1.3.0

Addition and Improvements

• New analysis/visualization programs:
  • LDA.py (Uses Linear Discriminant Analysis to visualize group-wise compositional differences)
  • diversity.py (Visualize alpha diversity as KDE-smoothed histograms)
• New API module
  • graph_util (Adds convenience methods for data visualization/graphing)
• biom_calc module:
  • Switched to using the official biom-format python library for parsing and handline BIOM files
  • Added arcsine square root transformation to the API and added as an option to several scripts:
    • iTol.py
    • LDA.py
• PCoA.py
  • Support for the new UniFrac format in QIIME 1.9
  • Adds the following command-line options:
    • Set font size
    • Set distance between axes and their labels
    • Set the azimuth and elevation for 3D plots
    • Set the graph styling to look like ggplot2 defaults
    • Add Sample ID annotations to graphed points
    • Replaces the --dpi option with --fig_size to set the figure size directly
• LDA.py: Added the option to save the LDA-transformed data out as a csv file.
• diversity.py
  • Added group coloring by specify a column in the mapping file
  • Support for multiple diversity metrics
  • Significance testing is now performed to compare alpha diversity between groups
    • Wilcoxon Signed Rank Test for two-group comparison
    • Kruskal-Wallis H-test for comparing three or more groups
• biom_relative_abundance.py: Support for BIOM-format input.
• biom_calc.py: Updated raw_abundance() function to handle BIOM format version 2.x input files.
• iTol.py: Updated BIOM file handling for iTol script (v2.x files).
• PhyloToAST documentation moved from separate repository into the 'docs' folder in the main code repository
• Overhauled the main page for the project documentation
• Added step-by-step instructions to the documentation for many of the executable scripts

Bug Fixes

• Prevents duplicate entries from being passed on into the output from restrict_repset.py.
• Fixes the --save_calculations option in diversity.py. Now prints out all metrics in a single column with the second column being group membership.
• Adds pad_taxonomy method (otu_condense.py) to ensure all taxonomy strings have all levels down to species.
• Cleans up error message for line parsing in prune_taxonomy. Makes file error message more readable.

1.2.0

Improvements

• Renamed "QIIME-tools" to "PhyloToAST".
• Added travis.yml file to implement continuous integration using Travis IC.
• Modified the README file to conform with the name change.
• Added PCOA.py script allowing users to create 2D or 3D plots.
• Added restrict_repset.py script, which allows users to create a new OTU representative set file from a filtered BIOM table.
• Updated imports in all the scripts to use "phylotoast" instead of "qiime_tools".
• Improved error handling mechanism in all binary scripts.
• Added try...catch blocks for ImportError and IOError for all third party imports and user required input file handles.
• Added user friendly error message to enable quick debugging.
• Improved and updated all API scripts with new functions.
• Binary scripts now import API scripts and use the functions from API, thus, reducing binary script complexities.
• Modified all scripts to conform to PEP8 format using flake8 module.

1.1.2

Improvements

• Cleans up the abundance calculation code and moves the output_relative_abundance() method to the biom_relative_abundance.py script.
• Modifies name extraction from each OTU level so that underscores in the name (after the initial double underscore) are allowed.
• Adds more detail and project badges (downloads,version,format) to the README.

Bug Fixes

• Restores accidental reversion of commit 9413c64 introduced by commit 91d6a39.

1.1.1

This version features full build compatibility with pypi, and is now available for download and install with pip:

$ pip install qiime-tools

Most of the changes in this release are related to project structure, edits necessary to get setuptools builds working for release on pypi, and bug fixes.

Additions and improvements

• SLURM template added for use with the multi_parallel_pick_otus script.
• New otu_calc module for working with abundance tables (BIOM) and providing calculations such as Shannon Diversity and relative abundance.
• otu_tax_name.py now handles classic (tsv) BIOM tables in addition to simple lists of OTU IDs.
• New script filter_keep_otus_by_sample.py as the opposite of the QIIME script filter_otus_by_sample.py

qiime-tools 1.0.0

First release of the qiime-tools project! Please visit (http://qiime-tools.readthedocs.org) for full documentation and tool explanation.

Please feel free to contribute by forking or opening issues.