trackplot 0.5.3__tar.gz → 0.5.4__tar.gz

{trackplot-0.5.3 → trackplot-0.5.4}/PKG-INFO

@@ -1,34 +1,30 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: trackplot
-Version: 0.5.3
+Version: 0.5.4
 Summary: The trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. https://sashimi.readthedocs.io/
-License: BSD-3
-Author: ygidtu
-Author-email: ygidtu@gmail.com
-Requires-Python: >=3.10,<3.13
-Classifier: License :: Other/Proprietary License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: adjusttext (>=0.7.3,<0.8.0)
-Requires-Dist: cairocffi (>=1.4.0,<2.0.0)
-Requires-Dist: click (>=8.1.3,<9.0.0)
-Requires-Dist: click-option-group (>=0.5.5,<0.6.0)
-Requires-Dist: filetype (>=1.2.0,<2.0.0)
-Requires-Dist: flask (>=2.3.2,<3.0.0)
-Requires-Dist: hicmatrix (>=17,<18)
-Requires-Dist: loguru (>=0.6.0,<0.7.0)
-Requires-Dist: matplotlib (>=3.6.3,<4.0.0)
-Requires-Dist: numpy (>=1.24.1,<2.0.0)
-Requires-Dist: pandas (>=1.5.3,<2.0.0)
-Requires-Dist: pybigwig (>=0.3.18,<0.4.0)
-Requires-Dist: pysam (>=0.21.0,<0.22.0)
-Requires-Dist: requests (>=2.28.2,<3.0.0)
-Requires-Dist: scipy (>=1.10.0,<2.0.0)
-Requires-Dist: seaborn (>=0.12.2,<0.13.0)
-Requires-Dist: xmltodict (>=0.13.0,<0.14.0)
+Author-email: ygidtu <ygidtu@gmail.com>
+License-Expression: BSD-3-Clause
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: adjusttext>=1.3.0
+Requires-Dist: cairocffi>=1.7.1
+Requires-Dist: click>=8.2.1
+Requires-Dist: click-option-group>=0.5.7
+Requires-Dist: filetype>=1.2.0
+Requires-Dist: flask>=3.1.1
+Requires-Dist: hicmatrix>=17.2
+Requires-Dist: loguru>=0.7.3
+Requires-Dist: matplotlib>=3.10.3
+Requires-Dist: numpy>=2.3.0
+Requires-Dist: pandas>=2.3.0
+Requires-Dist: pybigwig>=0.3.24
+Requires-Dist: pysam>=0.23.3
+Requires-Dist: requests>=2.32.4
+Requires-Dist: scipy>=1.15.3
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: xmltodict>=0.14.2
+Dynamic: license-file
 
 # trackplot
 
@@ -298,4 +294,3 @@ contact [Yiming Zhang](https://github.com/ygidtu) or
 If you use the tool in your publication, please cite by
 
 [Zhang Y, Zhou R, Liu L, et al. Trackplot: A flexible toolkit for combinatorial analysis of genomic data[J]. PLoS computational biology, 2023, 19(9): e1011477.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011477)
-

trackplot-0.5.4/pyproject.toml

@@ -0,0 +1,48 @@
+[project]
+name = "trackplot"
+version = "0.5.4"
+description = "The trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. https://sashimi.readthedocs.io/"
+authors = [
+    { name = "ygidtu", email = "ygidtu@gmail.com" }
+]
+license = "BSD-3-Clause"
+readme = "README.md"
+requires-python = ">=3.11"
+dependencies = [
+    "adjusttext>=1.3.0",
+    "cairocffi>=1.7.1",
+    "click>=8.2.1",
+    "click-option-group>=0.5.7",
+    "filetype>=1.2.0",
+    "flask>=3.1.1",
+    "hicmatrix>=17.2",
+    "loguru>=0.7.3",
+    "matplotlib>=3.10.3",
+    "numpy>=2.3.0",
+    "pandas>=2.3.0",
+    "pybigwig>=0.3.24",
+    "pysam>=0.23.3",
+    "requests>=2.32.4",
+    "scipy>=1.15.3",
+    "seaborn>=0.13.2",
+    "xmltodict>=0.14.2",
+]
+
+
+[build-system]
+requires = ["setuptools>=65.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+
+[tool.setuptools.packages.find]
+# 搜索目前目录下的trackplot和ui及其子文件夹
+where = ["."]
+include = ["trackplot*", "ui*"]  # 通配符匹配所有子包
+
+
+[tool.setuptools.package-data]
+# 不限定父目录(等号前为父目录)，包含其下匹配特定正则的文件
+"*" = [
+    "pyproject.toml", "*"
+]
+

trackplot-0.5.4/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

{trackplot-0.5.3 → trackplot-0.5.4}/trackplot/plot.py

@@ -30,7 +30,7 @@ logging.getLogger('matplotlib.font_manager').setLevel(logging.ERROR)
 faulthandler.enable()
 
 
-__version__ = "0.5.3"
+__version__ = "0.5.4"
 __author__ = "ygidtu & Ran Zhou"
 __email__ = "ygidtu@gmail.com"
 

{trackplot-0.5.3 → trackplot-0.5.4}/trackplot/plot_func.py

@@ -190,9 +190,6 @@ def init_graph_coords(region: GenomicLoci, exons: Optional[List[List[int]]] = No
                 for i in range(exons[1][1] +1, len(region)):
                     steps[i] = step
             graph_coords = list(map(int, itertools.accumulate(steps)))
-            #increments match exactly with original code
-            #for i, e in enumerate(graph_objects):
-            #    print(f"{i}\t{e}")
     else:
         # if there is not any exons, just init graph_coords by region
         for i, j in enumerate(range(region.start, region.end + 1)):
@@ -764,6 +761,7 @@ def plot_density(
         if data.strand_aware:
             max_used_y_val = max(abs(min_used_y_val), max_used_y_val)
             min_used_y_val = -max(abs(min_used_y_val), max_used_y_val) if data.minus is not None else 0
+            
     if jxns:
         # sort the junctions by intron length for better plotting look
         jxns_sorted_list = sorted(jxns.keys(), key=lambda x: (x.end - x.start, x.start, x.end), reverse=True)
@@ -775,11 +773,8 @@ def plot_density(
             min_junction_count = min(jxns.values())
         junction_count_gap = max_junction_count - min_junction_count
 
-        #recorded_pts = set()
         jxn_numbers = []
-
         for jxn_idx, jxn in enumerate(jxns_sorted_list):
-            #logger.info(f"junctions of {y_label}: {jxn} - {round(jxns[jxn], 2)}")
             leftss, rightss = jxn.start, jxn.end
 
             # junction must at least have one anchor located in plotted region
@@ -792,18 +787,15 @@ def plot_density(
             # the junction out of boundaries, set the boundaries as coordinate
             ss1_idx, ss1_modified = get_limited_index(leftss - region.start, len(graph_coords))
             ss2_idx, ss2_modified = get_limited_index(rightss - region.start, len(graph_coords))
-            #logger.info(f"{y_label} ss1_idx {ss1_idx} ss1_modified {ss1_modified} ss2_idx {ss2_idx} ss2_modified {ss2_modified}")
             u"""
             @2019.01.14
             add two new variables to make it clear which one is index, which one is genomic site 
             """
             ss1, ss2 = graph_coords[ss1_idx], graph_coords[ss2_idx]
             # AD = keep junction arcs on top
-            #min_used_y_val = 1
             jxn_on_top = True
-            min_used_y_val = 0
-            # draw junction on bottom
-            """
+
+            # draw junction on bottom 
             if kwargs.get("density_by_strand"):
                 jxn_on_top = jxn.strand == "+"
             else:
@@ -811,7 +803,7 @@ def plot_density(
                 #jxn_on_top = True # AD - keep all junctions on same strand
                 if abs(min_used_y_val) < max_used_y_val:
                     min_used_y_val = -max_used_y_val
-            """
+            
             if fill_step == "post":
                 ss1_idx = max(0, ss1_idx - 1)
             elif fill_step == "pre":
@@ -835,14 +827,7 @@ def plot_density(
                     -right_dens - current_height,
                     -right_dens if not ss2_modified else -right_dens - current_height
                 ]
-            """
-            if sum(pts) > 0:
-                pts_ = "_".join([str(x) for x in pts])
-                while pts_ in recorded_pts:
-                    pts[1], pts[2] = pts[1] * 1.1, pts[2] * 1.1
-                    pts_ = "_".join([str(x) for x in pts])
-                recorded_pts.add(pts_)
-            """
+  
             """
             @2018.12.26
             scale the junctions line width
@@ -853,39 +838,26 @@ def plot_density(
             else:
                 line_width = 0
             #line_width = max(.5,np.log())
-            #pts = [(ss1, pts[0]), (ss1, pts[1]), (ss2, pts[2]), (ss2, pts[3])]
-            
 
-            temp = np.linspace(0, 1.0, 100)
-            bdist = beta.pdf(temp, 3, 3)  # or  2, 2
-            bdist /= np.max(bdist) # max = 1
-            bdist *= jxns[jxn]
-            pts_x = np.linspace(ss1, ss2, 100)
-            
-            #pts = [(ss1, 0), (ss1+5, jxns[jxn]), (ss2-5, jxns[jxn]), (ss2, 0)]
-            path = Path(np.array([pts_x, bdist]).T)
-            patch = PathPatch(path, facecolor='none', edgecolor="#BA55D3", linewidth=line_width)
-            ax.add_patch(patch)
-            """
-            # pts = [(ss1, 0), (midpt-5, jxns[jxn]), (midpt+5, jxns[jxn]), (ss2, 0)]
+            pts = [(ss1, pts[0]), (ss1, pts[1]), (ss2, pts[2]), (ss2, pts[3])]
             ax.add_patch(PathPatch(Path(pts, [Path.MOVETO, Path.CURVE4, Path.CURVE4, Path.CURVE4]),
-                                   ec="#BA55D3", lw=line_width, fc='none'))
-                                   #ec=color, lw=line_width + 0.2, fc='none'))
-            """
+                                   ec=color, lw=line_width + 0.2, fc='none'))
+            
             if show_junction_number:
-                t = ax.text( (ss1+ss2)/2, jxns[jxn] * 1.1, 
-                            '{0}'.format(round(jxns[jxn], 2)),
-                            fontsize=junction_number_font_size, ha='center', va='center')
-                            #, backgroundcolor='w' ) AD - white here overrides transparency below
+                midpt = cubic_bezier(pts, .5)
+
+                t = ax.text(
+                    midpt[0], midpt[1],
+                    '{0}'.format(round(jxns[jxn], 2)),
+                    fontsize=junction_number_font_size,
+                    ha='center', va='center',
+                    backgroundcolor='w'
+                )
+
                 # @2018.12.19 transparent background
                 t.set_bbox(dict(alpha=0))
                 jxn_numbers.append(t)
 
-        # AD - this adds  a dot next to the counts
-        #try:
-        #    adjust_text(jxn_numbers, force_text=(0.2, 0.2), arrowprops=dict(arrowstyle="-", color='black', lw=1))
-        #except IndexError as err:
-        #    logger.debug(err)
 
     if obj and obj.title:
         ax.text(max(graph_coords) - len(obj.title), max_used_y_val, obj.title, color=color, fontsize=font_size)

trackplot-0.5.4/trackplot.egg-info/PKG-INFO

@@ -0,0 +1,296 @@
+Metadata-Version: 2.4
+Name: trackplot
+Version: 0.5.4
+Summary: The trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. https://sashimi.readthedocs.io/
+Author-email: ygidtu <ygidtu@gmail.com>
+License-Expression: BSD-3-Clause
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: adjusttext>=1.3.0
+Requires-Dist: cairocffi>=1.7.1
+Requires-Dist: click>=8.2.1
+Requires-Dist: click-option-group>=0.5.7
+Requires-Dist: filetype>=1.2.0
+Requires-Dist: flask>=3.1.1
+Requires-Dist: hicmatrix>=17.2
+Requires-Dist: loguru>=0.7.3
+Requires-Dist: matplotlib>=3.10.3
+Requires-Dist: numpy>=2.3.0
+Requires-Dist: pandas>=2.3.0
+Requires-Dist: pybigwig>=0.3.24
+Requires-Dist: pysam>=0.23.3
+Requires-Dist: requests>=2.32.4
+Requires-Dist: scipy>=1.15.3
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: xmltodict>=0.14.2
+Dynamic: license-file
+
+# trackplot
+
+[![PyPI version](https://badge.fury.io/py/trackplot.svg)](https://pypi.org/project/trackplot/)
+[![PyPI download](https://img.shields.io/pypi/dm/trackplot.svg)](https://pypi.org/project/trackplot/)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/trackplot/README.html)
+[![Documentation Status](https://readthedocs.org/projects/trackplot/badge/?version=latest)](https://trackplot.readthedocs.io/en/latest/)
+[![License: BSD 3-Clause](https://img.shields.io/badge/License-BSD%20v3-clause.svg)](https://www.gnu.org/licenses/agpl-3.0)
+[![DOI](https://img.shields.io/badge/DOI-10.1101%2F2022.11.02.514803%20-blue)](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011477)
+
+---
+
+![](example/diagram.png)
+
+[Tutorials](https://trackplot.readthedocs.io/en/latest/)
+
+## what is trackplot
+
+trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. 
+
+### Features of trackplot
+
+1. Support various file formats as input
+2. Support strand-aware coverage plot
+3. Visualize coverage by heatmap, including HiC diagram 
+4. Visualize protein domain based the given gene id
+5. Demultiplex the single-cell RNA/ATAC-seq which used cell barcode into cell population 
+6. Support visualizing individual full-length reads in read-by-read style
+7. Support visualize circRNA sequencing data
+
+## Input
+
+trackplot supports almost NGS data format, including
+
+- BAM
+- Bed
+- Depth file generated by `samtools depth`
+- bigBed [[pyBigWig](https://github.com/deeptools/pyBigWig) optional]
+- bigWig [[pyBigWig](https://github.com/deeptools/pyBigWig) optional]
+- naive Hi-C format [[hicmatrix](https://github.com/deeptools/HiCMatrix) optional]
+
+
+## Output
+
+The output will be a pdf and other image file formats which satisfy the requirement of the major journals, 
+and each track on output corresponds these datasets from config file.
+
+## Usage
+
+Trackplot is based on **Python3** `(python_requires='>=3.8')`, 
+and we have simplified the installation process on the main page. 
+For a more comprehensive installation guide, please refer to [this link](./docs/installation.md).
+
+### For impatient
+
+```shell
+pip install trackplot
+trackplot --help
+
+# or using trackplot by conda
+
+conda create -n trackplot -c bioconda -c conda-forge trackplot
+conda activate trackplot
+trackplot --help
+
+```
+
+###### Notes
+>1. For users on **Microsoft Windows**, **Mac (Apple Silicon)**, 
+    and **other ARM platforms**, 
+    please note that Trackplot may not be installable via PyPI or Conda due to compatibility issues with pysam, 
+    pybigwig, and hicmatrix libraries on these platforms. 
+    As an alternative, we recommend using the Docker image for installation.
+
+>2. If you encounter a `segment fault` error during multiple processing, 
+    you may want to consider using the Docker image or running the command with the `-p 1` flag. 
+
+>3. If you encounter the message `Please install pyBigWig and hicmatrix`, 
+    you can refer to the official documentation for [pyBigWig](https://github.com/deeptools/pyBigWig) and 
+    [hicmatrix](https://github.com/deeptools/HiCMatrix) to fulfill their requirements and resolve the issue.
+
+<details><summary>Using trackplot by a command line (click me) </summary>
+<p>
+
+
+1. install from PyPi 
+
+Before running this command line, please check python (>=3.8) was installed.
+
+```bash
+pip install trackplot
+# __Note:__ We noticed some pypi mirrors are not syncing some packages we depend on, 
+# therefore please try another pypi mirror once you encounter 
+# `No local packages or working download links found for xxx`
+```
+
+---
+
+2. [AppImage](https://github.com/ygidtu/trackplot/releases) (Linux/WSL x86_64 platform only)
+
+For a binary version of the tool and more comprehensive information, please visit [this link](./docs/installation.md).
+
+```bash
+# example with version v0.3.5, please using your interested version according to your needs
+export VERSION=0.3.5
+chmod +x trackplot-${VERSION}-x86_64.AppImage
+./trackplot-${VERSION}-x86_64.AppImage --help
+```
+
+---
+
+3. using docker image
+
+```bash
+docker pull ygidtu/trackplot
+docker run --rm ygidtu/trackplot --help
+```
+
+---
+
+
+4. install from bioconda
+
+```bash
+# install trackplot into the default conda env 
+conda install -c bioconda -c conda-forge trackplot
+
+# or install trackplot into an isolated environments
+conda create -n trackplot -c bioconda -c conda-forge trackplot
+
+# activate the trackplot environment and execute the command line tool
+conda activate trackplot
+trackplot --help
+```
+
+
+</p>
+</details>
+
+
+---
+<details><summary>Using trackplot by a local webserver (click me) </summary>
+<p>
+
+
+1. [AppImage](https://github.com/ygidtu/trackplot/releases) (Linux/WSL x86_64 only)
+
+```bash
+# example with version v0.3.3, please using your interested version according to your needs
+export VERSION=0.3.3
+gunzip trackplot-${VERSION}-x86_64.AppImage
+chmod +x trackplot-${VERSION}-x86_64.AppImage
+./trackplot-${VERSION}-x86_64.AppImage --help
+
+# startup webserver
+./trackplot-${VERSION}-x86_64.AppImage --start-server --host 0.0.0.0 --port 5000 --plots ./plots
+```
+    
+**Note:** the `--plots` were required while using appimages
+
+---
+
+2. Running using command line
+
+```bash
+trackplot --start-server --host 0.0.0.0 --port 5000 --plots ./plots
+```
+
+3. Running using docker image
+
+```bash
+docker pull ygidtu/trackplot
+
+# Deploy the server
+docker run --name trackplot \
+  --rm -v $PWD/example:/data -v $PWD/plots/:/plots -p 5000:5000 ygidtu/trackplot \
+  --start-server \
+  --host 0.0.0.0 \
+  --data /data \
+  --plots /plots
+```
+
+`-p`: public and private port for the server, default:5000(public):5000(private)
+- `-v`, `--volume`: mount the working directory to docker container, for example, the `$PWD/data` could replace by the path to your directory contains all necessary data
+- `--user`: prevent docker read and write file using root privileges
+
+</p>
+</details>
+
+---
+
+## Example
+
+The `example` folder is downloaded from [here.](https://github.com/ygidtu/trackplot/archive/refs/heads/main.zip) 
+And a more detailed tutorial could be found at [here.](https://trackplot.readthedocs.io/en/latest/)  
+
+```bash
+# example of basic plot types
+trackplot \
+  -e chr1:1270656-1284730:+ \
+  -r example/example.sorted.gtf.gz \
+  --interval example/interval_list.tsv \
+  --density example/density_list.tsv \
+  --show-junction-num \
+  --igv example/igv.tsv \
+  --heatmap example/heatmap_list.tsv \
+  --focus 1272656-1272656:1275656-1277656 \
+  --stroke 1275656-1277656:1277856-1278656@blue \
+  --sites 1271656,1271656,1272656 \
+  --line example/line_list.tsv \
+  -o example.png \
+  --dpi 300 \
+  --width 10 \
+  --height 1 \
+  --barcode example/barcode_list.tsv \
+  --domain --remove-duplicate-umi \
+  --normalize-format cpm \
+  --annotation-scale .3 \
+  -p 4
+```
+
+if trackplot was installed by docker, here is the cmd
+
+```bash
+## The absolute path is required in Docker env.
+ 
+cat $PWD/example/interval_list.tsv |grep -v '^#' | while read line; do echo $PWD/${line}; done > $PWD/example/interval_list.abspath.tsv
+cat $PWD/example/density_list.tsv |grep -v '^#' | while read line; do echo $PWD/${line}; done > $PWD/example/density_list.abspath.tsv
+cat $PWD/example/igv.tsv |grep -v '^#' | while read line; do echo $PWD/${line}; done > $PWD/example/igv.abspath.tsv
+cat $PWD/example/heatmap_list.tsv |grep -v '^#' | while read line; do echo $PWD/${line}; done > $PWD/example/heatmap_list.abspath.tsv
+
+docker run -v $PWD:$PWD -w $PWD --rm ygidtu/trackplot \
+  -e chr1:1270656-1284730:+ \
+  -r $PWD/example/example.sorted.gtf.gz \
+  --interval $PWD/example/interval_list.tsv \
+  --density $PWD/example/density_list.tsv \
+  --show-junction-num \
+  --igv $PWD/example/igv.tsv \
+  --heatmap $PWD/example/heatmap_list.tsv \
+  --focus 1272656-1272656:1275656-1277656 \
+  --stroke 1275656-1277656:1277856-1278656@blue \
+  --sites 1271656,1271656,1272656 \
+  --line $PWD/example/line_list.tsv \
+  -o example.png \
+  --dpi 300 \
+  --width 10 \
+  --height 1 \
+  --barcode $PWD/example/barcode_list.tsv \
+  --domain --remove-duplicate-umi \
+  --normalize-format cpm \
+  --annotation-scale .3 \
+  -p 4
+
+```
+
+here is the [output file](https://raw.githubusercontent.com/ygidtu/trackplot/main/example/example.png).
+
+
+## Questions
+
+Visit [issues](https://github.com/ygidtu/trackplot/issues) or 
+contact [Yiming Zhang](https://github.com/ygidtu) or 
+[Ran Zhou](https://github.com/zhou-ran)
+
+## Citation
+
+If you use the tool in your publication, please cite by
+
+[Zhang Y, Zhou R, Liu L, et al. Trackplot: A flexible toolkit for combinatorial analysis of genomic data[J]. PLoS computational biology, 2023, 19(9): e1011477.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011477)

trackplot-0.5.4/trackplot.egg-info/SOURCES.txt

@@ -0,0 +1,91 @@
+LICENSE
+README.md
+pyproject.toml
+trackplot/__init__.py
+trackplot/cli.py
+trackplot/plot.py
+trackplot/plot_func.py
+trackplot/plot_tests.py
+trackplot/server.py
+trackplot.egg-info/PKG-INFO
+trackplot.egg-info/SOURCES.txt
+trackplot.egg-info/dependency_links.txt
+trackplot.egg-info/requires.txt
+trackplot.egg-info/top_level.txt
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+trackplot/anno/__init__.py
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+trackplot/base/GenomicLoci.py
+trackplot/base/Junction.py
+trackplot/base/Protein.py
+trackplot/base/ReadDepth.py
+trackplot/base/Readder.py
+trackplot/base/Stroke.py
+trackplot/base/Transcript.py
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+trackplot/base/pyUniprot.py
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+trackplot/conf/config.py
+trackplot/conf/drawing.py
+trackplot/conf/ui.py
+trackplot/file/ATAC.py
+trackplot/file/Annotation.py
+trackplot/file/Bam.py
+trackplot/file/BedGraph.py
+trackplot/file/Bigwig.py
+trackplot/file/Depth.py
+trackplot/file/Fasta.py
+trackplot/file/File.py
+trackplot/file/HiCMatrixTrack.py
+trackplot/file/Junction.py
+trackplot/file/Motif.py
+trackplot/file/ReadSegments.py
+trackplot/file/__init__.py
+ui/index.html
+ui/vite.svg
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+ui/assets/Home-BV58jH3t.js
+ui/assets/Home-CDW3Zwoa.js
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+ui/assets/index-ns9n7-F7.css

trackplot-0.5.4/trackplot.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

trackplot-0.5.4/trackplot.egg-info/requires.txt

@@ -0,0 +1,17 @@
+adjusttext>=1.3.0
+cairocffi>=1.7.1
+click>=8.2.1
+click-option-group>=0.5.7
+filetype>=1.2.0
+flask>=3.1.1
+hicmatrix>=17.2
+loguru>=0.7.3
+matplotlib>=3.10.3
+numpy>=2.3.0
+pandas>=2.3.0
+pybigwig>=0.3.24
+pysam>=0.23.3
+requests>=2.32.4
+scipy>=1.15.3
+seaborn>=0.13.2
+xmltodict>=0.14.2

trackplot-0.5.4/trackplot.egg-info/top_level.txt

@@ -0,0 +1,2 @@
+trackplot
+ui

trackplot-0.5.4/ui/assets/Home-BV58jH3t.js

@@ -0,0 +1 @@
+import{d as _,c as m,a as u,b as e,t as c,w as t,E as f,o as g,e as h,f as n,u as i,_ as y}from"./index-C4Mi9Kmf.js";import{E as k,a as w,m as E,v,b}from"./el-divider-IbBQ8ZK2.js";const x={name:"Home",data(){return{msg:"Welcome to trackplot App",example:"https://trackplot.readthedocs.io/en/latest/imgs/diagram.png"}}},C=_({...x,setup(B){return(r,a)=>{const s=k,l=w,o=h,p=f,d=b;return g(),m("div",null,[u("h1",null,c(r.msg),1),e(s),e(p,null,{default:t(()=>[e(o,{span:12,offset:3},{default:t(()=>[e(l,{type:"primary",href:"/#/plot"},{default:t(()=>[...a[0]||(a[0]=[n("Create your own plot",-1)])]),_:1})]),_:1}),e(o,{span:6},{default:t(()=>[e(l,{type:"primary",href:"https://github.com/ygidtu/trackplot/issues",icon:i(E)},{default:t(()=>[...a[1]||(a[1]=[n("Report bug at Github",-1)])]),_:1},8,["icon"]),e(s,{direction:"vertical"}),e(l,{type:"primary",icon:i(v),href:"https://trackplot.readthedocs.io/en/latest/web/"},{default:t(()=>[...a[2]||(a[2]=[n("Read the tutorial",-1)])]),_:1},8,["icon"])]),_:1}),e(o,{span:6})]),_:1}),e(s),e(p,null,{default:t(()=>[e(o,{span:20,offset:2},{default:t(()=>[e(d,{src:r.example,width:"100%"},null,8,["src"])]),_:1})]),_:1})])}}}),V=y(C,[["__scopeId","data-v-3d7de397"]]);export{V as default};