Plot read counts of RiboSeq data from BAM format alignment files
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.
First release on PyPI.
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