Pygenometracks

===

Changes in dependencies:

- This version drops support for python 3.7.
- This version is compatible with matplotlib 3.8.

Enhancement:

- pyGenomeTracks now uses font type 42 for pdf and ps which helps modification with illustrator.

- 2 new display for bed: ``deletions`` which is helpful when you need to show a deletion with precise coordinates and ``inversions`` which displays arrows.
- New style to display bed: ``exonarrows`` which displays arrows with orientation in the exons.
- For the UCSC stlyle, the color of arrows on introns in customable
- Do not hesistate to check the updated documentation: [here](https://pygenometracks.readthedocs.io/en/latest/content/examples.html#examples-with-bed-and-gtf)

- Allow to rasterize rectangles/lines of maf tracks with ``rasterize = true``.

Bugfix:

- Fix the UTR/Coding of BED8/BED9.
- Fix a typo in options help text of bedgraph and bigwig: `tranform` instead of `transform`.

Enhancement:

- A new ``type`` was introduced in 3.7 (announcement has been forgotten): a ``vhighlight`` to be able to hightlight a whole region across all tracks.
- Much more parameters for vhighlight and vlines
- 'zorder' to set it on top or behind.
- 'line_width', 'color', 'alpha', 'border_color' for vhighlight and 'line_style' for vlines
- You can now set multiple vlines
- For gtf, the output of ``make_tracks_file`` set ``prefered_name`` to ``gene_name`` instead of ``transcript_name``.

Bugfix:

- Support mcool files for hic_matrix_square. This solves 404
- Works with gffutils version 0.11.0 where ValueError became gffutils.exceptions.EmptyInputError for empty gtf.
- The installation instructions have been updated
- Fixed a small bug in links track with "use_middle" enabled, where midpoints could have different ordering than start points (Thanks to Jeff1995 ).
- Fix a bug when plotting gtf in the middle of a large intron.
- Fix plot genes with ``orientation = inverted``
- Support Numpy 1.24, drop support below 1.20

Relax version control on matplotlib:

- Any version of matplotlib from 3.1.1 to 3.6.2 is now accepted.

Enhancements:

This release is full of new tracks and new parameters for existing tracks:

- Brand new tracks:

- ``fasta``: to display sequences with colored letters from a fasta file (Thanks GDelevoye for his contribution).

- ``maf`` (multiple alignment format): to display conservation between species.

- ``hic_matrix_square``: to display Hi-C matrices not in 'triangle' shape but in 'square' shape.
This allow to display identical regions but also interactions between 2 different regions.
This render plots close to [hicPlotMatrix](https://hicexplorer.readthedocs.io/en/latest/content/tools/hicPlotMatrix.html).

- New parameters for existing tracks:

- Related to ``hic_matrix_square``: we implemented a new ``display`` mode for ``bed`` and ``links_type`` for ``links``: ``squares``.
This allow to overlay TADs or loops on these Hi-C maps.

- For ``bed`` and ``gtf``:

- the ``fontstyle`` can be set to ``italic`` or ``oblique``.

- the ``arrowhead_fraction`` which controls the size of the arrowhead in the flybase style can be adjusted.

- the color of the backbone when you use flybase or UCSC style can be changed with ``color_backbone``.

- For ``gtf`` a new parameter ``merge_overlapping_exons = true`` help to get a better display when all transcripts are merged.

- For ``bedgraph_matrix``: when ``type = lines`` is set the colors of individual lines can be set by ``individual_color`` and the summary line by ``summary_color``

Minor enhancements:

- pyGenomeTracks display better error message when rtf files are used.

- the help message for BED has been improved to highlight the fact that the extension needs to be part of the output.

- if the directory of the output file does not exists, it is created.

Drop support for python 3.6

- The introduction of the new track for Maf forced us to drop support for python 3.6.

Relax version control on matplotlib:

- Any version of matplotlib from 3.1.1 to 3.5.1 is now accepted.

Bugfixes:

- The tick values for the x-axis are now accurate (see 333) and more informative.

- The y values for tracks like bigwig are not restricted to one decimal. If needed, the scientific notation can be used.

- pyGenomeTracks now allows to plot above chromosome size defined in bigwig or Hi-C matrices without raising an error.

- pyGenomeTracks now works with gtf without exons.

- pyGenomeTracks now closes figures after saving.

- The plotting part does not modify the tracks anymore. This solves 393.

Enhancements:

- A new parameter for pyGenomeTracks allow to fix the width of the central part: ``--plotWidth``

- For scale bars, you can now define the position using 2 parameters among ``x_center``, ``size``, ``scalebar_start_position`` and ``scalebar_end_position``.


Python dependency with conda:

- Using conda which is the way we recommand installation it is now possible to use Python 3.8.

Relax version control on matplotlib:

- Any version of matplotlib from 3.1.1 to 3.3.2 is now accepted.

Bugfixes:

- When the ``--fontSize`` parameter was used it happened that the colorbar labels were not corresponding to the colorbar ticks. This bug has been fixed (297).

- The colormap ``pink`` was not working because it was both the name of a color and a colormap. This bug has been fixed (295).

- When setting ``min_value``, ``max_value``, if the track was empty these values were ignored. This bug has been fixed.

- When using ``operation`` in bedgraph with a ``second_file``, BEDTools is now used to intersect the second file. ``use_middle`` is now taken into account on the second file.

- Different handling of string evaluation of color, colormap and operation.

Bugfixes:

- Get a message when bedtools is installed instead of crashing without any message (see 273, 278).

- Always test if a bedgraph is tabix indexed without checking the extension (see 13 )

- Fix a bug which was happening when ``operation`` or ``summary_method`` was used on bedgraph whereas the bedgraph had some missing intervals (see 277).

- Enforcing version 15 of HiCMatrix. Version 14 had a bug concerning the application of the correction factors of cool files.

Enhancements:

- pyGenomeTracks goes much faster:

- We now use bedtools to load only a portion of bed, gtf, bedgraph, narrowPeak, bedgraphMatrix, Epilogos, links. This speeds up the process dramatically especially for gtf files.

- When you use a cool matrix, only the plotted region is loaded, this speeds up the process. If multiple regions on different chromosomes are provided in a BED this option is not used.

- Unfortunately, it is not possible to speed the process with h5 matrices so you may want to convert them to cool with [hicConvertFormat](https://hicexplorer.readthedocs.io/en/latest/content/tools/hicConvertFormat.html>).

- pyGenomeTracks does not require sorted bed anymore.

- For coverage tracks (bedgraph and bigwig), there is a new parameter: ``grid`` which allows to display horizontal lines.

- For links, you can choose to use the middle of start1 and end1 and the middle of start2 and end2 thanks to ``use_middle`` instead of the extremities coordinates.

- For Hi-C matrices, mcool files are now supported.

- For vlines, the line_width can now be set.

Minor enhancements:

- Bedgraph with NA values in the 4-th column do not raise error anymore.

- There is a progress bar for links.

- For Hi-C matrices,

- there is no error when the plot goes over the chromosome size provided by the matrix.

- if the depth is smaller than binsize it makes an empty plot instead of raising errors.

- When the ``overlay_previous`` is set in the first track it is ignored and a warning is given instead of giving an error with a not meaningful error message.

- The color for negative values in coverage tracks (bigwig and bedgraph) is now part of the output of ``make_tracks_file``.

- Others output of ``make_tracks_file`` have been modified for better clarity.

- Others code related enhancements which are transparent to the users.

- The format of bed12 is more stringent (the blocks must span the chromStart and chromEnd).

- Improve the documentation regarding the installation. We highly recommand to use conda.

Bugfixes:

- For bed tracks when ``gene_rows`` or ``global_max_row`` was set the last row was very close to the bottom (sometimes even overlaying the next track). Now it is vertically centered and do not go over the track height.

- Solve some bugs how non conventional bed files are handle.

- Display more meaningful error messages.

- Only plot scale bar when in the region of plot.

- Do not show a warning when file_type is set for ``x_axis`` or ``spacer``.

- Solve some incompatibilities with python 3.8. However, python 3.8 is not officially supported by now as bioconda do not support it yet https://bioconda.github.io/user/versions.html#python.