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Merge pull request #5 from eggzilla/gtxconverter
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Gtxconverter
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eggzilla authored Jan 10, 2020
2 parents d10528f + d705b03 commit 1c3611d
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Showing 5 changed files with 14 additions and 7 deletions.
4 changes: 2 additions & 2 deletions .travis.yml
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Expand Up @@ -11,8 +11,8 @@ before_script:
script:
- docker create --name develcontainer devel
- mkdir Genbank
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.6.5/Genbank-2.0.0/x/GenbankConverter/build/GenbankConverter/GenbankConverter Genbank
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.6.5/Genbank-2.0.0/x/GenbankSequenceExtractor/build/GenbankSequenceExtractor/GenbankSequenceExtractor Genbank
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.6.5/Genbank-2.1.0/x/GenbankConverter/build/GenbankConverter/GenbankConverter Genbank
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.6.5/Genbank-2.1.0/x/GenbankSequenceExtractor/build/GenbankSequenceExtractor/GenbankSequenceExtractor Genbank
- cp LICENSE Genbank
- tar -cvzf Genbank.tar.gz Genbank

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2 changes: 1 addition & 1 deletion Biobase/Genbank/Export.hs
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Expand Up @@ -94,6 +94,6 @@ subFeatureToGFF3Entry gbkAccession _subFeature = subFeatureGFF3
_start = coordinatesFrom . head . setCoordinates . subFeatureCoordinates $ _subFeature
_stop = coordinatesTo . head . setCoordinates . subFeatureCoordinates $ _subFeature
_score = L.pack "."
_strand = if (complement . head . setCoordinates . subFeatureCoordinates $ _subFeature) then '+' else '-'
_strand = if (complement . head . setCoordinates . subFeatureCoordinates $ _subFeature) then '-' else '+'
_phase = L.pack "."
sfAttributes = V.fromList(map attributeToGFF3Attribute (subFeatureAttributes _subFeature))
2 changes: 1 addition & 1 deletion Biobase/Genbank/Import.hs
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Expand Up @@ -72,7 +72,7 @@ genParserGenbankFeatures :: GenParser Char st [Feature]
genParserGenbankFeatures = do
_ <- manyTill anyChar (try (string "FEATURES"))
_ <- many1 space
_ <- string "Location/Qualifiers\n"
_ <- string "Location/Qualifiers"
_ <- newline
_features <- many genParserFeature
_ <- optionMaybe (try (genParserField "CONTIG" "ORIGIN"))
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7 changes: 7 additions & 0 deletions ChangeLog.md
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@@ -1,4 +1,11 @@
-*-change-log-*-
### 2.1.0 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) 10. January 2020

* Fixed swapped strands when exporting to GFF3

### 2.0.1 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) 10. January 2020

* Fixed parsing feature header

### 2.0.0 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) 09. January 2020

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6 changes: 3 additions & 3 deletions Genbank.cabal
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@@ -1,5 +1,5 @@
name: Genbank
version: 2.0.0
version: 2.1.0
synopsis: Libary for processing the NCBI genbank format
description: Haskell cabal Genbank libary contains tools, parser and datastructures for the NCBI (National Center for Biotechnology Information) Genbank format.
.
Expand Down Expand Up @@ -40,8 +40,8 @@ source-repository head

source-repository this
type: git
location: https://github.com/eggzilla/Genbank/tree/2.0.0
tag: 2.0.0
location: https://github.com/eggzilla/Genbank/tree/2.1.0
tag: 2.1.0

library
-- Modules exported by the library.
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