ClustalParser 1.1.0 → 1.1.1

raw patch · 4 files changed

+22/−18 lines, 4 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• ClustalParser.cabal +10/−7
• README.md +5/−2
• changelog +3/−1
• src/Bio/ClustalParser.hs +4/−8

@@ -5,15 +5,18 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             1.1.0+version:             1.1.1 synopsis:            Libary for parsing Clustal tools output-description:         Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna+description:         Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna, cmalign                      .-                     For more information on clustal Tools refer to <http://www.clustal.org/>+	             Clustal tools are multiple sequence alignment tools for biological sequence like DNA, RNA and Protein.+                     For more information on clustal Tools refer to <http://www.clustal.org/>.                      .-                     ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences.+                     Mlocarna is a multiple sequence alignment tool for RNA sequences with secondary structure output. +                     For more information on mlocarna refer to <http://www.bioinf.uni-freiburg.de/Software/LocARNA/>.                      .-                     Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.+                     Cmalign is a multiple sequence alignment program based on RNA family models and produces+                     ,among others, clustal output. It is part of infernal <http://infernal.janelia.org/>.                       license:             GPL license-file:        LICENSE@@ -33,8 +36,8 @@  source-repository this   type:     git-  location: https://github.com/eggzilla/ClustalParser/tree/1.1.0-  tag:      1.1.0+  location: https://github.com/eggzilla/ClustalParser/tree/1.1.1+  tag:      1.1.1  library   -- Modules exported by the library.

@@ -1,7 +1,7 @@ ClustalParser [![Hackage](https://img.shields.io/hackage/v/ClustalParser.svg)](https://hackage.haskell.org/package/ClustalParser) [![Build Status](https://travis-ci.org/eggzilla/ClustalParser.svg)](https://travis-ci.org/eggzilla/ClustalParser) ============= -Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna+Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna, cmalign  Clustal tools are multiple sequence alignment tools for biological sequences  like DNA, RNA and Protein.@@ -9,7 +9,10 @@  Mlocarna is a multiple sequence alignment tool for RNA sequences with secondary structure output. -For more information on molocarna refer to <http://www.clustal.org/>.+For more information on mlocarna refer to <http://www.bioinf.uni-freiburg.de/Software/LocARNA/>.++cmalign is a multiple sequence alignment program based on RNA family models and produces+,among others, clustal output. It is part of infernal <http://infernal.janelia.org/>.   4 types of output are parsed 

@@ -1,6 +1,8 @@ -*-change-log-*-+1.1.1 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 2. July 2015+        * Added support for cmalign clustal output . 1.1.0 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 1. July 2015-        * Added Hspec test-suite for Parsing functions+        * Added Hspec test-suite for parsing functions 	* Added Show instances for ClustalAlignment and StructuralClustalAlignment 1.0.3 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 19. April 2015 	* Added Y (pyrimidine) and R (purine) to sequence characters

@@ -115,9 +115,7 @@ genParserClustalAlignment :: GenParser Char st ClustalAlignment genParserClustalAlignment = do   many1 (noneOf "\n")-  newline-  newline-  newline+  many1 newline   alignmentSlices <- many1 (try genParserClustalAlignmentSlice)   eof     return (mergealignmentSlices alignmentSlices)@@ -152,7 +150,7 @@ genParserClustalEntrySlice = do   sliceIdentifier <- many1 (noneOf " ")   spacer <- many1 (char ' ')-  sliceSequence <- many1 (oneOf "SNYRUAGCT-")+  sliceSequence <- many1 (oneOf ".SNYRUAGCT-uagct")   newline   return $ ClustalAlignmentEntrySlice sliceIdentifier sliceSequence (length spacer) @@ -199,9 +197,7 @@   string "Compute pair probs ..."   newline   string "Perform progressive alignment ..."-  newline-  newline-  newline+  many1 newline   return ""  mergeStructuralAlignmentSlices :: [StructuralClustalAlignmentSlice] -> String -> Double -> StructuralClustalAlignment@@ -227,7 +223,7 @@ genParserStructuralClustalEntrySlice = do   sliceIdentifier <- many1 (noneOf " ")   many1 (char ' ')-  sliceSequence <- many1 (oneOf "SNYRUAGCT-")+  sliceSequence <- many1 (oneOf ".SNYRUAGCT-uagtc")   newline   return $ StructuralClustalAlignmentEntrySlice (filter (/='\n') sliceIdentifier) sliceSequence