coolbox 0.1.4__tar.gz → 0.4.0__tar.gz

coolbox-0.4.0/PKG-INFO

@@ -0,0 +1,164 @@
+Metadata-Version: 2.4
+Name: coolbox
+Version: 0.4.0
+Summary: Jupyter notebook based genomic data visulization toolkit.
+Author-email: Weize Xu <vet.xwz@gmail.com>
+License: GPLv3
+Project-URL: Homepage, https://github.com/GangCaoLab/CoolBox
+Project-URL: Documentation, https://gangcaolab.github.io/CoolBox/index.html
+Project-URL: Repository, https://github.com/GangCaoLab/CoolBox
+Project-URL: Bug Tracker, https://github.com/GangCaoLab/CoolBox/issues
+Keywords: genomics,bioinformatics,visualization,Jupyter
+Classifier: Development Status :: 3 - Alpha
+Classifier: Operating System :: POSIX
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: <4,>=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scipy>=1.0.0
+Requires-Dist: numpy
+Requires-Dist: pandas>=1.0.0
+Requires-Dist: statsmodels
+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: h5py
+Requires-Dist: cooler
+Requires-Dist: numpydoc
+Requires-Dist: fire
+Requires-Dist: oxbow>=0.4.2
+Provides-Extra: doc
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+Requires-Dist: autodocsumm; extra == "doc"
+Requires-Dist: recommonmark; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
+Requires-Dist: sphinx_gallery; extra == "doc"
+Requires-Dist: sphinx-autobuild; extra == "doc"
+Provides-Extra: strawc
+Requires-Dist: strawC; extra == "strawc"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Dynamic: license-file
+
+<p align="center">
+  <img src="docs/images/banner.png">
+</p>
+
+<hr>
+
+<p align="center">
+
+  <a href="https://mybinder.org/v2/gh/GangCaoLab/CoolBox/master?filepath=tests%2FTestRegion.ipynb">
+    <img src="https://mybinder.org/badge_logo.svg" alt="Binder" />
+  </a>
+  
+  <a href="https://anaconda.org/bioconda/coolbox">
+    <img src="https://img.shields.io/conda/v/bioconda/coolbox" alt="Install with conda" />
+  </a>
+  
+  
+  <a href="https://pypi.python.org/pypi/coolbox/">
+    <img src="https://img.shields.io/pypi/v/coolbox.svg" alt="Install with PyPi" />
+  </a>
+  
+  <a href="https://hub.docker.com/r/nanguage/coolbox">
+  	<img src="https://img.shields.io/docker/v/nanguage/coolbox?label=docker&logo=docker&sort=semver" alt="Docker version">
+  </a>
+  
+  <a href="https://github.com/GangCaoLab/CoolBox/releases">
+  	<img src="https://img.shields.io/github/v/release/gangcaolab/coolbox?include_prereleases&label=github" alt="Github release">
+  </a>
+ 
+  <a href="https://gangcaolab.github.io/CoolBox/index.html">
+  	<img src="https://readthedocs.org/projects/ansicolortags/badge/?version=latest" alt="Documentation">
+  </a>
+  
+  <a href="https://pypi.python.org/pypi/coolbox">
+    <img src="https://img.shields.io/pypi/pyversions/coolbox.svg" alt="Version">
+  </a>
+  
+  <a href="https://pepy.tech/project/coolbox">
+    <img src="https://pepy.tech/badge/coolbox" alt="Downloads">
+  </a>
+
+  <a href="https://pepy.tech/project/coolbox">
+    <img src="https://pepy.tech/badge/coolbox/week" alt="Downloads per week">
+  </a>
+  
+  <a href="https://github.com/GangCaoLab/coolbox/actions/workflows/python-package-conda.yml">
+    <img src="https://github.com/GangCaoLab/coolbox/actions/workflows/python-package-conda.yml/badge.svg" alt="Build Status">
+  </a>
+
+  <a href="https://www.biorxiv.org/content/10.1101/2021.04.15.439923v1">
+    <img src="https://img.shields.io/badge/preprint-biorxiv-red" alt="biorxiv">
+  </a>
+
+  <a href="https://github.com/GangCaoLab/CoolBox/blob/master/LICENSE">
+    <img src="https://img.shields.io/github/license/GangCaoLab/coolbox" alt="license">
+  </a>
+
+</p>
+
+
+Flexible, user-friendly genomic data visualization toolkit. 
+
+![](docs/images/api_and_cli.png)
+
+## Highlights:
+
+* Multi-omics data interactively visualization.
+* User-friendly [API (ggplot2-like Python EDSL)](https://gangcaolab.github.io/CoolBox/quick_start_API.html) and [CLI](https://gangcaolab.github.io/CoolBox/quick_start_CLI.html).
+* Show within Jupyter notebook.
+* Ease to fetch data and in cooperation with other Python package.
+* Ease to implement/add custom track and integrate into CoolBox.
+
+More details please read the [documentation](https://gangcaolab.github.io/CoolBox/index.html).
+Interactively online demo: [binder](https://mybinder.org/v2/gh/GangCaoLab/CoolBox/master?filepath=tests%2FTestRegion.ipynb)
+
+## Develop
+
+See [CONTRIBUTING.md](https://github.com/GangCaoLab/CoolBox/blob/master/CONTRIBUTING.md) 
+
+## Citation
+
+```
+@article{xu2021coolbox,
+  title={CoolBox: A flexible toolkit for visual analysis of genomics data},
+  author={Xu, Weize and Zhong, Quan and Lin, Da and Zuo, Ya and Dai, Jinxia and Li, Guoliang and Cao, Gang},
+  journal={BMC bioinformatics},
+  volume={22},
+  number={1},
+  pages={1--9},
+  year={2021},
+  publisher={Springer}
+}
+```
+
+## Thanks
+
++ [pyGenomeTracks](https://github.com/deeptools/pyGenomeTracks),
+CoolBox's plot system is fork from it.
+
+### Contributors 
+This project exists thanks to all the people who contribute. 
+
+<a href="https://github.com/GangCaoLab/CoolBox/graphs/contributors">
+  <img src="https://contrib.rocks/image?repo=GangCaoLab/CoolBox" />
+</a>
+

coolbox-0.4.0/README.md

@@ -0,0 +1,106 @@
+<p align="center">
+  <img src="docs/images/banner.png">
+</p>
+
+<hr>
+
+<p align="center">
+
+  <a href="https://mybinder.org/v2/gh/GangCaoLab/CoolBox/master?filepath=tests%2FTestRegion.ipynb">
+    <img src="https://mybinder.org/badge_logo.svg" alt="Binder" />
+  </a>
+  
+  <a href="https://anaconda.org/bioconda/coolbox">
+    <img src="https://img.shields.io/conda/v/bioconda/coolbox" alt="Install with conda" />
+  </a>
+  
+  
+  <a href="https://pypi.python.org/pypi/coolbox/">
+    <img src="https://img.shields.io/pypi/v/coolbox.svg" alt="Install with PyPi" />
+  </a>
+  
+  <a href="https://hub.docker.com/r/nanguage/coolbox">
+  	<img src="https://img.shields.io/docker/v/nanguage/coolbox?label=docker&logo=docker&sort=semver" alt="Docker version">
+  </a>
+  
+  <a href="https://github.com/GangCaoLab/CoolBox/releases">
+  	<img src="https://img.shields.io/github/v/release/gangcaolab/coolbox?include_prereleases&label=github" alt="Github release">
+  </a>
+ 
+  <a href="https://gangcaolab.github.io/CoolBox/index.html">
+  	<img src="https://readthedocs.org/projects/ansicolortags/badge/?version=latest" alt="Documentation">
+  </a>
+  
+  <a href="https://pypi.python.org/pypi/coolbox">
+    <img src="https://img.shields.io/pypi/pyversions/coolbox.svg" alt="Version">
+  </a>
+  
+  <a href="https://pepy.tech/project/coolbox">
+    <img src="https://pepy.tech/badge/coolbox" alt="Downloads">
+  </a>
+
+  <a href="https://pepy.tech/project/coolbox">
+    <img src="https://pepy.tech/badge/coolbox/week" alt="Downloads per week">
+  </a>
+  
+  <a href="https://github.com/GangCaoLab/coolbox/actions/workflows/python-package-conda.yml">
+    <img src="https://github.com/GangCaoLab/coolbox/actions/workflows/python-package-conda.yml/badge.svg" alt="Build Status">
+  </a>
+
+  <a href="https://www.biorxiv.org/content/10.1101/2021.04.15.439923v1">
+    <img src="https://img.shields.io/badge/preprint-biorxiv-red" alt="biorxiv">
+  </a>
+
+  <a href="https://github.com/GangCaoLab/CoolBox/blob/master/LICENSE">
+    <img src="https://img.shields.io/github/license/GangCaoLab/coolbox" alt="license">
+  </a>
+
+</p>
+
+
+Flexible, user-friendly genomic data visualization toolkit. 
+
+![](docs/images/api_and_cli.png)
+
+## Highlights:
+
+* Multi-omics data interactively visualization.
+* User-friendly [API (ggplot2-like Python EDSL)](https://gangcaolab.github.io/CoolBox/quick_start_API.html) and [CLI](https://gangcaolab.github.io/CoolBox/quick_start_CLI.html).
+* Show within Jupyter notebook.
+* Ease to fetch data and in cooperation with other Python package.
+* Ease to implement/add custom track and integrate into CoolBox.
+
+More details please read the [documentation](https://gangcaolab.github.io/CoolBox/index.html).
+Interactively online demo: [binder](https://mybinder.org/v2/gh/GangCaoLab/CoolBox/master?filepath=tests%2FTestRegion.ipynb)
+
+## Develop
+
+See [CONTRIBUTING.md](https://github.com/GangCaoLab/CoolBox/blob/master/CONTRIBUTING.md) 
+
+## Citation
+
+```
+@article{xu2021coolbox,
+  title={CoolBox: A flexible toolkit for visual analysis of genomics data},
+  author={Xu, Weize and Zhong, Quan and Lin, Da and Zuo, Ya and Dai, Jinxia and Li, Guoliang and Cao, Gang},
+  journal={BMC bioinformatics},
+  volume={22},
+  number={1},
+  pages={1--9},
+  year={2021},
+  publisher={Springer}
+}
+```
+
+## Thanks
+
++ [pyGenomeTracks](https://github.com/deeptools/pyGenomeTracks),
+CoolBox's plot system is fork from it.
+
+### Contributors 
+This project exists thanks to all the people who contribute. 
+
+<a href="https://github.com/GangCaoLab/CoolBox/graphs/contributors">
+  <img src="https://contrib.rocks/image?repo=GangCaoLab/CoolBox" />
+</a>
+

coolbox-0.4.0/coolbox/__init__.py

@@ -0,0 +1 @@
+__version__ = '0.4.0'

coolbox-0.4.0/coolbox/__main__.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python
+
+from coolbox.cli import CLI
+import fire
+
+
+def main():
+    fire.Fire(CLI)
+
+
+if __name__ == "__main__":
+    main()

{coolbox-0.1.4 → coolbox-0.4.0}/coolbox/api.py

@@ -64,11 +64,13 @@ The rule of element composition:
 """
 
 import warnings
+
 warnings.filterwarnings('ignore')
 
 from coolbox.core.track import *
-from coolbox.core.frame import Frame
+from coolbox.core.frame import *
 from coolbox.core.feature import *
 from coolbox.core.coverage import *
 from coolbox.core.browser import *
-
+from coolbox.core.frame.superframe import JointView
+from coolbox.utilities.genome import GenomeRange

coolbox-0.4.0/coolbox/cli.py

@@ -0,0 +1,373 @@
+import os
+import os.path as osp
+import subprocess as subp
+from typing import Tuple
+import runpy
+
+import fire
+import nbformat as nbf
+
+import coolbox
+from coolbox.utilities import get_logger
+from coolbox.utilities.genome import GenomeRange
+from coolbox.api import *
+
+log = get_logger("CoolBox CLI")
+
+
+def get_element_type_by_str(elem_str):
+    import coolbox.api
+    try:
+        elem_tp = eval("coolbox.api." + elem_str)
+    except NameError:
+        log.error(
+            f"No element type name as {elem_tp}, all elements type see: " +
+            "https://gangcaolab.github.io/CoolBox/api.html"
+        )
+    return elem_tp
+
+
+def get_compose_code(elem_str, args, kwargs):
+    compose_code = elem_str + "("
+    compose_code += ", ".join(
+        [repr(arg) for arg in args] +
+        [f"{k} = {repr(v)}" for k, v in kwargs.items()]
+    )
+    compose_code += ")"
+    return compose_code
+
+
+FRAME_POS = ("left", "right", "top", "bottom", "center")
+
+
+class CLI(object):
+    """
+    CoolBox Command Line Interface
+
+    You can use this cli to create coolbox browser instance,
+    visualize your data directly in shell.
+
+    example:
+
+    1. Draw tracks within a genome range, save figure to a pdf file:
+
+        $ coolbox add XAxis - add BigWig test.bw - goto "chr1:5000000-6000000" - plot test.pdf
+
+    2. Generate a notebook and run jupyter to open browser:
+
+        $ coolbox add XAxis - add BigWig test.bw - goto "chr1:5000000-6000000" - run_jupyter
+
+    3. Run a independent web application.
+
+        $ coolbox add XAxis - add BigWig test.bw - goto "chr1:5000000-6000000" - run_webapp
+
+    """
+
+    def __init__(self, genome="hg19", genome_range: str = None, genome_range2: str = None):
+        self._indent = 0
+        self.current_range = [None, None]
+        self.goto(genome_range, genome_range2)
+        self.genome = genome
+        self.frame_pos = None
+        self.frames = {}
+
+    @staticmethod
+    def version():
+        """print coolbox version"""
+        print(coolbox.__version__)
+
+    def set_genome(self, genome):
+        """Set reference genome for browser object.
+
+        :param genome: Reference genome (hg19, hg38, mm9, mm10),
+        or the path to chromosomes size file(tab splited chromname-size).
+        """
+        self.genome = genome
+        return self
+
+    def goto(self, genome_range: str = None, genome_range2: str = None):
+        """Goto a genome range.
+
+        :param genome_range: Genome range string, like "chr9:4000000-6000000".
+        :param genome_range2: Genome range string, like "chr9:4000000-6000000. Only required in JointView mode".
+        """
+        if genome_range2 is None:
+            genome_range2 = genome_range
+        # validate genome range
+        if genome_range:
+            gr = GenomeRange(genome_range)
+        if genome_range2:
+            gr = GenomeRange(genome_range2)
+        log.info(f"Goto genome range '{genome_range}' '{genome_range2}'")
+        self.current_range = [genome_range, genome_range2]
+
+        return self
+
+    @staticmethod
+    def show_doc(elem_str):
+        """Print the document of specified Element type. For example: coolbox show_doc Cool"""
+        elem_tp = get_element_type_by_str(elem_str)
+        print(elem_tp.__doc__)
+
+    def joint_view(self, frame_pos: str = "top"):
+        """Start a new frame positioned at the specified frame_pos in the final joint view.
+        The center frame should be a single Cool, HicMat, DotHic track.
+
+        For example:
+        coolbox - \
+        joint_view top - \
+            add BigWig BW_PATH - \
+        joint_view right - \
+            add GTF BTF_PATH - \
+        joint_view center - \
+            add Cool - \
+        goto 'chr1:100000-200000' 'chr2:200000-30000' - \
+        plot /tmp/test_joint_view.svg
+
+        Parameters
+        ----------
+        frame_pos: str
+        Add a frame in the given position in the joint view.
+        Should be one of 'top', 'left', 'center', 'bottom', 'right'.
+
+        Returns
+        -------
+
+        """
+        if frame_pos not in FRAME_POS:
+            raise ValueError(f"Frame position should be one of {FRAME_POS}")
+        if frame_pos not in self.frames:
+            self.frames[frame_pos] = "frame = Frame()\n"
+        self.frame_pos = frame_pos
+
+        return self
+
+    def add(self, elem_str, *args, **kwargs):
+        """Add a Element(Track, Coverage, Feature), for example: coolbox add XAxis
+
+        :param elem_str: Element type string. Like BAM, BigWig, Cool ...
+        Full list of Track types
+        can be found here(https://gangcaolab.github.io/CoolBox/quick_start_API.html#Track-types).
+        :param args: Positional args for create elements.
+        :param kwargs: Keyword args for create elements.
+        """
+        if ("help" in args) or ("help" in kwargs):
+            self.show_doc(elem_str)
+            return
+        if self.frame_pos is None:
+            self.joint_view("top")
+
+        compose_code = get_compose_code(elem_str, args, kwargs)
+        log.info(f"Create element, compose code: {compose_code}")
+        self.frames[self.frame_pos] += "    " * self._indent + "frame += " + compose_code + "\n"
+        return self
+
+    def start_with(self, elem_str, *args, **kwargs):
+        """Start a 'with' block, apply the element to all elements within the block.
+
+        :param elem_str: Element type string. Like VLines, Color, MinValue ...
+        :param args: Positional args for create elements.
+        :param kwargs: Keyword args for create elements.
+        """
+        if ("help" in args) or ("help" in kwargs):
+            self.show_doc(elem_str)
+            return
+        if self.frame_pos is None:
+            self.joint_view("top")
+
+        compose_code = get_compose_code(elem_str, args, kwargs)
+        log.info(f"Create a with block, compose code: {compose_code}")
+        self.frames[self.frame_pos] += "    " * self._indent + f"with {compose_code}:\n"
+        self._indent += 1
+        return self
+
+    def end_with(self):
+        """End the with block"""
+        if self._indent <= 0:
+            raise ValueError("Expect a 'start_with' command before end_with clause.")
+        self._indent -= 1
+        return self
+
+    @staticmethod
+    def _fetch_frame_src(pos: str, source: str) -> Tuple[str, str]:
+        """
+
+        Parameters
+        ----------
+        pos
+        source
+
+        Returns
+        -------
+        Tuple[str, str].
+        The first string is the frame's variable name, and the second string is the function's source code
+        """
+        # center frame return the first track. expected a Cool, DotHiC, HicMat
+        if pos != 'center':
+            source += "return frame\n"
+        else:
+            source += "return list(frame.tracks.values())[0]\n"
+        source = "\n".join("    " + line for line in source.split("\n")) + "\n"
+        # generate function and call
+        frame_var = f"{pos}_frame"
+        source = f"def fetch_{frame_var}():\n" + source
+        source += f"{frame_var} = fetch_{frame_var}()\n"
+
+        return frame_var, source
+
+    def source(self) -> str:
+        num_frames = len(self.frames)
+        if num_frames == 0:
+            raise RuntimeError("No frame has been added yet.")
+
+        if num_frames > 1 and 'center' not in self.frames:
+            raise RuntimeError("JointView mode needs a center frame. "
+                               "Use `joint_view center ADD xxx` to add center track/frame.")
+        gr1, gr2 = self.current_range
+        if gr1 is None:
+            raise RuntimeError("No genome range found."
+                               "Use `goto chr1:5000000-6000000` to set the genome range.")
+
+        frame_dict = {}
+        source = ""
+        for pos, src in self.frames.items():
+            frame_var, frame_src = self._fetch_frame_src(pos, src)
+            source += frame_src
+            frame_dict[pos] = frame_var
+
+        if 'center' in self.frames:
+            source += f"frame = JointView({frame_dict['center']}, " \
+                      f"left={frame_dict.get('left')}, " \
+                      f"right={frame_dict.get('right')}, " \
+                      f"bottom={frame_dict.get('bottom')}, " \
+                      f"top={frame_dict.get('top')}" \
+                      f")\n"
+        else:
+            source += f"frame = {list(frame_dict.values())[0]}\n"
+
+        return source
+
+    def print_source(self):
+        """Print the browser composing code."""
+        print(self.source())
+
+    def gen_notebook(self, notebook_path, notes=True, figsave=True):
+        """Generate The notebook contain codes for run coolbox browser.
+
+        :param notebook_path: The output notebook path.
+        :param notes: Generate markdown notes in notebook or not.
+        :param figsave: Generate codes for saving figure or not.
+        """
+        code = nbf.v4.new_code_cell
+        markdown = nbf.v4.new_markdown_cell
+        nb = nbf.v4.new_notebook()
+        cells = []
+        if notes:
+            cells.append(
+                markdown("**Run the cell bellow to start the CoolBox browser.**")
+            )
+        cells.append(
+            code(
+                f"import os; os.chdir('{os.getcwd()}')\n"
+                "import coolbox.api\n" +
+                "from coolbox.api import *\n" +
+                self.source() +
+                f"bsr = Browser(frame, reference_genome='{self.genome}')\n" +
+                (f"bsr.goto('{str(self.current_range[0])}')\n" if self.current_range[0] else "") +
+                "bsr.show()"
+            ),
+        )
+        if figsave:
+            if notes:
+                cells.append(
+                    markdown("**Run the cell bellow to save your figure.**"),
+                )
+            cells.append(
+                code("bsr.save('test.pdf')"),
+            )
+        nb['cells'] = cells
+        nbf.write(nb, notebook_path)
+
+    def run_jupyter(self, jupyter_args="--ip=0.0.0.0"):
+        """Create a notebook according to command line, then start a jupyter process.
+
+        :param jupyter_args: Arguments for run jupyter.
+        """
+        i = 0
+        tmp_notebook = lambda: f"/tmp/coolbox_tmp.{i}.ipynb"
+        while osp.exists(tmp_notebook()):
+            i += 1
+        tmp = tmp_notebook()
+        self.gen_notebook(tmp)
+        subp.check_call(f"jupyter notebook {tmp} " + jupyter_args, shell=True)
+
+    def plot(self, fig_path, genome_range=None, genome_range2=None):
+        """Draw a figure within a genome range and save to file
+
+        :param fig_path: Figure save path
+        :param genome_range: Genome range string, like "chr9:4000000-6000000".
+        :param genome_range2: Genome range string, like "chr9:4000000-6000000".
+        """
+        if genome_range is None:
+            if self.current_range[0] is None:
+                raise ValueError("Should specify the gr")
+        else:
+            self.goto(genome_range, genome_range2)
+        source = "from coolbox.api import *\n" + self.source() + "\n"
+        gr1, gr2 = self.current_range
+        if 'center' in self.frames:
+            source += f"fig = frame.plot('{gr1}', '{gr2}')\n"
+            # TODO: svgutils.compose.Figure can only save to svg, convert it?
+            if not fig_path.endswith('.svg'):
+                fig_path = fig_path[:-4] + '.svg'
+                log.warning(f"The JointView only support save to svg now. Save fig to: {fig_path}.")
+            source += f"fig.save('{fig_path}')\n"
+        else:
+            source += f"fig = frame.plot('{gr1}')\n"
+            source += f"fig.savefig('{fig_path}')\n"
+        try:
+            code = compile(source, "coolbox_cli_source", "exec")
+            eval(code)
+        except Exception as e:
+            log.error(
+                "Error when execute the generated source code:\n\n" +
+                "------------------------\n" +
+                source + "\n" +
+                "------------------------\n\n"
+            )
+            if type(e) == NameError:
+                log.error(
+                    f"All elements type see: " +
+                    "https://gangcaolab.github.io/CoolBox/api.html"
+                )
+            raise e
+
+    def run_webapp(self, voila_args="--Voila.ip=0.0.0.0"):
+        """Run a independent coolbox browser web app.
+        (Create notebook and run voila)
+
+        :param voila_args: Arguments for run jupyter.
+        """
+        i = 0
+        tmp_notebook = lambda: f"/tmp/coolbox_tmp.{i}.ipynb"
+        while osp.exists(tmp_notebook()):
+            i += 1
+        tmp = tmp_notebook()
+        self.gen_notebook(tmp, notes=False, figsave=False)
+        subp.check_call(f"voila {tmp} " + voila_args, shell=True)
+
+    def load_module(self, mod_str):
+        """
+        Import custom tracks from a module/package for example:
+
+            $ coolbox - load_module ./my_custom.py - add XAxis - add CustomTrack - goto "chr1:5000000-6000000" - run_webapp
+
+        :param mod_str: Path to the module.
+        """
+        globals().update(runpy.run_path(mod_str, init_globals=globals()))
+        return self
+
+
+if __name__ == "__main__":
+    fire.Fire(CLI)
+