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* Created changelog Avoids hugging space on front page * Removed what's new -> changelog * Typo in help message
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| #CHANGELOG | ||
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| 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] (#installation) | ||
| - The program now also prints out the filtration options being used for the current analysis. | ||
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| v1.4.2 (13th Sep 2016) | ||
| - Fixed a bug that would cause Scoary to crash if ran without any -c options. | ||
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| 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. | ||
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| 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. | ||
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| 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) | ||
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| 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. | ||
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| v1.3.5 (PRE-RELEASE) (5th Jul 2016) | ||
| - You can now use the -w option with -r to write a reduced gene presence/absence file containing only the subset isolates. This ensures that the program will run much faster if you have a large dataset (1000s of isolates) but only want to analyze a subset. Scoary automatically opens and analyzes the newly written file. | ||
| - This is a pre-release version. There might still be bugs in the code, in which case I would be grateful if you report them. | ||
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| v1.3.4 (16th Jun 2016) | ||
| - Scoary no longer crashes when using Scipy 0.16 instead of 0.17. | ||
| - More information about what's going on is printed. (Useful for very large datasets that take long to analyze) | ||
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| v1.3.3 (9th Jun 2016) | ||
| - BUG FIX: Tree calculation had been broken since 1.3.2 yesterday. Sorry about that. | ||
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| v1.3.2 (8th Jun 2016) | ||
| - Scoary SHOULD now be compatible with Python 3.x. Please report back if you disagree. | ||
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| v1.3.1 (8th Jun 2016) | ||
| - Scoary is now packaged as a proper python package according to the PEP8 style guide (Thanks to Marco Galardini) | ||
| - A percentage counter is now shown when calculating pairs | ||
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| v1.3.0 (1st Jun 2016) | ||
| - Major changes to the pairwise comparisons algorithm. Scoary now calculates the maximum number of contrasting pairs, and given that maximum number tests the maximum number of pairs that SUPPORT A -> B (AB-ab pairs) and the maximum number of pairs that OPPOSE A -> B (Ab-aB pairs). The opposite is true for genes where the odds ratio is < 1 (i.e. that indicate A -> b). | ||
| - The p-values reported from the pairwise comparisons is now a range. It reports the best (lowest) p-value, which comes from the maximum number of supporting pairs and the minimum number of opposing (given a set total), as well as the worst (highest) p-value, which comes from the minimum number of supporting pairs and the maximum number of non-supporting, given a set total number of pairings. It does this at each node in the tree. | ||
| - Scoary can now print the UPGMA tree that is calculated internally from the Hamming distances of the gene_presence_absence matrix. Do this by using the -u flag. | ||
| - The elapsed time will now print when finished. | ||
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| v1.2.3 (30th May 2016) | ||
| - Odds ratios should now be correct again. These were behaving strangely since 1.2.0. Apologies. | ||
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| v1.2.2 (28th May 2016) | ||
| - Another bug fix related to the restrict_to option where Scoary would crash if it was NOT set. | ||
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| v1.2.1 (26th May 2016) | ||
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| - Bug fix. The --restrict_to option had become broken in 1.2.0 because one function was passing the full set of isolate names rather than the restricted set downstream in the analyses. This has been fixed. | ||
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| v1.2.0 (23rd May 2016) | ||
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| - Major changes. Scoary now implements the pairwise comparisons algorithm to account for population structure. | ||
| - Scoary now imports 4 classes: Matrix, QuadTree, PhyloTree and Tip. They two former are used for storing pairwise distances between isolates, and the two latter are used for the pairwise comparisons algorithm. Scoary_methods contain some new functions and most of the old ones have been altered to allow the pairwise comparisons implementation. However, there are no changes to how Scoary calculates the previously implemented statistics. | ||
| - There should now be a significant speed increase, as Scoary now stores Fisher's exact test p-values rather than re-calculating for every gene. Previously, a new calculation was made for every gene, even when the 2x2 table was identical. | ||
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| v1.1.2 (4th May 2016) | ||
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| - Fixed another bug related to Benjamini-Hochberg p-value adjustments. (Thanks again to cimendes). The numbers should now correspond to R's "p.adjust" method IF the number of tests are the same. (Scoary runs the correction on ALL genes, not just those with p<.05) | ||
| - Results are now printed with "" quotation marks around each cell to avoid weird cell breaks if annotations contain semicolons when opening in spreadsheets. | ||
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| v1.1.1 (3rd May 2016) | ||
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| - Fixed a bug where adjusted p-values were not being calculated and output correctly. (Thanks to cimendes). | ||
| - Benjamini-Hochberg p-values are now calculated from least to most significant (step-up) instead of step-down. | ||
| - Holm-Sidak p-values has been removed. | ||
| - The Scoary version is now displayed in the help message and if calling Scoary with the --version flag. (Thanks to EricDeveaud) | ||
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| v1.1 (29th Mar 2016) | ||
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| - Scoary now imports all methods from Scoary_methods in order to circumvent errors when trying to run Scoary under Python 3.x. | ||
| - Genes that have the same naïve p-value now have adjusted p-values penalized with the same factor rather than an increasing one. |
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