Name: bio Version: 0.5.1 License: LGPL License-file: LICENSE Cabal-Version: >= 1.6 Author: Ketil Malde Maintainer: ketil@malde.org Category: Bioinformatics Synopsis: A bioinformatics library Description: This is a collection of data structures and algorithms useful for building bioinformatics-related tools and utilities. . Current list of features includes: a Sequence data type supporting protein and nucleotide sequences and conversion between them. As of version 0.4, different kinds of sequence have different types. Support for quality data, reading and writing Fasta formatted files, reading TwoBit and phd formats, and Roche/454 SFF files. Rudimentary (i.e. unoptimized) support for doing alignments - including dynamic adjustment of scores based on sequence quality. Also Blast output parsing. Partly implemented single linkage clustering, and multiple alignment. Reading Gene Ontology (GO) annotations (GOA) and definitions\/hierarchy. . The Darcs repository is at: . Homepage: http://biohaskell.org/Libraries/Bio Tested-With: GHC==6.12.1 Build-Type: Simple Data-Files: README, Makefile Flag test Description: Build testing software Default: False Flag examples Description: Build example programs Default: True Library Build-Depends: base>=4 && <5, binary >=0.4 && <0.5, tagsoup>=0.8, bytestring >= 0.9.1, containers, array, parallel, parsec, mtl, directory, QuickCheck >= 2 Exposed-modules: Bio.Sequence, Bio.Sequence.SeqData, Bio.Sequence.Fasta, Bio.Sequence.FastQ, Bio.Sequence.TwoBit, Bio.Sequence.Phd, Bio.Sequence.Entropy, Bio.Sequence.HashWord, Bio.Sequence.GOA, Bio.Sequence.GeneOntology, Bio.Sequence.KEGG, Bio.Sequence.AminoProperties, Bio.Sequence.SFF, Bio.Sequence.SFF_name, Bio.Sequence.SFF_filters Bio.Alignment.BlastData, Bio.Alignment.BlastFlat, Bio.Alignment.Blast, Bio.Alignment.BlastXML, Bio.Alignment.AlignData, Bio.Alignment.Matrices, Bio.Alignment.SAlign, Bio.Alignment.AAlign, Bio.Alignment.QAlign Bio.Alignment.Multiple, Bio.Alignment.ACE, Bio.Alignment.Bowtie, Bio.Alignment.Soap, Bio.Alignment.BED, Bio.Alignment.PSL Bio.Clustering, Bio.Util, Bio.Util.Parsex Bio.Location.Strand, Bio.Location.Position, Bio.Location.ContigLocation, Bio.Location.Location, Bio.Location.LocMap, Bio.Location.OnSeq, Bio.Location.SeqLocation, Bio.Location.SeqLocMap, Bio.GFF3.Escape, Bio.GFF3.Feature, Bio.GFF3.FeatureHier, Bio.GFF3.FeatureHierSequences, Bio.GFF3.SGD Extensions: CPP, ParallelListComp if impl(ghc >= 6.12) Ghc-Options: -Wall -O2 -fexcess-precision -funbox-strict-fields -auto-all -fno-warn-unused-do-bind else Ghc-Options: -Wall -O2 -fexcess-precision -funbox-strict-fields -auto-all Source-Repository head Type: darcs Location: http://malde.org/~ketil/biohaskell/biolib Executable qc Main-Is: Test.hs Other-Modules: Bio.Util.TestBase, Bio.Util.Test, Bio.Alignment.Test, Bio.GFF3.Test, Bio.Location.Test, Bio.Sequence.Test, Bio.Clustering.Test Hs-Source-Dirs: . Build-Depends: base >= 3 && <5, process, containers, random, QuickCheck >= 2, old-time if flag(test) Buildable: True else Buildable: False -- Test.QuickBench needs to be ported to QC2. Or everything moved over to criterion. -- Executable qb -- Main-Is: Bench.hs -- Other-Modules: Test.QuickBench, Bio.Util.TestBase, Bio.Util.Test, -- Bio.Alignment.Test, Bio.Sequence.Test, Bio.Clustering.Test -- Hs-Source-Dirs: . -- Build-Depends: base >= 3 && <5, process, containers, random Executable flx Main-Is: Flx.hs Hs-Source-Dirs: examples . Other-Modules: Bio.Sequence.SFF Build-Depends: base >= 3 && <5, bytestring if flag(examples) Buildable: True else Buildable: False Executable fastout Main-Is: FastOut.hs Hs-Source-Dirs: examples . Build-Depends: base >= 3 && <5 if flag(examples) Buildable: True else Buildable: False Executable frecover Main-Is: FRecover.hs Hs-Source-Dirs: examples . Build-Depends: base >= 3 && < 5 Ghc-Options: -Wall if flag(examples) Buildable: True else Buildable: False Executable frename Main-Is: FRename.hs Hs-Source-Dirs: examples . Build-Depends: base >= 3 && < 5, bytestring >= 0.9.1 Ghc-Options: -Wall if flag(examples) Buildable: True else Buildable: False Executable flowclip Main-Is: FlowClip.hs Hs-Source-Dirs: examples . Build-Depends: base >= 3 && < 5 Ghc-Options: -Wall if flag(examples) Buildable: True else Buildable: False Executable orf Main-Is: Orf.hs Hs-Source-Dirs: examples . Build-Depends: base >= 3 && < 5 Ghc-Options: -Wall if flag(examples) Buildable: True else Buildable: False Executable rselect-pe Main-Is: RSelectPE.hs Hs-Source-Dirs: examples . Build-Depends: base >= 3 && < 5, random Ghc-Options: -Wall if flag(examples) Buildable: True else Buildable: False