ClustalParser 1.0.2 → 1.0.3

raw patch · 4 files changed

+44/−5 lines, 4 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• ClustalParser.cabal +6/−3
• README.md +27/−0
• changelog +9/−0
• src/Bio/ClustalParser.hs +2/−2

@@ -5,7 +5,7 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             1.0.2+version:             1.0.3 synopsis:            Libary for parsing Clustal tools output description:         Currently contains parsers and datatypes for: clustalw2, clustalo                      .@@ -24,14 +24,17 @@ build-type:          Simple cabal-version:       >=1.8 +extra-source-files:+  README.md changelog+ source-repository head   type:     git   location: https://github.com/eggzilla/ClustalParser  source-repository this   type:     git-  location: https://github.com/eggzilla/ClustalParser/tree/1.0.2-  tag:      1.0.2+  location: https://github.com/eggzilla/ClustalParser/tree/1.0.3+  tag:      1.0.3  library   -- Modules exported by the library.

@@ -0,0 +1,27 @@+ClustalParser   [![Build Status](https://travis-ci.org/eggzilla/ClustalParser.svg)](https://travis-ci.org/eggzilla/ClustalParser)+=============++Currently contains parsers and datatypes for: clustalw2, clustalo++Clustal tools are multipe sequence aligenment tools for biological sequences +like DNA, RNA and Protein.+For more information on clustal Tools refer to <http://www.clustal.org/>.+++4 types of output are parsed++ - Alignment file (.aln): +  * Parsing with readClustalAlignment from filepath (Bio.ClustalParser)+  * Parsing with parseClustalAlignment from String (Bio.ClustalParser)+  +- Alignment file with secondary structure (.aln): +  * Parsing with readStructuralClustalAlignment from filepath (Bio.ClustalParser)+  * Parsing with parsStructuralClustalAlignment from String (Bio.ClustalParser)++ - Summary (printed to STDOUT):+  * Parsing with readClustalSummary from filepath (Bio.ClustalParser)+  * Parsing with parseClustalSummary from String (Bio.ClustalParser)++ - Phylogenetic Tree (.dnd):+  * Parsing with readGraphNewick from filepath (Bio.Phylogeny)+  * Parsing with readGraphNewick from String (Bio.Phylogeny)

@@ -0,0 +1,9 @@+-*-change-log-*-+1.0.3 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 19. April 2015+	* Added Y (pyrimidine) and R (purine) to sequence characters+1.0.2 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 19. March 2015+	* Linebreaks are now filtered from structural alignment sequence identifiers+1.0.1 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 27. October 2014+	* Fixed compiler warnings and updated documentation to mention structural clustal format+	* Added -Wall and -O2 compiler options+	* Added support for clustal alignments with secondary structure annotation

@@ -152,7 +152,7 @@ genParserClustalEntrySlice = do   sliceIdentifier <- many1 (noneOf " ")   spacer <- many1 (char ' ')-  sliceSequence <- many1 (noneOf "\n")+  sliceSequence <- many1 (oneOf "NYRUAGCT-")   newline   return $ ClustalAlignmentEntrySlice sliceIdentifier sliceSequence (length spacer) @@ -231,7 +231,7 @@ genParserStructuralClustalEntrySlice = do   sliceIdentifier <- many1 (noneOf " ")   many1 (char ' ')-  sliceSequence <- many1 (oneOf "NUAGCT-")+  sliceSequence <- many1 (oneOf "NYRUAGCT-")   newline   return $ StructuralClustalAlignmentEntrySlice (filter (/='\n') sliceIdentifier) sliceSequence