = self.get_no_comment_line(iter=file_iter, count=False)
         fields = to_string(fields)
-        line_values = fields.split()
+        line_values = fields.split("\t")
 
         if len(line_values) == 3:
             self.file_type = 'bed3'

coolbox/utilities/hic/wrap.py

@@ -35,7 +35,7 @@ class StrawWrap(object):
         self.chromosomes, self.resolutions, self.masterindex, self.genome, self.metadata = self.__info()
         self.fetched_binsize = None
 
-    def fetch(self, genome_range1, genome_range2=None):
+    def fetch(self, gr1, gr2=None):
         """
         Return
         ------
@@ -43,26 +43,34 @@ class StrawWrap(object):
         """
         from coolbox.utilities.genome import GenomeRange
 
-        if genome_range2 is None:
-            genome_range2 = genome_range1
-        genome_range1 = to_gr(genome_range1)
-        genome_range2 = to_gr(genome_range2)
+        flip = False
 
-        if isinstance(genome_range1, str):
-            genome_range1 = GenomeRange(genome_range1)
-        if isinstance(genome_range2, str):
-            genome_range2 = GenomeRange(genome_range2)
+        if gr2 is None:
+            gr2 = gr1
+        gr1 = to_gr(gr1)
+        gr2 = to_gr(gr2)
+        if gr2.start < gr1.start:
+            flip = True
+            gr1, gr2 = gr2, gr1
 
-        if genome_range1.chrom.startswith("chr"):
-            genome_range1.change_chrom_names()
-        if genome_range2.chrom.startswith("chr"):
-            genome_range2.change_chrom_names()
+        if isinstance(gr1, str):
+            gr1 = GenomeRange(gr1)
+        if isinstance(gr2, str):
+            gr2 = GenomeRange(gr2)
 
-        binsize = self.infer_binsize(genome_range1)
+        if gr1.chrom.startswith("chr"):
+            gr1.change_chrom_names()
+        if gr2.chrom.startswith("chr"):
+            gr2.change_chrom_names()
+
+        binsize = self.infer_binsize(gr1)
         self.fetched_binsize = binsize  # expose fetched binsize
 
-        straw_iter = self.__fetch_straw_iter(genome_range1, genome_range2, binsize)
-        return self.__straw_to_matrix(straw_iter, genome_range1, genome_range2, binsize)
+        straw_iter = self.__fetch_straw_iter(gr1, gr2, binsize)
+        mat = self.__straw_to_matrix(straw_iter, gr1, gr2, binsize)
+        if flip:
+            mat = mat.T
+        return mat
 
     def infer_binsize(self, genome_range):
         from .tools import infer_resolution

{coolbox-0.3.8.dist-info → coolbox-0.3.9.dist-info}/METADATA

@@ -1,13 +1,12 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: coolbox
-Version: 0.3.8
+Version: 0.3.9
 Summary: Jupyter notebook based genomic data visulization toolkit.
 Home-page: https://github.com/GangCaoLab/CoolBox
 Author: Weize Xu
 Author-email: vet.xwz@gmail.com
 License: GPLv3
 Keywords: genomics,bioinformatics,visualization,Jupyter
-Platform: UNKNOWN
 Classifier: Development Status :: 3 - Alpha
 Classifier: Operating System :: POSIX
 Classifier: Programming Language :: Python
@@ -20,18 +19,19 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.7, <4
-Requires-Dist: scipy (>=1.0.0)
+License-File: LICENSE
+Requires-Dist: scipy>=1.0.0
 Requires-Dist: numpy
-Requires-Dist: pandas (>=1.0.0)
+Requires-Dist: pandas>=1.0.0
 Requires-Dist: statsmodels
-Requires-Dist: matplotlib (>=3.1.1)
-Requires-Dist: jupyter (>=1.0.0)
-Requires-Dist: ipywidgets (>=7.5.1)
+Requires-Dist: matplotlib>=3.8.4
+Requires-Dist: jupyter>=1.0.0
+Requires-Dist: ipywidgets>=7.5.1
 Requires-Dist: nbformat
 Requires-Dist: voila
 Requires-Dist: svgutils
 Requires-Dist: intervaltree
-Requires-Dist: dna-features-viewer
+Requires-Dist: dna_features_viewer
 Requires-Dist: h5py
 Requires-Dist: cooler
 Requires-Dist: pybbi
@@ -39,7 +39,15 @@ Requires-Dist: numpydoc
 Requires-Dist: fire
 Requires-Dist: pytest
 Requires-Dist: strawC
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 See https://github.com/GangCaoLab/CoolBox
-
-

{coolbox-0.3.8.dist-info → coolbox-0.3.9.dist-info}/RECORD

@@ -1,6 +1,6 @@
-coolbox/__init__.py,sha256=-QLfj7uUl-2aJTKOCtcCtcWgBazpxqPKSvaS_ubTbxk,22
+coolbox/__init__.py,sha256=gbDwVXQgqJCrp_LBD8s-Ao23kHOWEZvGI_dULd1w5y8,22
 coolbox/api.py,sha256=kFF91EQBjVhJt0_TWzOea9_K15lORsqpwS6lB33hMec,1371
-coolbox/cli.py,sha256=Q4JpKmWqV-XzwEgjKpbPS3s7htxzf3udxMSiL4g7nZ8,13072
+coolbox/cli.py,sha256=ZnnuBlLQIn-SfSnpO8s5XKwEbNBv1fGfLx7F1seyfwU,13032
 coolbox/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 coolbox/core/feature.py,sha256=uS_lxkSY5XiEDV3Sy7kvSptZSLKjUXyGYdqU0jItK1Y,4783
 coolbox/core/browser/__init__.py,sha256=sSnKCwXPqLX8Lj349CWohF6zt6ORYjl68EtXNPev85c,1188
@@ -10,53 +10,53 @@ coolbox/core/browser/widgets/base.py,sha256=7JqUcbm6JiEKGAV7tTgS9dxdv5iLy5VTNkfg
 coolbox/core/browser/widgets/full.py,sha256=tTzIpGqi3zDdkHkDk8T7V03HO8q1wsr_iURZn271ZBc,1380
 coolbox/core/browser/widgets/navigation.py,sha256=uZaspuG_ihYo1fijUE9GT1qxUlQTbf14F_NO11XaqzY,10329
 coolbox/core/browser/widgets/simple.py,sha256=edMR5ATFyNfeZ9vF0WgfdbkfV1cOivQ7vdhsCqJslko,858
-coolbox/core/coverage/__init__.py,sha256=S3NkyPxwWy-ut2Gi-MR3XsRTrWXUzBE64N0HPO8Oou4,629
+coolbox/core/coverage/__init__.py,sha256=kbnMBT9CmUnHCNLxE4avQSkPHoQ-HYUooRs5YZzlSBo,629
 coolbox/core/coverage/base.py,sha256=hybOLXk0H0Btz7zJ308i0mrx7YaG8lFA4INp8KNVQdc,6075
-coolbox/core/coverage/highlights.py,sha256=3buduSzFNDTmKq_amS7Bnjl_Z0uWWzOyo3nTRs_qHvQ,6292
+coolbox/core/coverage/highlights.py,sha256=elXU0In66521Cg2hM-TvbxhtuCqtFfcccdlxoyW5OSI,6294
 coolbox/core/coverage/hlines.py,sha256=f-v54Mgz82peaJAZ3qsrqASo_0PiUzSNI9CvHCEfoaY,1744
 coolbox/core/coverage/vlines.py,sha256=6JPrFdkyHgmiGFMHLTJCAfpXGtJHv09pwJo-1Rt28xQ,3798
 coolbox/core/frame/__init__.py,sha256=uNle3cyOXuSsoneUzr0Zu8v6YNVSaKLRkR1D6Xic1Ts,59
 coolbox/core/frame/base.py,sha256=TOd-X_Cs6zQbC-xgGXMmqGjx6Vh2F9pIxdLHDwJyJpg,10645
-coolbox/core/frame/frame.py,sha256=KjSjtz_M-LbURNZ0geDC0kHehXkdSbz448pKuEfTh-0,7305
+coolbox/core/frame/frame.py,sha256=Ltrsty0xj_iSMDkNqVEZL8dCT6Trrol3P7VvpfTLkFw,7823
 coolbox/core/frame/superframe/__init__.py,sha256=GmuujYuf1O9Dy9LcU_Q774cCK_GV1R9R9rGIY82qYQk,33
 coolbox/core/frame/superframe/base.py,sha256=eX-Vx6_bjREyFJzlx7wcIxH64c2PF8hebiX5k1bvIYc,2270
 coolbox/core/frame/superframe/jointview.py,sha256=lTD20hOgl_bCo8H6Jlzm9OAFtXtBKMv0AXGJO7cRYec,9474
-coolbox/core/track/__init__.py,sha256=sKAkB6LJCw_jJft_DA9Wv25GsqQV6GPVUbM4I9cGVCs,449
+coolbox/core/track/__init__.py,sha256=GNsVAhhq3kcJtWdanlJo1IQaI4JkMQo8tO3FnVKtU4s,465
 coolbox/core/track/bam.py,sha256=eLFpbIjNXql81GBJDI8KW-ZoeRmoW5RKOwMKzEJMeiY,3297
 coolbox/core/track/base.py,sha256=UA21GuqrbWGIO4LxvGbrMViMlSzAHrWevHysLtrF0k8,8027
-coolbox/core/track/gtf.py,sha256=WNyF25pc-BF36zkuC2P8JqTAgVeRzdXo7HPvEveNjcE,5395
-coolbox/core/track/ideogram.py,sha256=hSG_W96ZKtU9oo-X4odvCSCjWrt8flANBiTHqh4_vgY,4250
-coolbox/core/track/pseudo.py,sha256=LGH9vsIHcBmlcGTzjKKj_3edFRTkJBUsBwmN4t8eyss,4813
+coolbox/core/track/gtf.py,sha256=ZgmL_Pjvb2FuznGikbRJJ9_X8MI1voFrDZvkj70mlUk,5341
+coolbox/core/track/ideogram.py,sha256=vbdIi3_Yp6kP-uwAR7HQ1KxZnJLB0cw_nMfv_orva5M,4522
+coolbox/core/track/pseudo.py,sha256=qyBpD2PqEKJoQivZ2QaKN5XJJpzLvH_cOXc_Iuzmls0,4969
+coolbox/core/track/tad.py,sha256=P7hhqWjACW47qszDzjnA4TuBJU-79lY7rIotp_qYdyo,7791
 coolbox/core/track/arcs/__init__.py,sha256=rdZHnRJ11jC2Sp1fwx29gNMteUoqkeNvS7MsN0hWIIw,553
 coolbox/core/track/arcs/base.py,sha256=kIZR-vEPGZ7ygUHDA2HGqdWVK0-2lL-sa_QzKrsPuSU,3147
 coolbox/core/track/arcs/bedpe.py,sha256=bxyXjD3a6lui4y-5lkPzjPtqF_pp1VR7gFLnuGF1wfs,2628
 coolbox/core/track/arcs/fetch.py,sha256=_VE_Aixx9Kx0s0mP50stika0d5yx7UKYBxBG_dCsvIc,660
 coolbox/core/track/arcs/hicpeaks.py,sha256=XZWU9L1MM36EN2Zvg5dWZGcxoLgChMMae-Im4y6bZTY,540
 coolbox/core/track/arcs/pairs.py,sha256=j8xNMBBGbLzEfuQMVBDeBWCKprJ6ALLhiDRtLN7TmpE,1316
-coolbox/core/track/arcs/plot.py,sha256=cIiWGAsVlax1xArmqAmYhnlEErqF35GWhMbnTNklIRo,8298
-coolbox/core/track/bed/__init__.py,sha256=Z-4E2W5utvF_aw9Ecn078dOhGzE4CygWVVJjRWkZGFQ,67
-coolbox/core/track/bed/base.py,sha256=0m8Eh7p3FzQfjn9laTg_YzdaHbdLJjdgx8VmevAfLNY,3898
-coolbox/core/track/bed/bed.py,sha256=UlICZQHVqWfj9qFKIcsiM58RdUgSfzKHxAHWQEoFZUs,929
-coolbox/core/track/bed/fetch.py,sha256=SRVJjkWEybI6uTuo1VOrCVufHPaYzAeqdzLTIqVEvIY,2018
-coolbox/core/track/bed/plot.py,sha256=z2-0WStFOkQ5L0TUMV-BMcqBvKIX2qRM9pWzbsMs0dU,23523
-coolbox/core/track/bed/tad.py,sha256=RUK371ljvanrktc1tY9PLwDyqEFlrYd7185j8Mx7DTI,371
+coolbox/core/track/arcs/plot.py,sha256=nJk9OM3QmScA2kKpNQgooBzZW37cZmerMN8td1eox08,8402
+coolbox/core/track/bed/__init__.py,sha256=Jfr1EhUYCTpJdepIFq-89bk83Fr8LDaP1twiUWrFCQI,46
+coolbox/core/track/bed/base.py,sha256=dNioGhgFCOLeoiu3mhv8ExokonHGL6CrkNzf6KLKpro,5486
+coolbox/core/track/bed/bed.py,sha256=7tSL25mU3_1heg1ftdXs-3kn79trv7faQbR3t1t4KIw,1739
+coolbox/core/track/bed/fetch.py,sha256=IR2wAeCUS1YS0qEkelkwhZNI33fjKR4e9IepAGcyK9Q,2019
+coolbox/core/track/bed/plot.py,sha256=07lnIh0-xclFbBVMyDeUmCtfSIUDveGCnWv436KDS0s,17190
 coolbox/core/track/hicmat/__init__.py,sha256=JHuqWKQ3icSRvN1DUiROizvGrGHdEfHZlokQoQRCWc0,146
-coolbox/core/track/hicmat/base.py,sha256=a9Kya9Yff3DLSH9jdSxb351MMjA2ybb39CtK6zxpyKc,5416
-coolbox/core/track/hicmat/cool.py,sha256=4PJABTzxnptWFugS_WAs6f0vTTfPzhVX_PiCmebNVtE,2676
-coolbox/core/track/hicmat/dothic.py,sha256=p61bmkhUeqY7rOGWDU-r_aXDXstl2pEsAWVKcmhbVyQ,2781
+coolbox/core/track/hicmat/base.py,sha256=vIoTfqXneugynhw0wkNCqob6Ptt4IVTkPdSWUQiUhJk,5693
+coolbox/core/track/hicmat/cool.py,sha256=FGs6JsHjG2Iy4vDjETzfhticctEaOuprzgHTyk4OBcg,2668
+coolbox/core/track/hicmat/dothic.py,sha256=M7gD85juT1vQOmbkFuoCXGF9RWI_iFyo6cfYsG7yO-0,2741
 coolbox/core/track/hicmat/hicmat.py,sha256=ZOnCN3sFJxILW11Qcw2JIU7phIjOhsbvWd9Trq7unSI,814
-coolbox/core/track/hicmat/plot.py,sha256=Vm7zjG2He75Zpcl08r1DD1PY3Lxoxu2Co1tV4KBxeME,9226
+coolbox/core/track/hicmat/plot.py,sha256=STFiEJEo8scg9GcJiVr4fgrt8DbDY0hUlyDvHl4t4OM,9411
 coolbox/core/track/hicmat/process.py,sha256=ETl2dufEVyrejcsSjyyqMvhhMLh28eV_fSMGaEY_J4g,5672
 coolbox/core/track/hicmat/hicdiff/__init__.py,sha256=7Ce79XaFBTrpG9isJykt3e7dM5p5IXJgGe1OeJKAAn0,55
 coolbox/core/track/hicmat/hicdiff/diff.py,sha256=Xu6kON7rhTurmhn7hUgnmSaEjQT-OOWWzrZyfigL1Ys,2818
 coolbox/core/track/hicmat/hicdiff/selfish.py,sha256=HRaeemZwO4MyBZAx4R4Z_NaNlwmZ1qhZwD5dlmD8USY,5184
-coolbox/core/track/hist/__init__.py,sha256=uasp1W_Hr3VhTlF6rw16jFpFpBdd8KNryhYFxhRDZR8,889
+coolbox/core/track/hist/__init__.py,sha256=GzKbiXG9kR7dfr_NZlM2EmWXl5GzzKPEcNZlzrii7FE,1090
 coolbox/core/track/hist/bam.py,sha256=tskPKPX2LdrNuuNcbxw4qcKAQJF6V3sOGNtQarNpN_E,1111
 coolbox/core/track/hist/base.py,sha256=3l34G8pGtVDHJEf_gGCQpYz75-25emUV_c3uSzYq6UY,4408
 coolbox/core/track/hist/bedgraph.py,sha256=5JCXE3pjgv_Pu4HFhaAY3Q01-nmOFZxKP_cWjbLbJCc,1609
-coolbox/core/track/hist/bigwig.py,sha256=yFU99oKJKH8d4IAJw7htqIRpQSO3rN6VFoBd8hUlfE8,3728
+coolbox/core/track/hist/bigwig.py,sha256=ZwFJAUrB9w4mTpPB3LZadtfFzGo6aGUOPi2Fp6RZjJI,3343
 coolbox/core/track/hist/hicfeature.py,sha256=d9EyUU3GNvsjzyf9hS3J-22qtdc5hfu6fbu2Q7O3-mw,9371
-coolbox/core/track/hist/plot.py,sha256=iVUWqGEAnT4vmjKbdJQObW6fovItBFy19JlQBEj8D3I,7879
+coolbox/core/track/hist/plot.py,sha256=RkN2lzhV-z6cQYIezBLUUF_KXzKCF2Zjk21vFAR4XaU,8199
 coolbox/core/track/hist/snp.py,sha256=iSn7r4CowSZMDkJ2zfRwavfQYDJhRinP5cwZVnoNLZY,3354
 coolbox/genome/hg19.txt,sha256=IdcU4R0MhT9t4wC0GyvXMiJmZAHizjPpHOzdPzyjy70,423
 coolbox/genome/hg38.txt,sha256=8LUJl2Mc9PDszabammK1DRV7Wpf7PDBvMiRjBdOHJtg,423
@@ -64,7 +64,7 @@ coolbox/genome/mm10.txt,sha256=vzWeqUgcJwoWaKFMO-p2vEQJi-Sp1C5CWhquvpu6H44,372
 coolbox/genome/mm9.txt,sha256=Hdpx0s3MmDbahX1lIuO8FEMZ5BlnrgpGZ9IG6RDT8Ho,372
 coolbox/utilities/__init__.py,sha256=yH4OKxaB2CC2KMMESC_8VswEPa60jb-QBSOLp_d2FFg,2411
 coolbox/utilities/bam.py,sha256=qR9Gey4sk2m8KjYw4jFlTKn_hYKIjyaRwE4EkehoDH4,2338
-coolbox/utilities/bed.py,sha256=j2XVZ6EteycjNZmMFsuq0UMsokFrD8kYU9ltrTOYkkY,17800
+coolbox/utilities/bed.py,sha256=s0KSgC2vXjKTzFPI3klGiyigcF14d0PGshEZH46SEz0,17804
 coolbox/utilities/doctool.py,sha256=ZfC6jLBhkATJR6iO8ghpdW3C8th7Gv7QNokfh5mo5FQ,4413
 coolbox/utilities/figtools.py,sha256=3SmHIyP8hQBHaBSVt2jgTAEtBwY9JptR6D4Z8utPcQU,4664
 coolbox/utilities/filetool.py,sha256=aEqqa7VBMZyqHtct48Qn8WizGmU65EIVi-zv9k4M9gY,2378
@@ -74,10 +74,10 @@ coolbox/utilities/logtools.py,sha256=-AY2Hb_RPv7Qydlb6ShwAknDqDPFKwXKq867AF8E99A
 coolbox/utilities/hic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 coolbox/utilities/hic/straw.py,sha256=OccMxjTnvR6_tmdQajRzDSWhubdKUka_mbMA-YH0AYk,30655
 coolbox/utilities/hic/tools.py,sha256=d2jYcrMVSVp7Ft7MholvFmdMlFzPJYagI_Od5ewH4Tk,1818
-coolbox/utilities/hic/wrap.py,sha256=JiSUIza9DTzl4KktLcDKyIE25DIBc12gZNeL1Iy7vqU,12561
-coolbox-0.3.8.data/scripts/coolbox,sha256=82rDcSSoAUZ8YUiahT-lSv77QZho8FCr1xPpbN_dK_c,67
-coolbox-0.3.8.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-coolbox-0.3.8.dist-info/METADATA,sha256=5iosVK1cDjUOLtSGolerjzQZUEgLK-pvjwryATjdwEE,1450
-coolbox-0.3.8.dist-info/WHEEL,sha256=OqRkF0eY5GHssMorFjlbTIq072vpHpF60fIQA6lS9xA,92
-coolbox-0.3.8.dist-info/top_level.txt,sha256=0n3TkrhoWU8tLVxqBDHrQNeqiV2IelFbwI4UIZC7R14,8
-coolbox-0.3.8.dist-info/RECORD,,
+coolbox/utilities/hic/wrap.py,sha256=Kq_EsP78gt3sT7oFqgzb7j19G395geMoXOAu87CtUFQ,12492
+coolbox-0.3.9.data/scripts/coolbox,sha256=82rDcSSoAUZ8YUiahT-lSv77QZho8FCr1xPpbN_dK_c,67
+coolbox-0.3.9.dist-info/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+coolbox-0.3.9.dist-info/METADATA,sha256=FAMWtEhJF3eJN11hbMbV-HbwieoB4dkELvoOMKCdA_A,1635
+coolbox-0.3.9.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+coolbox-0.3.9.dist-info/top_level.txt,sha256=0n3TkrhoWU8tLVxqBDHrQNeqiV2IelFbwI4UIZC7R14,8
+coolbox-0.3.9.dist-info/RECORD,,

{coolbox-0.3.8.dist-info → coolbox-0.3.9.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.36.2)
+Generator: setuptools (75.8.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

coolbox/core/track/bed/tad.py

@@ -1,18 +0,0 @@
-from .bed import BED
-from .base import BedBase
-
-
-class TAD(BED):
-    """
-    Tad tack from bed file
-    """
-
-    DEFAULT_PROPERTIES = {
-        'style': BedBase.STYLE_TAD,
-        'alpha': 0.3,
-    }
-
-    def __init__(self, file, **kwargs):
-        properties = TAD.DEFAULT_PROPERTIES.copy()
-        properties.update(kwargs)
-        super().__init__(file, **properties)