Releases: KatyBrown/CIAlign
1.1.0
A detailed description of all changes associated with the release is in the attached PDF.
CIAlign_v1.1.0_Improvements.pdf
Briefly:
The “remove insertions” function now runs much faster, particularly when the maximum insertion size is very large
A new “crop divergent” function is now available, which allows the user to isolate the most conserved region of the alignment.
CIAlign can now generate position weight, position probability and position frequency matrices.
Users can now specify, using the retain functions, sequences which they would like CIAlign not to remove.
The plot_coverage function is now the plot_stats function and will generate three plots, showing coverage, Shannon entropy and information content per column.
Users can now extract part of an alignment based on their own coordinates, using the get_section function.
An additional colour palette is now available for mini alignments and sequence logos,
It is now possible to convert T to U in alignments, as well as U to T.
The CIAlign manual is now hosted at ReadTheDocs - https://cialign.readthedocs.io/ - and is more readable and comprehensive.
Unit test coverage is now 100% across all module files (excluding import lines and logging)
What's Changed
- Retain sequences by @KatyBrown in #45
- Crop divergent by @KatyBrown in #46
- Multiple changes for release of version 1.1.0 by @KatyBrown in #47
Full Changelog: v1.0.17...v1.1.0
Contributors
Assets 2
1.0.17
1.0.16
1.0.15
v1.0.14
v1.0.11
Changelog:
- Changed how the main CIAlign.py script works internally (but not the results) by moving the argument parser to argP.py and the code to run CIAlign from CIAlign.py to runCIAlign.py and split it up into functions, added extra comments and docstrings
- Added an option to the miniAlignments to keep the numbering from the initial alignment in the mini alignment for the output (e.g. if the input is 1, 2, 3, 4 and 3 is removed the rows in the output will be numbered 1, 2, 4 rather than 1, 2, 3.
- Added default, minimum and maximum values to all the numeric parameters
- Added two additional amino acids - U and O - to the mini alignment colour dictionary
- Added an option to parse non-CIAlign log files to the benchmarking AlignmentStats find_removed_cialign function
- Added --clean, --interpret, --visualise options to run multiple functions
- Added --logo_start, --logo_end to make a sequence logo for partial sequences
- Additional scripts to show how benchmarking was performed
- Generated online figures and online tables for manuscript
- Minor fixes to unit tests to accomodate changes in the main code
- Minor bug fixes and additional documentation
v1.0.10
v1.0.9
v1.0.8
Changelog:
- Resolved issue with pip install
- Added small additional functionality to makeSimilarityMatrix function to count positions with one gap and one non-gap
- Allowed for ambiguous amino acid codes
- Added checks that files are valid FASTA files and that all residues are recognised
- Minor debugging
v1.0.5
Changelog
- Updated miniAlignments to work with large alignments in the latest version of matplotlib
- Small performance improvements to remove_insertions
- Changed the _removed.txt log file to allow automated processing
- Improved log file to remove unnecessary logging
- Changed minimum number of sequences in an alignment to two where this is appropriate
- Formatting to match pep8 standard
- Improved error messages
- Minor bug fixes