name: BiobaseBlast version: 0.3.1.0 author: Christian Hoener zu Siederdissen, Florian Eggenhofer maintainer: choener@bioinf.uni-leipzig.de homepage: https://github.com/choener/BiobaseBlast bug-reports: https://github.com/choener/BiobaseBlast/issues copyright: Christian Hoener zu Siederdissen, 2013 - 2019 category: Bioinformatics license: GPL-3 license-file: LICENSE build-type: Simple stability: experimental cabal-version: >= 1.10.0 tested-with: GHC == 8.4.4 synopsis: BLAST-related tools description: This library contains BLAST-related functionality: . - Parser for tabular NCBI BLAST+ output - Parser for JSON2 NCBI BLAST+ output - Parsers for BLOSUM and PAM matrices. - Specialized substitution functions for (in)complete amino acid / nucleotide triplet substitution. - Incomplete nucleotide patterns map one or two nucleotides to an amino acid (need for indel editing in the mitochondria of certain species like /p.polycephalum/). . The matrices are currently not provided but can be found here: extra-source-files: changelog.md README.md tests/succeed/*.golden tests/succeed/*.test -- because nobody would ever want to distribute files without extensions ... :( sources/PamBlosum/BLOSUM45.50 sources/PamBlosum/BLOSUM45 sources/PamBlosum/BLOSUM40.50 sources/PamBlosum/BLOSUM40 sources/PamBlosum/BLOSUM35.50 sources/PamBlosum/BLOSUM35 sources/PamBlosum/BLOSUM30.50 sources/PamBlosum/BLOSUM30 sources/PamBlosum/BLOSUM100.50 sources/PamBlosum/BLOSUM100 sources/PamBlosum/BLOSUM90 sources/PamBlosum/BLOSUM85.50 sources/PamBlosum/BLOSUM85 sources/PamBlosum/BLOSUM80.50 sources/PamBlosum/BLOSUM80 sources/PamBlosum/BLOSUM75.50 sources/PamBlosum/BLOSUM75 sources/PamBlosum/BLOSUM70.50 sources/PamBlosum/BLOSUM70 sources/PamBlosum/BLOSUM65.50 sources/PamBlosum/BLOSUM65 sources/PamBlosum/BLOSUM62.50 sources/PamBlosum/BLOSUM62 sources/PamBlosum/BLOSUM60.50 sources/PamBlosum/BLOSUM60 sources/PamBlosum/BLOSUM55.50 sources/PamBlosum/BLOSUM55 sources/PamBlosum/BLOSUM50.50 sources/PamBlosum/BLOSUM50 sources/PamBlosum/PAM160.cdi sources/PamBlosum/PAM160 sources/PamBlosum/PAM150 sources/PamBlosum/PAM140 sources/PamBlosum/PAM130 sources/PamBlosum/PAM120.cdi sources/PamBlosum/PAM120 sources/PamBlosum/PAM110 sources/PamBlosum/PAM100 sources/PamBlosum/PAM10 sources/PamBlosum/NUC.4.4 sources/PamBlosum/NUC.4.2 sources/PamBlosum/MATCH sources/PamBlosum/IDENTITY sources/PamBlosum/GONNET sources/PamBlosum/DAYHOFF sources/PamBlosum/BLOSUMN.50 sources/PamBlosum/BLOSUMN sources/PamBlosum/BLOSUM90.50 sources/PamBlosum/PAM310 sources/PamBlosum/PAM300 sources/PamBlosum/PAM30 sources/PamBlosum/PAM290 sources/PamBlosum/PAM280 sources/PamBlosum/PAM270 sources/PamBlosum/PAM260 sources/PamBlosum/PAM250.cdi sources/PamBlosum/PAM250 sources/PamBlosum/PAM240 sources/PamBlosum/PAM230 sources/PamBlosum/PAM220 sources/PamBlosum/PAM210 sources/PamBlosum/PAM200.cdi sources/PamBlosum/PAM200 sources/PamBlosum/PAM20 sources/PamBlosum/PAM190 sources/PamBlosum/PAM180 sources/PamBlosum/PAM170 sources/PamBlosum/PAM490 sources/PamBlosum/PAM480 sources/PamBlosum/PAM470 sources/PamBlosum/PAM460 sources/PamBlosum/PAM450 sources/PamBlosum/PAM440 sources/PamBlosum/PAM430 sources/PamBlosum/PAM420 sources/PamBlosum/PAM410 sources/PamBlosum/PAM40.cdi sources/PamBlosum/PAM400 sources/PamBlosum/PAM40 sources/PamBlosum/PAM390 sources/PamBlosum/PAM380 sources/PamBlosum/PAM370 sources/PamBlosum/PAM360 sources/PamBlosum/PAM350 sources/PamBlosum/PAM340 sources/PamBlosum/PAM330 sources/PamBlosum/PAM320 sources/PamBlosum/PAM90 sources/PamBlosum/PAM80.cdi sources/PamBlosum/PAM80 sources/PamBlosum/PAM70 sources/PamBlosum/PAM60 sources/PamBlosum/PAM500 sources/PamBlosum/PAM50 library build-depends: base >= 4.7 && < 5.0 , aeson >= 1.0 , attoparsec >= 0.13 , binary >= 0.7 , bytestring , cereal >= 0.4 , containers , deepseq >= 1.3 , directory , file-embed >= 0.0.10 , lens >= 4.0 , log-domain >= 0.12 , mtl >= 2.0 , text , unordered-containers , vector >= 0.11 , vector-th-unbox >= 0.2 -- , BiobaseENA == 0.0.0.* , BiobaseTypes == 0.2.0.* , BiobaseXNA == 0.11.0.* , PrimitiveArray == 0.9.1.* , SciBaseTypes == 0.1.0.* default-language: Haskell2010 default-extensions: BangPatterns , DataKinds , DeriveGeneric , FlexibleContexts , MultiParamTypeClasses , MultiWayIf , PolyKinds , TemplateHaskell , TypeApplications , TypeFamilies , TypeOperators , UnicodeSyntax exposed-modules: Biobase.BLAST Biobase.BLAST.Import Biobase.BLAST.Types Biobase.SubstMatrix Biobase.SubstMatrix.Embedded Biobase.SubstMatrix.Hints Biobase.SubstMatrix.Import Biobase.SubstMatrix.Types ghc-options: -O2 test-suite properties type: exitcode-stdio-1.0 main-is: properties.hs ghc-options: -O2 -threaded -rtsopts -with-rtsopts=-N hs-source-dirs: tests default-language: Haskell2010 default-extensions: BangPatterns , OverloadedStrings , ScopedTypeVariables , TemplateHaskell build-depends: base , bytestring , containers , filepath , split >= 0.2.3 , tasty >= 0.11 , tasty-quickcheck >= 0.8 , tasty-silver >= 3.1.9 , tasty-th >= 0.1 , text -- , BiobaseBlast source-repository head type: git location: https://github.com/choener/BiobaseBlast source-repository this type: git location: https://github.com/choener/BiobaseBlast/tree/0.3.1.0 tag: 0.3.1.0