Hello community,
here is the log from the commit of package ghc-ViennaRNAParser for
openSUSE:Factory checked in at 2017-04-14 13:34:28
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/ghc-ViennaRNAParser (Old)
and /work/SRC/openSUSE:Factory/.ghc-ViennaRNAParser.new (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "ghc-ViennaRNAParser"
Fri Apr 14 13:34:28 2017 rev:2 rq:483917 version:1.3.2
Changes:
--------
--- /work/SRC/openSUSE:Factory/ghc-ViennaRNAParser/ghc-ViennaRNAParser.changes
2017-03-24 02:07:09.319167852 +0100
+++
/work/SRC/openSUSE:Factory/.ghc-ViennaRNAParser.new/ghc-ViennaRNAParser.changes
2017-04-14 13:34:29.734742253 +0200
@@ -1,0 +2,5 @@
+Sun Feb 12 14:18:43 UTC 2017 - [email protected]
+
+- Update to version 1.3.2 with cabal2obs.
+
+-------------------------------------------------------------------
Old:
----
ViennaRNAParser-1.2.9.tar.gz
New:
----
ViennaRNAParser-1.3.2.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ ghc-ViennaRNAParser.spec ++++++
--- /var/tmp/diff_new_pack.Ymu2pr/_old 2017-04-14 13:34:30.874581165 +0200
+++ /var/tmp/diff_new_pack.Ymu2pr/_new 2017-04-14 13:34:30.878580600 +0200
@@ -19,7 +19,7 @@
%global pkg_name ViennaRNAParser
%bcond_with tests
Name: ghc-%{pkg_name}
-Version: 1.2.9
+Version: 1.3.2
Release: 0
Summary: Libary for parsing ViennaRNA package output
License: GPL-3.0
@@ -27,6 +27,7 @@
Url: https://hackage.haskell.org/package/%{pkg_name}
Source0:
https://hackage.haskell.org/package/%{pkg_name}-%{version}/%{pkg_name}-%{version}.tar.gz
BuildRequires: ghc-Cabal-devel
+BuildRequires: ghc-ParsecTools-devel
BuildRequires: ghc-parsec-devel
BuildRequires: ghc-process-devel
BuildRequires: ghc-rpm-macros
@@ -43,7 +44,7 @@
For more information on the ViennaRNA package refer to
<http://www.tbi.univie.ac.at/RNA/>.
-The libary is tested with Version 2.2.4 of the ViennaRNA package.
+The libary is tested with Version 2.3.2 of the ViennaRNA package.
%package devel
Summary: Haskell %{pkg_name} library development files
++++++ ViennaRNAParser-1.2.9.tar.gz -> ViennaRNAParser-1.3.2.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/ViennaRNAParser-1.2.9/ViennaRNAParser.cabal
new/ViennaRNAParser-1.3.2/ViennaRNAParser.cabal
--- old/ViennaRNAParser-1.2.9/ViennaRNAParser.cabal 2016-03-23
19:54:17.000000000 +0100
+++ new/ViennaRNAParser-1.3.2/ViennaRNAParser.cabal 2017-01-20
10:12:13.000000000 +0100
@@ -5,13 +5,13 @@
-- PVP summary: +-+------- breaking API changes
-- | | +----- non-breaking API additions
-- | | | +--- code changes with no API change
-version: 1.2.9
+version: 1.3.2
synopsis: Libary for parsing ViennaRNA package output
description: Currently contains parsers and datatypes for: RNAalifold,
RNAcode, RNAdistance, RNAcofold, RNAfold, RNAplex, RNAup, RNAz.
.
For more information on the ViennaRNA package refer to
<http://www.tbi.univie.ac.at/RNA/>.
.
- The libary is tested with Version 2.2.4 of the ViennaRNA
package.
+ The libary is tested with Version 2.3.2 of the ViennaRNA
package.
license: GPL
license-file: LICENSE
author: Florian Eggenhofer
@@ -30,8 +30,8 @@
source-repository this
type: git
- location: https://github.com/eggzilla/ViennaRNAParser/tree/1.2.9
- tag: 1.2.9
+ location: https://github.com/eggzilla/ViennaRNAParser/tree/1.3.2
+ tag: 1.3.2
library
-- Modules exported by the library.
@@ -58,7 +58,7 @@
ghc-options: -Wall -O2 -fno-warn-unused-do-bind
-- Other library packages from which modules are imported.
- build-depends: base >=4.5 && <5, parsec>=3.1.9, process, transformers
+ build-depends: base >=4.5 && <5, parsec>=3.1.9, process, transformers,
ParsecTools
-- Directories containing source files.
hs-source-dirs: src
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/ViennaRNAParser-1.2.9/changelog
new/ViennaRNAParser-1.3.2/changelog
--- old/ViennaRNAParser-1.2.9/changelog 2016-03-23 19:54:17.000000000 +0100
+++ new/ViennaRNAParser-1.3.2/changelog 2017-01-20 10:12:13.000000000 +0100
@@ -1,4 +1,11 @@
-*-change-log-*-
+1.3.2 Florian Eggenhofer <[email protected]> 20. January 2017
+ * Fix for RNAalifold systemcall function
+1.3.1 Florian Eggenhofer <[email protected]> 23. October 2016
+ * Improvements to RNAcode parser,
+ * Improvements to travis testing
+1.3.0 Florian Eggenhofer <[email protected]> 6. September 2016
+ * Added support for new prefilter fields in RNAplex output
1.2.8 Florian Eggenhofer <[email protected]> 11. February 2016
* Fixed special character parsing of identifiers in RNAcode
1.2.7 Florian Eggenhofer <[email protected]> 4. January 2016
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/ViennaRNAParser-1.2.9/src/Bio/RNAalifoldParser.hs
new/ViennaRNAParser-1.3.2/src/Bio/RNAalifoldParser.hs
--- old/ViennaRNAParser-1.2.9/src/Bio/RNAalifoldParser.hs 2016-03-23
19:54:17.000000000 +0100
+++ new/ViennaRNAParser-1.3.2/src/Bio/RNAalifoldParser.hs 2017-01-20
10:12:13.000000000 +0100
@@ -17,7 +17,7 @@
--- | Run external RNAalifold command and read the output into the
corresponding datatype
systemRNAalifold :: String -> String -> String -> IO ExitCode
-systemRNAalifold options inputFilePath outputFilePath = system ("RNAalifold "
++ options ++ " < " ++ inputFilePath ++ " > " ++ outputFilePath)
+systemRNAalifold options inputFilePath outputFilePath = system ("RNAalifold "
++ options ++ " " ++ inputFilePath ++ " > " ++ outputFilePath)
-- | Parse the consenus of RNAz results
genParserRNAalifold :: GenParser Char st RNAalifold
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/ViennaRNAParser-1.2.9/src/Bio/RNAcodeData.hs
new/ViennaRNAParser-1.3.2/src/Bio/RNAcodeData.hs
--- old/ViennaRNAParser-1.2.9/src/Bio/RNAcodeData.hs 2016-03-23
19:54:17.000000000 +0100
+++ new/ViennaRNAParser-1.3.2/src/Bio/RNAcodeData.hs 2017-01-20
10:12:13.000000000 +0100
@@ -22,8 +22,9 @@
data RNAcodeHit = RNAcodeHit
{
hss :: Int,
- frame :: Double,
- length :: Int,
+ strand :: Char,
+ frame :: Int,
+ hitLength :: Int,
from :: Int,
to :: Int,
name :: String,
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/ViennaRNAParser-1.2.9/src/Bio/RNAcodeParser.hs
new/ViennaRNAParser-1.3.2/src/Bio/RNAcodeParser.hs
--- old/ViennaRNAParser-1.2.9/src/Bio/RNAcodeParser.hs 2016-03-23
19:54:17.000000000 +0100
+++ new/ViennaRNAParser-1.3.2/src/Bio/RNAcodeParser.hs 2017-01-20
10:12:13.000000000 +0100
@@ -19,6 +19,7 @@
import qualified Control.Exception.Base as CE
import Text.Parsec.Language (haskell)
import Control.Applicative ((<*>),(<$>),(<$),pure)
+import Text.Parsec.Numbers
-- | Run external RNAcode command and read the output into the corresponding
datatype
systemRNAcode :: String -> String -> String -> IO ExitCode
@@ -33,21 +34,29 @@
-- | Parse the input as RNAcodeHit
genParseRNAcodeTabularHit :: GenParser Char st RNAcodeHit
genParseRNAcodeTabularHit = do
- _hss <- natural haskell
- _frame <- integer haskell
- _length <- natural haskell
- _from <- natural haskell
- _to <- natural haskell
- _name <- identifier haskell
- --_name <- identifier haskell
+ _hss <- parseIntegral
+ tab
+ _strand <- oneOf "+-"
+ tab
+ _frame <- parseIntegral
+ tab
+ _length <- parseIntegral
+ tab
+ _from <- parseIntegral
+ tab
+ _to <-parseIntegral
+ tab
_name <- many1 (oneOf
"AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz1234567890_-")
- string ("\t")
- _start <- natural haskell
- _end <- natural haskell
- _score <- many1 (oneOf "1234567890e.-+")
- many space
- _pvalue <- float haskell
- return $ RNAcodeHit (fromInteger _hss) (fromInteger _frame) (fromInteger
_length) (fromInteger _from) (fromInteger _to) _name (fromInteger _start)
(fromInteger _end) (read _score ::Double) _pvalue
+ tab
+ _start <- parseIntegral
+ tab
+ _end <- parseIntegral
+ tab
+ _score <- parseFloat
+ tab
+ _pvalue <- parseFloat
+ newline
+ return $ RNAcodeHit _hss _strand _frame _length _from _to _name _start _end
_score _pvalue
-- | Parse the input as RNAcode datatype
@@ -82,20 +91,29 @@
genParseRNAcodeHit :: GenParser Char st RNAcodeHit
genParseRNAcodeHit = do
many (char ' ')
- _hss <- natural haskell
- _frame <- integer haskell
- _length <- natural haskell
- _from <- natural haskell
- _to <- natural haskell
- --_name <- identifier haskell
+ _hss <- parseIntegral
+ tab
+ _strand <- oneOf "+-"
+ tab
+ _frame <- parseIntegral
+ tab
+ _length <- parseIntegral
+ tab
+ _from <- parseIntegral
+ tab
+ _to <- parseIntegral
+ tab
_name <- many1 (oneOf
"AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz1234567890_-")
- string ("\t")
- _start <- natural haskell
- _end <- natural haskell
- _score <- float haskell
- _pvalue <- many1 (try (choice [digit,char '.']))
+ tab
+ _start <- parseIntegral
+ tab
+ _end <- parseIntegral
+ tab
+ _score <- parseFloat
+ tab
+ _pvalue <- parseFloat
newline
- return $ RNAcodeHit (fromInteger _hss) (fromInteger _frame) (fromInteger
_length) (fromInteger _from) (fromInteger _to) _name (fromInteger _start)
(fromInteger _end) _score (read _pvalue :: Double)
+ return $ RNAcodeHit _hss _strand _frame _length _from _to _name _start _end
_score _pvalue
-- | parse RNAcode from input string
parseRNAcode :: String -> Either ParseError RNAcode
@@ -109,7 +127,7 @@
-- | parse RNAcode from input string
parseRNAcodeTabular :: String -> Either ParseError RNAcode
-parseRNAcodeTabular = parse genParseRNAcodeTabular "parseRNAcode"
+parseRNAcodeTabular = parse genParseRNAcodeTabular "parseRNAcodeTabular"
-- | parse RNAcode from input filePath
readRNAcodeTabular :: String -> IO (Either ParseError RNAcode)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/ViennaRNAParser-1.2.9/src/Bio/RNAplexData.hs
new/ViennaRNAParser-1.3.2/src/Bio/RNAplexData.hs
--- old/ViennaRNAParser-1.2.9/src/Bio/RNAplexData.hs 2016-03-23
19:54:17.000000000 +0100
+++ new/ViennaRNAParser-1.3.2/src/Bio/RNAplexData.hs 2017-01-20
10:12:13.000000000 +0100
@@ -17,6 +17,9 @@
duplexEnergy :: Double,
duplexEnergyWithoutAccessiblity :: Maybe Double,
queryAccessiblity :: Maybe Double,
- targetAccessibility :: Maybe Double
+ targetAccessibility :: Maybe Double,
+ prefilterStart :: Maybe Int,
+ prefilterStop :: Maybe Int,
+ prefilterEnergy :: Maybe Double
}
deriving (Show, Eq)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/ViennaRNAParser-1.2.9/src/Bio/RNAplexParser.hs
new/ViennaRNAParser-1.3.2/src/Bio/RNAplexParser.hs
--- old/ViennaRNAParser-1.2.9/src/Bio/RNAplexParser.hs 2016-03-23
19:54:17.000000000 +0100
+++ new/ViennaRNAParser-1.3.2/src/Bio/RNAplexParser.hs 2017-01-20
10:12:13.000000000 +0100
@@ -9,7 +9,8 @@
import Bio.RNAplexData
import Bio.ViennaRNAParserLibrary
-import Text.ParserCombinators.Parsec
+import Text.ParserCombinators.Parsec
+import Text.Parsec.Numbers
import Control.Monad
-- | Parse the input as list of RNAplexInteraction datatype
@@ -30,34 +31,44 @@
newline
_secondaryStructure <- many1 (oneOf "&().,")
many1 space
- _targetDuplexBegin <- many1 digit
+ _targetDuplexBegin <- parseIntegral
char ','
- _targetDuplexEnd <- many1 digit
+ _targetDuplexEnd <- parseIntegral
many1 space
char ':'
many1 space
- _queryDuplexBegin <- many1 digit
+ _queryDuplexBegin <- parseIntegral
char ','
- _queryDuplexEnd <- many1 digit
+ _queryDuplexEnd <- parseIntegral
many1 space
char '('
- optional space
- _duplexEnergy <- many1 (noneOf (" )"))
- optional space
+ optional (string " ")
+ _duplexEnergy <- parseFloat
+ optional (string " ")
optional (char '=')
- optional space
- _duplexEnergyWithoutAccessiblity <- optionMaybe (try (many1 (noneOf (" )"))))
- optional space
+ optional (string " ")
+ _duplexEnergyWithoutAccessiblity <- optionMaybe (try parseFloat)
+ optional (string " ")
optional (char '+')
- optional (many1 space)
- _queryAccessiblity <- optionMaybe (try (many1 (noneOf (" )"))))
- optional space
+ optional (many1 (string " "))
+ _queryAccessiblity <- optionMaybe (try parseFloat)
+ optional (string " ")
optional (char '+')
optional (many1 space)
- _targetAccessibility <- optionMaybe (try (many1 (noneOf (")"))))
+ _targetAccessibility <- optionMaybe (try parseFloat)
char ')'
+ many (oneOf " ")
+ optional (string "i:")
+ _prefilterStart <- optionMaybe (try parseIntegral)
+ optional (string ",")
+ optional (string "j:")
+ _prefilterEnd <- optionMaybe (try parseIntegral)
+ many (oneOf " ")
+ optional (string "<")
+ _prefilterEnergy <- optionMaybe (try parseFloat)
+ optional (string ">")
newline
- return $ RNAplexInteraction _targetIdentifier _queryIdentifier
_secondaryStructure (readInt _targetDuplexBegin) (readInt _targetDuplexEnd)
(readInt _queryDuplexBegin) (readInt _queryDuplexEnd) (readDouble
_duplexEnergy) (liftM readDouble _duplexEnergyWithoutAccessiblity) (liftM
readDouble _queryAccessiblity) (liftM readDouble _targetAccessibility)
+ return $ RNAplexInteraction _targetIdentifier _queryIdentifier
_secondaryStructure _targetDuplexBegin _targetDuplexEnd _queryDuplexBegin
_queryDuplexEnd _duplexEnergy _duplexEnergyWithoutAccessiblity
_queryAccessiblity _targetAccessibility _prefilterStart _prefilterEnd
_prefilterEnergy
-- | parse RNAplexOutput from input string
parseRNAplex :: [Char] -> Either ParseError [RNAplexInteraction]
