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Merge pull request #269 from deeptools/develop
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PGT 3.5
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@lldelisle
lldelisle authored Jul 17, 2020
2 parents c5a24fa + 970b232 commit 709aa6e
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1 change: 0 additions & 1 deletion .gitignore
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# Unit test / coverage reports
.coverage
coverage.*
.tox
nosetests.xml
htmlcov
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13 changes: 9 additions & 4 deletions README.md
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[![PyPI Version](https://img.shields.io/pypi/v/pyGenomeTracks.svg?style=plastic)](https://pypi.org/project/pyGenomeTracks/) [![bioconda-badge](https://img.shields.io/conda/vn/bioconda/pyGenomeTracks.svg?style=plastic)](https://anaconda.org/bioconda/pygenometracks)
[![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=plastic)](http://bioconda.github.io)
[![Build Status](https://travis-ci.org/deeptools/pyGenomeTracks.svg?branch=master)](https://travis-ci.org/deeptools/pyGenomeTracks)

![Coverage](./docs/coverage.svg)

pyGenomeTracks
==============
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------------
pyGenomeTracks works with python >=3.6.

Currently, the best way to install pyGenomeTracks is with anaconda
The recommended way to install pyGenomeTracks is via conda

```bash
$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks python=3.7
```
To get a specific version, one can specify it. For example:

```bash
$ conda install -c bioconda -c conda-forge pygenometracks
$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks=3.5 python=3.7
```

Also, pyGenomeTracks can be installed using pip
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Our [documentation](http://pygenometracks.readthedocs.io/) provide [examples](http://pygenometracks.readthedocs.org/en/latest/content/examples.html), as well as the [full list of possible parameters](http://pygenometracks.readthedocs.org/en/latest/content/possible-parameters.html) and [guidelines for developers who would like to add a new track type](http://pygenometracks.readthedocs.org/en/latest/content/adding-new-tracks.html).

<!-- I do not know what to do with that, is it External users?
<!-- I do not know what to do with that, is it External users?
pyGenomeTracks is used by [HiCExporer](https://hicexplorer.readthedocs.io/) and [HiCBrowser](https://github.com/maxplanck-ie/HiCBrowser) (See e.g. [Chorogenome navigator](http://chorogenome.ie-freiburg.mpg.de/) which is made with HiCBrowser)
-->
External users
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6 changes: 3 additions & 3 deletions docs/content/all_default_properties_rst.txt
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Expand Up @@ -3,7 +3,7 @@ parameter :doc:`tracks/x_axis` :doc:`tracks/epilogos`
========================= ========================= ========================= ========================= ========================= ========================= ========================= ========================= ========================= ========================= ========================= ========================= ========================= =========================
overlay_previous no no no no no no no no no no no no no
where bottom left
fontsize 15 12 12 12 12
fontsize 15 12 12 12
categories_file not set
orientation not set not set not set not set not set not set not set not set not set not set not set
links_type arcs
Expand All @@ -15,6 +15,7 @@ max_value
min_value not set not set not set not set not set not set not set not set
ylim not set
compact_arcs_level 0
use_middle false false
border_color black black black
prefered_name transcript_name transcript_name transcript_name
merge_transcripts false false false
Expand Down Expand Up @@ -45,12 +46,11 @@ log_pseudocount
y_axis_values transformed transformed
second_file* not set not set
operation* file file
use_middle false
grid false false
rasterize false true true
pos_score_in_bin center
plot_horizontal_lines false
colormap viridis RdYlBu_r
region not set
depth 100000
show_masked_bins false
scale_factor 1
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8 changes: 6 additions & 2 deletions docs/content/all_possible_properties.txt
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Expand Up @@ -24,6 +24,10 @@

- for *links*: 0, 1, 2

- **use_middle**:

- for *links, bedgraph*: true, false

- **merge_transcripts**:

- for *domains, bed, gtf*: true, false
Expand Down Expand Up @@ -94,9 +98,9 @@

- for *bigwig, bedgraph*: true, false

- **use_middle**:
- **grid**:

- for *bedgraph*: true, false
- for *bigwig, bedgraph*: true, false

- **rasterize**:

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45 changes: 17 additions & 28 deletions docs/content/all_tracks.rst
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All available tracks
====================


:doc:`tracks/bed`

:doc:`tracks/bedgraph`

:doc:`tracks/bedgraph_matrix`

:doc:`tracks/bigwig`

:doc:`tracks/domains`

:doc:`tracks/epilogos`

:doc:`tracks/gtf`

:doc:`tracks/hic_matrix`

:doc:`tracks/hlines`

:doc:`tracks/links`

:doc:`tracks/narrow_peak`

:doc:`tracks/scalebar`

:doc:`tracks/spacer`

:doc:`tracks/x_axis`
.. toctree::
:maxdepth: 1

tracks/bed
tracks/bedgraph
tracks/bedgraph_matrix
tracks/bigwig
tracks/domains
tracks/epilogos
tracks/gtf
tracks/hic_matrix
tracks/hlines
tracks/links
tracks/narrow_peak
tracks/scalebar
tracks/spacer
tracks/x_axis
12 changes: 9 additions & 3 deletions docs/content/examples.rst
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Expand Up @@ -106,12 +106,18 @@ The output file of some 4C-seq pipeline are bedgraph where the coordinates are t

.. literalinclude:: ../../pygenometracks/tests/test_data/bedgraph_useMid.ini
:language: INI

We can generate two zooms using a bed instead of regions:

.. literalinclude:: ../../pygenometracks/tests/test_data/regions_imbricated_chr2.bed

.. code:: bash
$ pyGenomeTracks --tracks bedgraph_useMid.ini --region chr2:73,800,000-75,744,000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o master_bedgraph_useMid.pdf
$ pyGenomeTracks --tracks bedgraph_useMid.ini --BED regions_imbricated_chr2.bed --trackLabelFraction 0.2 --width 38 --dpi 130 -o master_bedgraph_useMid.png
.. image:: ../../pygenometracks/tests/test_data/master_bedgraph_useMid_chr2-73800000-75744000.png

The output is available `here <https://github.com/deeptools/pyGenomeTracks/raw/master/pygenometracks/tests/test_data/master_bedgraph_useMid.pdf>`_.
.. image:: ../../pygenometracks/tests/test_data/master_bedgraph_useMid_chr2-74000000-74800000.png


Examples with peaks
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Log transform and Operation Examples
--------------------------
------------------------------------

With the parameter ``operation`` you can make operations between one or two files (here two bigwig files but this is also working with two bedgraph files). For example, difference, log ratio, scaling...

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22 changes: 13 additions & 9 deletions docs/content/installation.rst
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Expand Up @@ -4,7 +4,7 @@ Installation
Remember -- pyGenomeTracks is available for **command line usage** as well as for
**integration into Galaxy servers**!

.. contents::
.. contents::
:local:

Requirements
Expand All @@ -19,15 +19,20 @@ Requirements
* matplotlib >= 3.1.1
* gffutils >=0.9

The fastest way to obtain **Python 3.6 together with numpy** is
via the `Anaconda Scientific Python
Distribution <https://store.continuum.io/cshop/anaconda/>`_.
Just download the version that's suitable for your operating system and
follow the directions for its installation. All of the requirements for pyGenomeTracks can be installed in Anaconda with:
Command line installation using ``conda``
-----------------------------------------

We encourage users to use ``conda`` installation to install pygenometracks. All of the requirements for pyGenomeTracks can be installed via Anaconda with:

.. code:: bash
$ conda install -c bioconda -c conda-forge pygenometracks
$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks python=3.7
To get a specific version, one can specify it. For example:

.. code:: bash
$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks=3.5 python=3.7
Command line installation using ``pip``
-----------------------------------------
Expand All @@ -45,11 +50,10 @@ If you need to specify a specific path for the installation of the tools, make u
$ pip install --install-option="--prefix=/MyPath/Tools/pyGenomeTracks" git+https://github.com/deeptools/pyGenomeTracks.git
Command line installation without ``pip``
-------------------------------------------

You are highly recommended to use `pip` rather than these more complicated steps.
You are highly recommended to use `conda install` rather than the following complicated steps.

1. Install the requirements listed above in the "requirements" section. This is done automatically by `pip`.

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37 changes: 15 additions & 22 deletions docs/content/releases.rst
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Releases
========

:doc:`releases/3.4`
"""""""""""""""""""
:doc:`releases/3.3`
"""""""""""""""""""
:doc:`releases/3.2.1`
"""""""""""""""""""""
:doc:`releases/3.2`
"""""""""""""""""""
:doc:`releases/3.1.2`
"""""""""""""""""""""
:doc:`releases/3.1.1`
"""""""""""""""""""""
:doc:`releases/3.1`
"""""""""""""""""""
:doc:`releases/3.0`
"""""""""""""""""""
:doc:`releases/2.1`
"""""""""""""""""""
:doc:`releases/2.0`
"""""""""""""""""""
:doc:`releases/1.0`
"""""""""""""""""""
.. toctree::
:maxdepth: 1

releases/3.5
releases/3.4
releases/3.3
releases/3.2.1
releases/3.2
releases/3.1.2
releases/3.1.1
releases/3.1
releases/3.0
releases/2.1
releases/2.0
releases/1.0

Main changes in configuration files:
Since v3.2:
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10 changes: 8 additions & 2 deletions docs/content/releases/3.3.rst
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===

Release 3.3 adds:
^^^^^^^^^^^^^^^^^

- a documentation on readthedocs: https://pygenometracks.readthedocs.io
- progress bar for bed, gtf, bedgraph, narrowPeak, epilogos
- all colors can be set as ``(r, g, b)`` with r, g, b values between 0 and 1.
- all colormap can be set as an array of colors, for example ``[red, white, (0, 0, 0.5)]``
- the titles on the right can be align left, right or center with the argument ``--trackLabelHAlign``
- for the links track,

- for the links track
- ``compact_arcs_level`` to be able to see both very long arcs and very small arcs.
- ``ylim`` to be able to zoom and see small arcs.

- a new track type: ``file_type = scalebar`` which by default is close to the UCSC scale bar.
- for the bed tracks:

- for the bed tracks
- a new gene type: ``tssarrow``
- ``border_color`` and ``color_utr`` can be set to ``bed_rgb``.
- ``all_labels_inside`` allow to put the name of the region on the left if it ends after the plotted region.
- ``labels_in_margin`` allow to put the name of the region in the margin if it ends after the plotted region.

- ``line_width`` can now be set in the narrowPeak tracks.
- ``colormap`` can now be set in bedgraphMatrix tracks.

bug fixes:
^^^^^^^^^^

- if a bed with no interval is provided, pgt no longer exit.
- When an exon had both UTR start and UTR end within it, only the UTR start was considered.
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