The holy handgrenade

v1.6.16 (Aug 2017)

• Bug fixes to vcf2scoary

v1.6.15 (Jul 2017)

• Deleted a function that would prevent scoary from being installed through pip for some users

v1.6.13 (Jul 2017)

• Fixed a bug where Scoary would not handle converted VCF files due to different headers
• Changed the parameters of --test
• Fixed the GUI that was broken since 1.6.12 due to introduction of --include_input_columns
• Include_input_columns now correctly handles the ALL keyword
• Added the ExampleVCFTrait.csv file to test VCF functionality

v1.6.12 (Jun 2017)

• Convert VCF files to Roary/Scoary format, allowing analysis on a wide range of variants (SNPs, indels, structural variations etc)
• Grab columns from the Roary input and put in the output (To get strain-specific protein names, for example)
• Scoary now comes with a manual, located under docs/tex/scoary_manual.pdf
• The log now includes the original command line

v1.6.11 (Apr 2017)

• Blank values in trait files will now correctly be read as missing. Fixes (#54)
• Added --no_pairwise option for simple set differences / categorical enrichment analysis without causal hypothesis (As requested among others in (#53)
• Modified GUI with no_pairwise and slightly modified look.
• Added ExampleTree.nwk to exampledata
• Added support for travis. (CI tests will be further developed)
• Added example cases in README.md
• Fixed broken links in README.md

v1.6.10 (Jan 2017)

• Scoary now creates a log file (both in terminal and GUI mode)
• Fixed a bug where empirical p-values would exceed 1.0
• Fixed a bug where Scoary would crash when pruning many isolates from the internally calculated phylogenetic tree

v1.6.9 (Dec 2016)

• Scoary now handles missing data specified in the traits file as "NA", "-" or ".".
• Now also handles missing isolates (rows) in the traits file.
• Stylistic changes, including line lengths formats to conform with PEP8.

v1.6.8 (29th Nov 2016)

• Bugfix: Addition of numpy.float64 and long were causing problems on some systems. Now converted to float beforehand. (Fixes #43)

v1.6.7 (28th Nov 2016)

• Scoary article is now out! Updated Readme and citation.

Blind unicorn

#CHANGELOG
v1.6.6 (9th Nov 2016)

• Changed citation.
• Scoary is now available through Zenodo.

v1.6.5 (25th Oct 2016)

• Added the README_pypi.md file so that setup.py can be used to build/install locally if pip not installed.

v1.6.4 (18th Oct 2016)

• Made the permutations algorithm faster by implementing a dynamic cutoff

v1.6.3 (14th Oct 2016)

• Removed OR calculation from PhyloTree class
• Now prints collapse option to stdout
• Cleaned up threading method

v1.6.2 (13th Oct 2016)

• Collapsing correlated genes is now optional, controlled with the --collapse flag
• Fixed a bug where the collapsing duplicated some genes
• Collapsing is default to False in GUI mode

v1.6.1 (7th Oct 2016)

• Added a GUI, callable as scoary_GUI
• Added post-analysis label-switching permutations, and the option to filter on empirical p-values
• Added multiprocessing to speed up permutations
• Added a second column in the phenotype exampledata
• Adds an outdir option
• Now available through PyPi

v1.5.1 (22nd Sep 2016)

• Users can now provide a custom tree that will be used for analysis instead of the internally calculated one.
• Changed the way trees are written to file. Leaf nodes will no longer have "double" distance. The tree files are now also rooted, which allows them to be read by other software
• Fixed some typos and added a lot of exception throwing for when the user is trying strange things, such as pointing to files that don't exist.

Slow loris

"Slow loris" is the latest Scoary release.

v1.5.0 (13th Sep 2016)

• Scoary is now installable via pip! (Thanks go to Anders Goncalves da Silva). The scoary.py script will now be deprecated, but is still available for legacy use. See Installation
• The program now also prints out the filtration options being used for the current analysis.
• Changes will now be in a dedicated changelog rather than in the readme.

Version 1.4.2 - Home laboratory

v1.4.2 (13th Sep 2016)

Fixed a bug that would cause Scoary to crash if ran without any -c options.

v1.4.1 (8th Sep 2016)

Fixed a bug where results in the output file did not have quotes around them. This could interfere with annotations that have delimiters (like commas) in them.

v1.4.0 (7th Sep 2016)

-The correction options are now a lot more sophisticated, and allow multiple restrictions with individual p-values to be set.
-Fixed a bug that would sometimes result in a too strict Bonferroni p-value in the results.
-No-time now also applies to the reduced gene presence/absence file.
-The results sorting now works a little differently. When using only pairwise comparisons filtering, results will be sorted by these p-values. When other filters (Individual, Bonferroni, Benjamini-Hochberg) are used, results will be sorted by these instead.
-Fixed a bug where the program would crash if you specified a very large max_hits.
-The citation option has been added, and includes a nifty ASCII logo.
-Some optimization when using pairwise comparison to filter results.

v1.3.7 (2nd Sep 2016)

-The no-time argument can now be used to avoid output files (results and tree file) to come with a timestamp in the name. Should make it easier to implement Scoary in automated pipelines. (Credits: Marco Galardini)
-Comma is now the default delimiter in input and output files. The user can specify another input/output delimiter with the delimiter argument. (Note that the two input files and the output files will all have the same delimiter)
-Bug fixes that caused python3 problems in 1.3.6 (Credits: Marco Galardini)

v1.3.6 (28th Jul 2016)

-Simulated example data is included in the exampledata folder. This is primarily intended as a guide to how input files can look, as well as giving users a quick view at what the program can do. Running Scoary with the --test flag will overrun all other options (except --version) and automatically run the exampledata with default options.

Morning glory

This is the pre-release version of Scoary.