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Merge pull request #474 from deeptools/develop
Release 3.19
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‎MANIFEST.in

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prune pygenometracks/tests

‎README.md

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Here is a scheme which describe how pyGenomeTracks is working (graphical abstract of [Lopez-Delisle et al. 2020](https://doi.org/10.1093/bioinformatics/btaa692)):
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![pyGenomeTracks](./docs/content/images/graphicalabstract.png)
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![pyGenomeTracks](https://github.com/deeptools/pyGenomeTracks/blob/b8918d43b0bd1ca9dd2939fdd0d93a5a297d0453/docs/content/images/graphicalabstract.png)
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pyGenomeTracks can make plots with or without Hi-C data. The following is an example output of
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pyGenomeTracks from [Ramírez et al. 2017](https://www.nature.com/articles/s41467-017-02525-w)
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![pyGenomeTracks example](./docs/content/images/hic_example_nat_comm_small.png)
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![pyGenomeTracks example](https://github.com/deeptools/pyGenomeTracks/blob/b8918d43b0bd1ca9dd2939fdd0d93a5a297d0453/docs/content/images/hic_example_nat_comm_small.png)
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Table of content
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----------------
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Installation
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------------
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pyGenomeTracks works with python >=3.7.
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pyGenomeTracks works with python >=3.8.
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The recommended way to install pyGenomeTracks is via conda
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```bash
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conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks python=3.7
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conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks
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```
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To get a specific version, one can specify it. For example:
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You first need to create the environment and install mamba:
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```bash
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conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.7
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conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.9
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```
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Then activate the environment and install pygenometracks with mamba:
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Description of other possible arguments:
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<!--- Start of possible arguments of pgt -->
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``` text
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optional arguments:
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options:
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-h, --help show this help message and exit
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--tracks TRACKS File containing the instructions to plot the tracks.
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The tracks.ini file can be genarated using the

‎azure-pipelines.yml

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vmImage: 'ubuntu-latest'
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strategy:
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matrix:
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Python37LowMatplotlib:
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python.version: '3.7'
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matplotlib.version: '3.1.1'
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Python37HighMatplotlib:
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python.version: '3.7'
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matplotlib.version: '3.5.3'
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Python38LowMatplotlib:
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python.version: '3.8'
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matplotlib.version: '3.1.1'
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Python38HighMatplotlib:
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python.version: '3.8'
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matplotlib.version: '3.6.2'
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matplotlib.version: '3.6.0'
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Python39HighMatplotlib:
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python.version: '3.9'
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matplotlib.version: '3.6.2'
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matplotlib.version: '3.7.3'
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Python310HighMatplotlib:
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python.version: '3.10'
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matplotlib.version: '3.8.4'
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steps:
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- bash: |
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- bash: |
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conda config --set always_yes yes --set changeps1 no
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conda info -a
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cat requirements_CI.txt | awk -v v=$(matplotlib.version) '{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt
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conda create -n pygenometracks --yes -c conda-forge -c bioconda python=$(python.version) mamba
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cat requirements_CI.txt | awk -v v=$(matplotlib.version) -v vp=$(python.version) 'BEGIN{print "python =="vp}{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt
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conda create -n pygenometracks --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt
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source activate pygenometracks
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mamba install --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt
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python setup.py install
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python -m pip install .
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displayName: installing dependencies
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- script: |
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source activate pygenometracks
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vmImage: 'macOS-11'
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strategy:
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matrix:
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Python37LowMatplotlib:
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python.version: '3.7'
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matplotlib.version: '3.1.1'
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Python37HighMatplotlib:
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python.version: '3.7'
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matplotlib.version: '3.5.1'
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python.version: '3.8'
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matplotlib.version: '3.1.1'
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- bash: |
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conda config --set always_yes yes --set changeps1 no
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conda info -a
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cat requirements_CI.txt | awk -v v=$(matplotlib.version) '{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt
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conda create -n pygenometracks --yes -c conda-forge -c bioconda python=$(python.version) mamba
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source activate pygenometracks
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mamba install --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt
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python setup.py install
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cat requirements_CI.txt | awk -v v=$(matplotlib.version) -v vp=$(python.version) 'BEGIN{print "python =="vp}{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt
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conda create -n pygenometracks --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt
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python -m pip install .
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displayName: installing dependencies
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- script: |
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source activate pygenometracks
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container: python:3.8
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steps:
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- script: |
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python setup.py sdist bdist_wheel
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python -m pip install --upgrade pip
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pip install build
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python -m build
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python -m pip install --user --upgrade twine
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python -m twine upload -r pypi dist/*
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env:

‎bin/make_tracks_file

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‎bin/pgt

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‎bin/pyGenomeTracks

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‎docs/content/all_default_properties.csv

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color_backbone,,,,,black,black,,,,,,,,,,,
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height_utr,,,,,1,1,,,,,,,,,,,
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arrow_length,,,,,not set,not set,,,,,,,,,,,
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height_intron,,,,,0.5,0.5,,,,,,,,,,,
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all_labels_inside,,,,,false,false,,,,,,,,,,,
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labels_in_margin,,,,,false,false,,,,,,,,,,,
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fontstyle,,,,,normal,normal,,,,,,,,,,,
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color_arrow,,,,,black,black,,,,,,,,,,,
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show_data_range,,,,,,,true,true,true,true,true,,,,,,
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show_labels,,,,,,,true,,,,,,,,,,
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use_summit,,,,,,,true,,,,,,,,,,
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second_file*,,,,,,,,not set,not set,,,,,,,,
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operation*,,,,,,,,file,file,,,,,,,,
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grid,,,,,,,,false,false,,,,,,,,
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rasterize,,,,,,,,,false,true,,true,true,,,,
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rasterize,,,,,,,,,false,true,,true,true,false,,,
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pos_score_in_bin,,,,,,,,,,center,,,,,,,
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plot_horizontal_lines,,,,,,,,,,false,,,,,,,
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colormap,,,,,,,,,,viridis,,RdYlBu_r,RdYlBu_r,,,,

‎docs/content/all_default_properties_rst.txt

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color_backbone black black
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height_utr 1 1
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arrow_length not set not set
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height_intron 0.5 0.5
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all_labels_inside false false
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labels_in_margin false false
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fontstyle normal normal
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color_arrow black black
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show_data_range true true true true true
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show_labels true
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use_summit true
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second_file* not set not set
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operation* file file
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grid false false
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rasterize false true true true
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rasterize false true true true false
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pos_score_in_bin center
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plot_horizontal_lines false
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colormap viridis RdYlBu_r RdYlBu_r

‎docs/content/all_possible_properties.txt

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- **overlay_previous**:
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- for *x_axis, epilogos, links, domains, bed, gtf, narrow_peak, bigwig, bedgraph, bedgraph_matrix, hlines, hic_matrix, hic_matrix_square, maf, scalebar, fasta, spacer*: no, yes, share-y
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- for *x_axis, epilogos, links, domains, bed, gtf, narrow_peak, bigwig, bedgraph, bedgraph_matrix, hlines, hic_matrix, hic_matrix_square, maf, scalebar, spacer, fasta*: no, yes, share-y
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- **where**:
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- **style**:
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- for *bed, gtf*: flybase, UCSC, tssarrow
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- for *bed, gtf*: flybase, UCSC, tssarrow, exonarrows
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- **display**:
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- for *bed*: collapsed, triangles, interleaved, stacked, squares
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- for *gtf*: collapsed, triangles, interleaved, stacked
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- for *bed, gtf*: collapsed, triangles, interleaved, stacked, squares, deletions, inversions
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- for *bedgraph, bedgraph_matrix, hic_matrix, hic_matrix_square*: true, false
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- for *bedgraph, bedgraph_matrix, hic_matrix, hic_matrix_square, maf*: true, false
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- **pos_score_in_bin**:
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