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.
History
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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