Plot read counts of RiboSeq data from BAM format alignment files
Project description
RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).
There are two programs in the package:
riboplot
Plot and output read counts (csv) for a single transcript.
ribocount
Output read counts for all transcripts in an alignment.
Free software: GPL license.
Documentation: http://pythonhosted.org/riboplot.
PyPI: https://pypi.python.org/pypi/riboplot.
Github Repository: https://github.com/vimalkvn/riboplot.
Online: http://ribogalaxy.ucc.ie (under RiboSeq Analysis/RiboPlot).
History
0.3.1 (2017-03-04)
Bugfix: ribocount: allow creation of zip files larger than 2GB.
0.3.0 (2015-12-10)
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.
0.2.5 (2015-11-30)
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].
0.2.4 (2015-11-25)
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.
0.2.3 (2015-11-24)
Bugfix: Recalculate read frame positions after applying offset.
Add sequence to CSV output.
0.2.2 (2015-10-29)
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.
0.2.1 (2015-10-16)
Fix: Add mock again to setup requirements. Matplolib install under Galaxy fails otherwise.
0.2.0 (2015-10-15)
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 → 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
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.
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].
0.1.1 (2015-09-08)
Remove invalid Python 3 version (whl).
Remove unused test data files.
Remove strict dependence on matplotlib and pysam versions.
Cleanup MANIFEST.
0.1.0 (2015-08-24)
First release on PyPI.
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