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This repository has been archived by the owner on Nov 25, 2023. It is now read-only.
* Bugfix: Use known versions of libraries as dependencies in setup.py.
Otherwise, pip installs latest versions which haven't been tested.
* Remove Codons label, change START to AUG [riboplot].
* Bugfix: ribocount now returns correct read counts if an offset is p…
…rovided.
* Bugfix: Don't include read counts in the longest ORF start or stop positions
i.e., only include reads upstream or downstream of the start or stop positions.
* Use default linewidth (riboplot), Minor changes to default plot style.
* Use 'Agg' as the default matplotlib backend (prevent $DISPLAY errors).
* Use smaller images for the help section.
* Fix typo in HISTORY.rst.
* Update Github repository URL.
**riboplot**
* Support for color schemes - options: default, colorbrewer, rgb, greyorfs.
* Plot changes - colored, light background for ORF architecture, legend moved down.
* Image DPI change 300 |srarr| 600.
* Sample scripts to plot multiple transcripts and multiple color schemes.
**ribocount**
* Ability to output read counts in 5'(``-v``) and 3'(``-r``) leader region.
Bugfixes
1. Report error if a bam index could not be generated (ex. bam sorted using
reference names instead of chromosome coordinates).
2. No start/stop values when transcript sequences are in lower case.
Tests
* Split into three different files.
* Updated test configuration.
Minor
* XML wrapper changes - remove 'leader', add help text and output label change [ribocount].
* Remove unused pysam import [riboplot].
* Replace doc includes with sym links (breaks Galaxy toolshed otherwise).
* Updated CSS/Table styles (removed number column from table).
* y limit is now 1.25x [riboplot].
* Removed line width on bars [riboplot].
* Remove invalid Python 3 version (whl).
* Remove unused test data files.
* Remove strict dependence on matplotlib and pysam versions.
* Cleanup MANIFEST.