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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:


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:

Online: (under RiboSeq Analysis/RiboPlot).


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 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)


  • 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.


  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.


  • 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].

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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