riboplot 0.3

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:

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 (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

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.

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.