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Release History

1.3.0 (2016-02-26)

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 (2015-01-29)

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 (2014-09-19)

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 (2014-09-16)

The most notable change is the project is now structured to be installable via setuptools and compatible with (and available on) PyPI:

$ pip install qiime-setuptools

Or if you prefer to build from source:

$ python setup.py install

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

Bug Fixes

  • In iTol.py: fixes an issue where some or all of the OTU IDs in a newick-format tree have single-quotes surrounding them ('OTU_ID'), causing the script to crash.
  • otu_name_biom() in the otu_calc method now returns a value as it was meant to

1.0.0 (2014-05-17)

First release!