PGT 3.5

[lldelisle]

• The _version.py needs to be updated for pypi deploy.

[lldelisle]

3.5

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.

• 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.

[lldelisle]

Note: on linux the current version of libopenblas make segmentation faults (on my laptop and on travis at least).
For the bioconda recipe, I propose that we modify it to add:

libopenblas < 0.3.10

To avoid issues and we will relax it in the next release if it is fixed.

[lldelisle]

I would say, let's go...