cobot-io 0.1.2.4 → 0.1.2.5

raw patch · 5 files changed

+22/−12 lines, 5 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• ChangeLog.md +4/−0
• cobot-io.cabal +2/−2
• src/Bio/FASTA/Parser.hs +9/−8
• src/Bio/FASTA/Type.hs +2/−1
• test/FASTASpec.hs +5/−1

@@ -2,6 +2,10 @@  ## [Unreleased] +## [0.1.2.5] - 2019-12-24+### Fixed+- Possibility to have spaces in Fasta sequences.+ ## [0.1.2.4] - 2019-12-23 ### Added - Preprocessing for pdb-files.

@@ -4,10 +4,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: 1ecc108258e91fab1cf40b3e7a3dbb217465d2d0d4b32b76560469f2cf1ca543+-- hash: 0e861a80d499c39e6ac8b1c1cb2b2fbcb63c09cd506f31744cbba112b69d71c5  name:           cobot-io-version:        0.1.2.4+version:        0.1.2.5 synopsis:       Biological data file formats and IO description:    Please see the README on GitHub at <https://github.com/less-wrong/cobot-io#readme> category:       Bio

@@ -2,12 +2,13 @@   ( fastaP   ) where -import           Bio.FASTA.Type         (Fasta, FastaItem(..))-import           Bio.Sequence           (BareSequence, bareSequence)-import           Data.Attoparsec.Text   (Parser, many', many1', char, endOfLine, letter,-                                            takeWhile, choice, endOfInput)-import           Data.Text              (Text, strip)-import           Prelude         hiding (takeWhile)+import           Bio.FASTA.Type       (Fasta, FastaItem (..))+import           Bio.Sequence         (BareSequence, bareSequence)+import           Data.Attoparsec.Text (Parser, char, choice, endOfInput,+                                       endOfLine, letter, many', many1',+                                       takeWhile)+import           Data.Text            (Text, strip)+import           Prelude              hiding (takeWhile)  -- | Parser of .fasta file. --@@ -23,8 +24,8 @@ fastaSeq :: Parser (BareSequence Char) fastaSeq = bareSequence . mconcat <$> many' line -line :: Parser (String)-line = many1' letter <* eol+line :: Parser String+line = concat <$> many1' (many1' letter <* many' (char ' ')) <* eol  eol :: Parser () eol = tabs *> choice [slashN, endOfInput]

@@ -7,7 +7,8 @@ import           Data.Text    (Text)  -- | Type alias for FASTA file.---  satisfies the following format : >(\s|\t)*[^\n\r]+(\s|\t)*(\n|\r)*(\w(\n|\r)*)*+--  satisfies the following format : >(\s|\t)*[^\n\r]+(\s|\t)*(\n|\r)*((\w|\s)(\n|\r)*)*+-- type Fasta a = [FastaItem a]  -- | One record in FASTA file.

@@ -10,7 +10,11 @@ import           Test.Hspec  correctFasta :: Fasta Char-correctFasta = [FastaItem "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL"), FastaItem "7HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")]+correctFasta = [ FastaItem "3HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")+               , FastaItem "7HMX:A|PDBID|CHAIN|SEQUENCE" (bareSequence "EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLL")+               , FastaItem "With_spaces" (bareSequence "MDFFDLDIEIKQERLPAECSLNSPLNYSLSAQLTDRMTPRTENVRRQRERMDFFDLDIEIKQERLPAECSLNSPLNYSLSAQLTDRMTPRTENVRRQRERMDFFDLDIEIKQERLPAECSLNSPLNYSLSAQLTDRMTPRTENVRRQRER")+               , FastaItem "Empty_ha_ha_ha" (bareSequence "")+               ]  fastaSpec :: Spec fastaSpec = describe "Fasta file parser." $ do