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HISTORY.md

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Changelog for Coral

0.5.0 (2016-02-20)

  • Separated ssDNA (single-stranded) and DNA (implicitly double-stranded) classes. Convert between them using .to_ds() and .to_ss() methods, respectively.
  • coral.Primer instances now contain ssDNA instances, not DNA.
  • feature_type is now an optional argument when initializing new Feature instances. The default is 'misc_feature'.
  • Added to_feature() convenience method to coral.DNA for generating a feature from a given DNA instance.
  • Fixed an issue where coral.analysis.tm returned an arcane message when the input is a non-DNA character.
  • Fixed an issue where read_sequencing returned ssDNA.
  • Overhauled alignment and Sanger sequencing analysis modules. Added support for using the MAFFT command-line tool as an alignment method, located at coral.analysis.MAFFT. Added MAFFT as an option for the Sanger analysis class. Added a new function, needle_msa, that generates a reference-aligned MSA representation of a set of Needleman-Wunsch pairwise alignments. Added coral.analysis.substitution_matrices module, which adds a SubstitutionMatrix class for easily specifying customized substitution matrices for Needleman-Wunsch alignment as well as built-in matrices such as BLOSUM62, DNA, and DNA_SIMPLE.
  • dev note: started using zest.releaser to automate releases.

0.4.1-0.4.3

  • Bugfixes to 0.4.0 (brown-bag style bugs, fixed immediately after elease).

0.4.0

  • Renamed coral.DNA.rotate() method to coral.DNA.rotate_to().
  • Created new coral.DNA.rotate() method that rotates a sequence 'counter-clockwise', acting as a deque.
  • Created new coral.DNA.rotate_to_feature, which rotates a sequence to a given feature's start location.
  • Created new coral.DNA.excise feature, which removes a feature's sequence from a circular DNA object, generating a linear product (useful for swapping out features).
  • Improved coral.DNA __getitem__ behavior.
  • Added .material property to all sequence types for pseudo-type checking.
  • Made coral.DNA.top() and coral.DNA.bottom() methods into properties (coral.DNA.top and coral.DNA.bottom) that can be overwritten and accessed directly.
  • Replaced coral.DNA.topology and coral.DNA.stranded properties (which were strings) with boolean-valued .circular and .ds values, respectively.
  • Re-wrote (and renamed) the coral.analysis.NUPACK and coral.analysis.ViennaRNA packages to be more feature-complete.
  • Fixed an issue where re-running coral.DNA.display() in a Jupyter notebook resulted in non-updated text labels.

0.3.3

  • Added Python 2 version check to prevent installation on Python 3.

0.3.2

  • Removed cython dependencies entirely to ease installation.

0.3.1

  • Fixed issues with PCR simulation and annealing, can now handle all cases of primer directionality and overlaps, linear and circular templates.
  • Added pyx to package manifest for case where user already has cython installed.

0.3.0

  • Separated out annealing behavior into analysis function (analysis.anneal).
  • Functions that use annealing (e.g. reaction.pcr) can now accept partial annealing + overhang matches due to annealing overhaul.
  • Gibson reactions now retain features of the inputs.
  • Added strip() method to coral.DNA.
  • Installation now works on Mac OS X.
  • Made most dependencies optional.
  • Fixed issue where features were not being copied, resulting in unexpected behavior (assign by reference vs. value).
  • Fixed an issue where slicing the last N bases of a sequence (e.g. y =x[-4:]) would modify the feature locations of the parent (x).

0.2.1

  • Added HISTORY.md (this file) changelog.
  • Fixed version bump issue, added javascript to manifest, added dev-requirements.txt.

0.2.0

  • plasmid visualizations for iPython notebooks using coral.DNA.display.
  • features are now searchable using coral.DNA.select_features.
  • seqio.read_dna now keeps all feature qualifiers when reading genbank files (thanks @eyu-bolthreads!).

0.1.0

Initial Release.