poly-v0.9.0

BREAKING CHANGES

• fasta parsing has been moved to its own separate sub-package and is no longer supported with previous syntax or in CLI. It also no longer parses to Sequence struct by default.

• All sequences that are translated are now forced to uppercase.

• All CLI commands that don't involve file converting or file hashing functionality have been deprecated in anticipation of an overhaul.

• Poly only ships one sequence hashing standard seqhashv1 and has deprecated all support for other hashing functions. You can still use Booth Least Rotation in combo with your favorite hash function.

Changelog

9bf2993 Add random protein sequence function (#121)
17f27e4 Added Fasta parser (#113)
7937615 Adds force upper case during translations (#158)
72be193 All iupac variants (#106)
f8cbd8f Fixed EOF error call (#167)
f7c6987 Fixed pichia error by adding multiline genbank feature locations (#125)
9d2eea8 Make writes to temporary files in io tests (#149)
b98f224 Markdown cleanup (#112)
dd81ed2 Rebase parser (#111)
7825244 Simplified names in parsers (#168)
e69df2e Uniprot XML parser (#156)
f6e7dec added barcoding functions (#87)
6886868 bump golang to 1.16 (#150)
a1ba1c5 integrated new linter, removed deadcode, and deprecated parts of CLI and hashing. (#116)

poly-v0.8.1

Changelog

a0b539f Added CompromiseCodonTable to Poly (#85)
3a11af6 Fixed panics during large file parsing (#86)
acfec4a Seqhash v1 (#82)

poly-v0.7.1

Changelog

63573e9 Add Codon Table JSON input / output (#73)
a3f9b1d Add support for Gz'd flat files (#79)
5e9178c Adds func for reading multi and flat genbank files (#76)

poly-v0.6.1

Changelog

c31aaf6 Update doc.go

poly-v0.6.0

BREAKING CHANGES

Optimization functions have been renamed.
Odd variety of hash command printout have been deprecated.

Changelog

f8da3dc Hash flag test (#64)
9b00bd6 Refactor commands (#66)
903b8b5 added doc files for pkg.go.dev. (#68)
4c95242 improving test coverage (#65)
9f0f049 increase test coverage (#63)
bbd5da0 updated variable names in io.go.

poly-v0.5.0

BREAKING CHANGES

parse functions now except bytes instead of strings.
boothLeastRotation, DefaultCodonTables*, and GetCodonFrequency were made private.

Changelog

9cd47eb Refactor docs (#60)
67bc453 added FASTA IO example tests.

poly-v0.4.0

BREAKING CHANGES

This version of poly has breaking changes. AnnotatedSequence and Sequence has merged into one unified struct also called Sequence.

Also, the previous blake3 and Generichashsequence methods have been deprecated and merged into one function hashSequence() which is exposed through a new .Hash() interface.

Changelog

a54050d Refactor io (#59)
7304bf6 refactored hash.go. Now exposes only two hashing methods. (#58)

poly-v0.3.1

Changelog

7fbfb93 Repackage (#57)

• This is a minor version bump. Poly's command line utility and library have been separated such that godocs should now render.

poly-v0.3.0

Changelog

7b0947a Add optimization and translation functions for sequences (#11)
49d4f53 Create FUNDING.yml
4e7ba37 Delete discord.yml
f2cec4c Read a FASTA file containing multiple sequences, extract the definition and sequence from each. (#37)
6145b4f Update installation.md
bd89570 added BuildFASTA function.
9471438 added GetSequence methods and tests. (#48)
5f1251c added issues and issue comments to discord notifications.
84f2367 create discord.yml.
9e993f8 fixed comment whitespace in io.go
37b2d28 implements CalcTM, which calculates primer melt temp (no mismatches) (#34)
58b967f tidying up comments in io.go and dependencies in go.mod and go.sum.
f5eca20 updated comments in io.go.

poly-v0.2.0

Changelog

f66c140 added a buildGbk() function and related command. (#33)