Merge pull request #229 from deeptools/develop

[WIP] Release 3.4

.travis.yml

@@ -29,8 +29,7 @@ jobs:
     - LINT=1
     - TRAVIS_OS_NAME=linux
     before_install:
-    - curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -o
-      miniconda.sh
+    - curl -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh
     - bash miniconda.sh -b -p $HOME/miniconda
     - PATH_WITHOUT_CONDA="$PATH"
     - export PATH="$HOME/miniconda/bin:$PATH"
@@ -46,10 +45,10 @@ before_install:
 - export TEST_DATA_DIR="`pwd`/pygenometracks/test/test_data/"
 - echo $TEST_DATA_DIR
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
-  curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh
+  curl -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh
   ; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then curl
-  https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o miniconda.sh
+- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then 
+  curl -L https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o miniconda.sh
   ; fi
 - bash miniconda.sh -b -p $HOME/miniconda
 - PATH_WITHOUT_CONDA="$PATH"
@@ -60,10 +59,7 @@ before_install:
 - conda info -a
 install:
 - conda install --yes -c bioconda -c conda-forge python=$TRAVIS_PYTHON_VERSION --file requirements.txt
-- conda install --yes -c conda-forge -c bioconda pytest
-- conda install --yes -c conda-forge -c bioconda nose
-- conda install --yes -c conda-forge -c bioconda ghostscript
-- conda install --yes pathlib
+- conda install --yes -c conda-forge -c bioconda pytest nose ghostscript pathlib
 - python setup.py install
 script:
 - py.test pygenometracks --doctest-modules

README.md

@@ -112,6 +112,9 @@ optional arguments:
                         By default, the horizontal alignment of the track
                         labels is left. This alignemnt can be changed to right
                         or center.
+  --decreasingXAxis     By default, the x-axis is increasing. Use this option
+                        if you want to see all tracks with a decreasing
+                        x-axis.
   --version             show program's version number and exit
 ```
 <!--- End of possible arguments of pgt -->

docs/conf.py

@@ -23,14 +23,13 @@
 
 # import mock
 
-MOCK_MODULES = ['numpy', 'numpy.core', 'numpy.core.multiarray', 'numpy.distutils.core', 'pandas', 'pysam', 'intervaltree',
-                'scipy', 'scipy.sparse', 'scipy.stats', 'scipy.ndimage', 'scipy.special',
-                'matplotlib', 'matplotlib.pyplot', 'matplotlib.gridspec', 'matplotlib.ticker',
-                'matplotlib.textpath', 'matplotlib.patches', 'matplotlib.colors', 'matplotlib.cm',
-                'mpl_toolkits', 'mpl_toolkits.axisartist', 'mpl_toolkits.mplot3d', 'mpl_toolkits.axes_grid1',
-                'Bio', 'Bio.Seq', 'Bio.Alphabet', 'pyBigWig', 'tables', 'pytables', 'future', 'past', 'past.builtins',
-                'future.utils', 'cooler', 'logging', 'unidecode', 'hic2cool', 'hicmatrix', 'hicmatrix.HiCMatrix',
-                'hicmatrix.lib', 'pybedtools']
+MOCK_MODULES = ['pygenometracks.tracksClass',  # (required for both)
+                # For plotTracks in plotTracks
+                'matplotlib',
+                # For plotTracks in utilities
+                'numpy',
+                'tqdm',
+                'intervaltree']
 
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = Mock()

docs/content/all_possible_properties.txt

@@ -1,12 +1,16 @@
+- **overlay_previous**:
+
+  - for *x_axis, epilogos, links, domains, bed, gtf, narrow_peak, bigwig, bedgraph, bedgraph_matrix, hlines, hic_matrix, scalebar, spacer*: no, yes, share-y
+
 - **where**:
 
-  - for *x-axis*: top, bottom
+  - for *x_axis*: top, bottom
 
   - for *scalebar*: left, right, top, bottom
 
 - **orientation**:
 
-  - for *epilogos, links, domains, bed, narrow_peak, bigwig, bedgraph, bedgraph_matrix, hlines, hic_matrix*: inverted, not set
+  - for *epilogos, links, domains, bed, gtf, narrow_peak, bigwig, bedgraph, bedgraph_matrix, hlines, hic_matrix*: inverted, not set
 
 - **links_type**:
 
@@ -22,35 +26,35 @@
 
 - **merge_transcripts**:
 
-  - for *domains, bed*: true, false
+  - for *domains, bed, gtf*: true, false
 
 - **style**:
 
-  - for *bed*: flybase, UCSC, tssarrow
+  - for *bed, gtf*: flybase, UCSC, tssarrow
 
 - **display**:
 
-  - for *bed*: collapsed, triangles, interleaved, stacked
+  - for *bed, gtf*: collapsed, triangles, interleaved, stacked
 
 - **labels**:
 
-  - for *bed*: true, false
+  - for *bed, gtf*: true, false
 
 - **global_max_row**:
 
-  - for *bed*: true, false
+  - for *bed, gtf*: true, false
 
 - **arrowhead_included**:
 
-  - for *bed*: true, false
+  - for *bed, gtf*: true, false
 
 - **all_labels_inside**:
 
-  - for *bed*: true, false
+  - for *bed, gtf*: true, false
 
 - **labels_in_margin**:
 
-  - for *bed*: true, false
+  - for *bed, gtf*: true, false
 
 - **type**:
 
@@ -76,6 +80,16 @@
 
   - for *bedgraph*: mean, average, max, min, stdev, dev, coverage, cov, sum, not set
 
+- **transform**:
+
+  - for *bigwig, bedgraph*: no, log, log1p, -log, log2, log10
+
+  - for *hic_matrix*: no, log, log1p, -log
+
+- **y_axis_values**:
+
+  - for *bigwig, bedgraph*: original, transformed
+
 - **nans_to_zeros**:
 
   - for *bigwig, bedgraph*: true, false
@@ -96,10 +110,6 @@
 
   - for *bedgraph_matrix*: true, false
 
-- **transform**:
-
-  - for *hic_matrix*: no, log, log1p, -log
-
 - **show_masked_bins**:
 
   - for *hic_matrix*: true, false

docs/content/all_tracks.rst

@@ -0,0 +1,31 @@
+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`

docs/content/examples.rst

@@ -1,7 +1,7 @@
 Examples
 ========
 
-These examples and the input data for these examples can found in the `examples/ <https://github.com/deeptools/pyGenomeTracks/tree/master/examples>`_ or `test_data/ <https://github.com/deeptools/pyGenomeTracks/tree/master/tests/test_data>`_ folders of the github repository.
+These examples and the input data for these examples can found in the `examples/ <https://github.com/deeptools/pyGenomeTracks/tree/master/examples>`_ or `test_data/ <https://github.com/deeptools/pyGenomeTracks/tree/master/pygenometracks/tests/test_data>`_ folders of the github repository.
 
 
 .. contents:: 
@@ -267,3 +267,46 @@ The configuration file for this image is:
     $ pyGenomeTracks  --tracks browser_tracks_hic.ini --region X:2500000-3500000 --trackLabelFraction 0.23 --width 38 --dpi 130 -o master_plot_hic.png
 
 
+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...
+
+.. image:: ../../pygenometracks/tests/test_data/master_operation.png
+
+The configuration file for this image is:
+
+.. literalinclude:: ../../pygenometracks/tests/test_data/operation.ini
+    :language: INI
+
+.. code:: bash
+
+    $ pyGenomeTracks --tracks operation.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o master_operation.png
+
+With the parameter ``transformation`` you can log transform your data and decide to put on the y axis either the transformed values or the original values:
+
+.. image:: ../../pygenometracks/tests/test_data/master_log1p.png
+
+The configuration file for this image is:
+
+.. literalinclude:: ../../pygenometracks/tests/test_data/log1p.ini
+    :language: INI
+
+.. code:: bash
+
+    $ pyGenomeTracks --tracks log1p.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o master_log1p.png
+
+With ``operation`` you can also do log transformation however nothing will be written on the left of the y axis:
+
+.. image:: ../../pygenometracks/tests/test_data/master_log.png
+
+The configuration file for this image is:
+
+.. literalinclude:: ../../pygenometracks/tests/test_data/log.ini
+    :language: INI
+
+.. code:: bash
+
+    $ pyGenomeTracks --tracks log.ini  --region chr2:73,800,000-75,744,000 --trackLabelFraction 0.2 --width 38 --dpi 130  -o master_log.png
+
+

docs/content/releases.rst

@@ -0,0 +1,37 @@
+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`
+"""""""""""""""""""
+
+Main changes in configuration files:
+Since v3.2: 
+
+- there is no more space in the name of the parameters (``line width`` become ``line_width``)
+- all on/off, yes/no, 0/1 become true/false
+
+Since v3.4:
+
+- gtf has its own file_type (``file_type = gtf``).
+
+**Warning** in version 4.0 the old configuration files will not work anymore

docs/content/releases/1.0.rst

@@ -0,0 +1,4 @@
+1.0
+===
+
+This version added python3 compatibility to the code

docs/content/releases/2.0.rst

@@ -0,0 +1,16 @@
+2.0
+===
+
+This release makes it **very easy to add new tracks**! See the Readme for examples on how to do that.
+
+Furthermore, this release:
+
+* Adds Hi-C tracks
+* Allows a track be plotted over the previous. There is not limit on the tracks that can be plotted on top of each other
+* Removed unnecessary empty space around the resulting image
+* Enlarged the README.md file with new examples and a mini-tutorial on how to add new tracks.
+* Added chromosome name and title to x-axis plot 
+* Added option to plot links as 'triangles'. This is useful to overlay links with Hi-C data to identify the contact pixel.
+* Added line width to bed track
+* Added 'bed graph' track
+* Added a track that can plot .narrowPeaks

docs/content/releases/2.1.rst

@@ -0,0 +1,6 @@
+2.1
+===
+
+* Support for epilogos  #38 
+* HiC improvements and migration to use `HiCMatrix <https://github.com/deeptools/HiCMatrix>`_. Thanks to *@joachimwolff* for these changes.
+* Different coloring of negative and positive bigwig values is now possible. Thanks to *@Phlya* for this improvement.

docs/content/releases/3.0.rst

@@ -0,0 +1,6 @@
+3.0
+===
+
+- support for Python 2 has been removed.
+- regions smaller than 200000 can be plotted with a warning message for plotting TADs.
+- non existing chromosomes in some or all of the input files can be asked as regions to plot the tracks.

docs/content/releases/3.1.1.rst

@@ -0,0 +1,5 @@
+3.1.1
+=====
+
+* small bug fix for summit usage (@lldelisle)
+* I added a vertical bar in the narrowPeaks when plotted as box to be able to see the summits (@lldelisle)

docs/content/releases/3.1.2.rst

@@ -0,0 +1,4 @@
+3.1.2
+=====
+
+change infos to warnings

docs/content/releases/3.1.rst

@@ -0,0 +1,8 @@
+3.1
+===
+
+* add the ability to control alpha of bedgraph tracks (thanks to @mikewolfe)
+* add GTF support (thanks to @lldelisle)
+* add support for various BED flavors (thanks to @lldelisle)
+* adopt codebase to lastest matplotlib changes (thanks to @lldelisle)
+* various new tests, code cleanups and smaller fixes all over

docs/content/releases/3.2.1.rst

@@ -0,0 +1,7 @@
+3.2.1
+=====
+
+- Small bug fix in parser when the parameter had spaces in the name and was a boolean (for example show data range instead of show_data_range).
+
+
+**Warning:** In version 4.0 no parameter with space will be accepted.

docs/content/releases/3.2.rst

@@ -0,0 +1,33 @@
+3.2
+===
+
+This is a major release with a lot of new features but also some deprecations in preparation for a new 4.0 release.
+
+During the years we have introduced several ways to enable/disable settings.
+We have used on/off, yes/no, 0/1, true/false. From now on we recommend to only use true/false so that we can unify our config files and make it more intuitive for all pgt-users.
+
+We also removed all 2/3/4 words items and concatenate them now by ``_`` `#132 <https://github.com/deeptools/pyGenomeTracks/pull/132>`_.
+For example ``line width`` is now ``line_width``. Thanks @LeilyR!
+
+A few new features in this release:
+
+* Every config is now checked for syntax errors before anything is executed (@lldelisle)
+* Added the possibility to merge transcripts into one single gene representation when using gtf (@lldelisle)
+* Added the possibility to rasterize bedgraph plots (@lldelisle)
+* Added the possibility to use summary functions on bedgraphs (@lldelisle)
+* Generate an empty track if a requested region is not in the given track-files. Fixed `#120 <https://github.com/deeptools/pyGenomeTracks/issues/120>`_ (@LeilyR)
+* Generate an empty track if a chromosome is missing in bedgraph files (@lldelisle)
+* Improved UCSC style for intron arrows (@lldelisle)
+* Flybase style now supports color_utr and height_uts (@lldelisle)
+* A new tracktype ``hlines`` was added (@lldelisle)
+* Allow to plot the arcs of the links with a color scale based on scores as proposed in `#30 <https://github.com/deeptools/pyGenomeTracks/issues/30>`_ (@lldelisle)
+* Allow to plot rectangle on a heatmap for loops. Fixed `#47 <https://github.com/deeptools/pyGenomeTracks/issues/47>`_ (@Phlya, @lldelisle)
+* A lot of HiC Matrix improvements (@lldelisle)
+* The ``alpha`` property can now be used nearly everywhere (@lldelisle)
+
+Also checkout our updated `readme <https://github.com/deeptools/pyGenomeTracks/blob/master/README.md>`_).
+
+Special thanks to @lldelisle & @LeilyR for such a feature-rich release.
+
+Merry Xmas and a happy new year!
+Your PGT team!