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Add stats to codon tables #350

Merged
merged 38 commits into from
Nov 15, 2023
Merged

Add stats to codon tables #350

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14d574a
add stats to codon tables
cachemoi Sep 18, 2023
9e5dc10
revert unintended error message removal
cachemoi Sep 19, 2023
1b3009f
separate stats into its own codon analyzer struct
cachemoi Sep 19, 2023
e21ea46
Update synthesis/codon/analyzer_test.go
cachemoi Sep 19, 2023
1770a10
remove analyzer
cachemoi Sep 21, 2023
57c2b06
stats struct
cachemoi Sep 21, 2023
35f8854
turn codonTable into TranslationTable, which holds the required data …
cachemoi Sep 21, 2023
5a40bc3
generate translation and optimisation maps in constructors
cachemoi Sep 21, 2023
1cee443
return pointer
cachemoi Sep 21, 2023
ad22177
return pointer, table interface no longer necessary
cachemoi Sep 21, 2023
6f6fa7b
update the Compromise and Add funcs to copy the first table when merg…
cachemoi Sep 21, 2023
a371a42
imports and error
cachemoi Sep 21, 2023
7d0e6a9
add gene count to stats
cachemoi Sep 21, 2023
8f21d0b
DRY tests with new structures
cachemoi Sep 21, 2023
7938cd8
DRY examples with new structures
cachemoi Sep 21, 2023
888d800
update synthesis code to use the codontable's Optimize func
cachemoi Sep 21, 2023
fdaa508
update amino acid weights through setter
cachemoi Sep 21, 2023
0e2a1a3
bubble up table weight update errs
cachemoi Oct 18, 2023
03e99bc
make stats part of the table struct so we can track them across a tab…
cachemoi Oct 18, 2023
a2f8fc7
add comments
cachemoi Oct 18, 2023
299e45a
make translation table stats public rather than use a getter
cachemoi Oct 18, 2023
6429150
add table test for optimisation
cachemoi Oct 18, 2023
4d8020b
fix fatal err case
cachemoi Oct 18, 2023
f613bde
add test case
cachemoi Oct 18, 2023
4fcd51e
missed an item in updateWeights
cachemoi Oct 18, 2023
436ed93
proper gene count
cachemoi Oct 18, 2023
eb0036f
move stats below other interfaces
cachemoi Nov 1, 2023
04b7c82
add translate to table interface
cachemoi Nov 1, 2023
d3a9454
update comments
cachemoi Nov 1, 2023
08becb9
update comment
cachemoi Nov 1, 2023
58a511c
update changelog
cachemoi Nov 5, 2023
2062760
comment NewStats
cachemoi Nov 8, 2023
c4ff8d7
add weight update err test
cachemoi Nov 8, 2023
aaf961b
newAminoAcidChoosers test
cachemoi Nov 8, 2023
36f255c
UpdateWeights test
cachemoi Nov 8, 2023
a65fbe0
Compromise/Add codon table tests
cachemoi Nov 8, 2023
0d107ac
add an example for using manual codon weights
cachemoi Nov 8, 2023
caef839
fix lint
cachemoi Nov 13, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added
- Alternative start codons can now be used in the `synthesis/codon` DNA -> protein translation package (#305)
- Added a parser and writer for the `pileup` sequence alignment format (#329)
- Added statistics to the `synthesis/codon` package (keeping track of the observed start codon occurrences in a translation table) (#350)

### Fixed
- `fastq` parser no longer becomes de-aligned when reading (#325)
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