RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).
There are two programs in the package:
Plot and output read counts (csv) for a single transcript.
Output read counts for all transcripts in an alignment.
Free software: GPL license.
Github Repository: https://github.com/vimalkvn/riboplot.
Online: http://ribogalaxy.ucc.ie (under RiboSeq Analysis/RiboPlot).
- Bugfix: ribocount: allow creation of zip files larger than 2GB.
- Support for multiple read lengths and corresponding offsets.
- Optional arguments check is now split into multiple steps.
- Remove the calculation of read lengths present in the BAM alignment.
- 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 provided.
- 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.
- Bugfix: Recalculate read frame positions after applying offset.
- Add sequence to CSV output.
- 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.
Fix: Add mock again to setup requirements. Matplolib install under Galaxy fails otherwise.
- Support for color schemes - options: default, colorbrewer, rgb, greyorfs.
- Plot changes - colored, light background for ORF architecture, legend moved down.
- Image DPI change 300 → 600.
- Sample scripts to plot multiple transcripts and multiple color schemes.
- Ability to output read counts in 5’(-v) and 3’(-r) leader region.
- Report error if a bam index could not be generated (ex. bam sorted using
reference names instead of chromosome coordinates).
- No start/stop values when transcript sequences are in lower case.
- Split into three different files.
- Updated test configuration.
- 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.
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