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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[Unreleased]

[2.0.2.post1]

Changed

  • Retaining FASTA header comments in output.

[2.0.2]

Fixed

  • Typo in melt_duplex.
  • Duplicated output from melt_duplex when -F is not used.
  • Wrong variable name in duplex module.

Changed

  • Version tag now stored in const module.
  • Now using black for code formatting.

##[2.0.1.post5]

Added

  • Version control of scripts and --version flag.
  • melt_duplex output in FASTA format.
  • FASTA header key-value delimiter as option.

Changed

  • FASTA input parsed with biopython SimpleFastaParser.

Fixed

  • Proper script help page formatting.
  • Bug that duplicated every line in the output.

[2.0.1]

Changed

  • Re-packed software for pypi.

Added

  • Default parameter values.

[1.4.5]

Fixed

  • Fixed issue with new interaction type labeling system.

Added

  • Automatic R packages installation (argparser and ggplot2).

Changed

  • Separated curve calculation and fraction calculation to different functions.
  • Harmonized melt_X.py scripts output.
  • Better fasta reading management: not kept in memory and considering sequences with same header as separate fasta items.

Added

  • plot_melt_curves_coupled.R for single-oligo coupled melting curve plot.
  • Allowed for initial formamide and sodium concentration for melting temperature correction.

[1.4.4]

Changed

  • Renamed oligomeltlib.py to meltlib.py.
  • Renamed oligomelt.py to melt_duplex.py.

Added

  • melt_second.py to perform formamide correction and melting curve calculation for secondary structures predicted with OligoArrayAux.

[1.4.3]

Added

  • Melting curve plotting script (from fish-conditions repo).

Changed

  • Moved functions to separate library

Fixed

  • Now melting curves show the proper (inverted) dissociation curve.

[1.4.2]

Changed

  • Now using user-defined formamide m-value for wright correction.

[1.4.0]

Added

  • New feature: formamide correction.

[1.3.0]

Added

  • New feature: temperature curve calculation. Proper fasta input.

[1.2.2]

Fixed

  • Allawi and Freier thermodynamic tables.

[1.2.1]

Fixed

  • Introduced Sugimoto (DNA:RNA) thermodynamic table.

[1.2.0]

Added

  • New feature: DNA/RNA and RNA/DNA duplex calculation.

[1.1.0]

Added

  • New input file mode.

Fixed

  • Mg2+ correction now skips Na+ correction.

[1.0.0]