elynx-seq 0.4.1 → 0.5.0

raw patch · 5 files changed

+42/−32 lines, 5 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• ChangeLog.md +10/−0
• README.md +27/−27
• elynx-seq.cabal +1/−1
• src/ELynx/Data/Character/Codon.hs +3/−3
• src/ELynx/Data/Sequence/Translate.hs +1/−1

@@ -5,6 +5,16 @@ ## Unreleased changes  +## Version 0.5.0++-   `modLen`, `modSup`.+-   Newtype wrappers for branch length, branch support, and node name. Those data+    types and some functions were also renamed.+-   Add `Path`, and `getSubTreeUnsafe` to tree zipper.+-   Rename `unsafe` functions so that `unsafe` is at the end.+-   Many small changes.++ ## Version 0.4.1  -   Improve `TimeSpec` (Point process).

@@ -2,7 +2,7 @@  # The ELynx Suite -Version: 0.4.1.+Version: 0.5.0. Reproducible evolution made easy.  <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -90,9 +90,9 @@      slynx --help | head -n -16 -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]                   [-f|--force] [--no-elynx-file] COMMAND@@ -137,9 +137,9 @@      slynx concatenate --help -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE       Concatenate sequences found in input files.@@ -158,9 +158,9 @@      slynx examine --help -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site]       Examine sequences. If data is a multi sequence alignment, additionally analyze columns.@@ -180,9 +180,9 @@      slynx filter-rows --help -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH]                               [--shorter-than LENGTH] [--standard-characters]@@ -203,9 +203,9 @@      slynx filter-columns --help -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE                                  [--standard-chars DOUBLE]@@ -227,9 +227,9 @@      slynx simulate --help -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]                            [-m|--mixture-model MODEL] [-e|--edm-file NAME] @@ -306,9 +306,9 @@      slynx sub-sample --help -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE                             (-n|--number-of-sites INT)@@ -336,9 +336,9 @@      slynx translate --help -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT)                            (-u|--universal-code CODE)@@ -361,9 +361,9 @@      tlynx --help | head -n -16 -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]                   [-f|--force] [--no-elynx-file] COMMAND@@ -401,9 +401,9 @@      tlynx compare --help -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect]                           [-f|--newick-format FORMAT] NAMES@@ -430,9 +430,9 @@      tlynx examine --help -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT]       Compute summary statistics of phylogenetic trees.@@ -454,9 +454,9 @@      tlynx simulate --help -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: tlynx simulate (-t|--nTrees INT) (-n|--nLeaves INT) PROCESS                            [-u|--sub-sample DOUBLE] [-s|--summary-statistics] @@ -491,9 +491,9 @@      elynx --help | head -n -16 -    ELynx Suite version 0.4.1.+    ELynx Suite version 0.5.0.     Developed by Dominik Schrempf.-    Compiled on October 16, 2020, at 12:46 pm, UTC.+    Compiled on November 10, 2020, at 14:29 pm, UTC.          Usage: elynx COMMAND       Validate and redo past ELynx analyses

@@ -1,6 +1,6 @@ cabal-version:  2.2 name:           elynx-seq-version:        0.4.1+version:        0.5.0 synopsis:       Handle molecular sequences description:    Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>. category:       Bioinformatics

@@ -18,7 +18,7 @@ -- - https://en.wikipedia.org/wiki/Genetic_code module ELynx.Data.Character.Codon   ( Codon (Codon),-    unsafeFromVec,+    fromVecUnsafe,     UniversalCode (..),     translate,     translateX,@@ -50,8 +50,8 @@  -- | Unsafe conversion from vector with at least three elements; only the first -- three elements are used, the rest is discarded.-unsafeFromVec :: V.Vector v a => v a -> Codon a-unsafeFromVec xs =+fromVecUnsafe :: V.Vector v a => v a -> Codon a+fromVecUnsafe xs =   Codon (V.head xs, V.head . V.tail $ xs, V.head . V.tail . V.tail $ xs)  -- | Universal codes.

@@ -49,5 +49,5 @@   | rf < 0 = error "translateVecWith: reading frame is negative."   | otherwise = aas   where-    codons = map unsafeFromVec $ chopVec 3 $ V.drop rf cs+    codons = map fromVecUnsafe $ chopVec 3 $ V.drop rf cs     aas = V.fromList $ map f codons