Bio.Uniprot.Parser

Documentation

data NameType

Describes possible name type of DE section.

Constructors

RecName

AltName

SubName

Flags

None

Instances

Show NameType

Methods

showsPrec :: Int -> NameType -> ShowS

show :: NameType -> String

showList :: [NameType] -> ShowS

parseID :: Parser ID

Parses ID line of UniProt-KB text file.

parseAC :: Parser AC

Parses AC lines of UniProt-KB text file.

parseDT :: Parser DT

Parses 3 DT lines of UniProt-KB text file.

parseDE :: Parser DE

Parses DE lines of UniProt-KB text file.

parseGN :: Parser [GN]

Parses DE lines of UniProt-KB text file.

parseOS :: Parser OS

Parses OS lines for one record of UniProt-KB text file.

parseOG :: Parser OG

Parser OG line of UniProt-KB text file.

parseOC :: Parser OC

Parser OC line of UniProt-KB text file.

parseOX :: Parser OX

Parses OX lines of UniProt-KB text file.

parseOH :: Parser OH

Parses OH line of UniProt-KB text file.

parseRef :: Parser Reference

Parses RN, RP, RC, RX, RG, RA, RT and RL lines of UniProt-KB text file.

parseCC :: Parser CC

Parses CC lines of UniProt-KB text file.

parseDR :: Parser DR

Parses DR lines of UniProt-KB text file.

parsePE :: Parser PE

Parses PE line of UniProt-KB text file.

parseKW :: Parser KW

Parses KW lines of UniProt-KB text file.

parseFT :: Parser FT

Parses FT lines of UniProt-KB text file. One FT section is parsed.

parseSQ :: Parser SQ

Parses SQ lines of UniProt-KB text file.

parseEnd :: Parser ()

Parses end of one UniProt record.

parseRecord :: Parser Record

Parses whole UniProt-KB record.

parseEvidence :: Parser Text

optional :: Parser a -> Parser (Maybe a)

Transforms any parser to a parser of maybe value.

>>> parseOnly (optional digit) "1"
Right (Just 1)

>>> parseOnly (optional digit) ""
Right Nothing

parseNodes

Arguments

:: Text

Start 2-letter mark.

-> Char

Delimeter char, that splits the nodes.

-> Char

Terminal char, that ends the node list.

-> Parser [Text]

Parses lines, that contain nodes splitted by del and ended by end.

parseTillEnd :: Parser String

Parses line till the end.

parseMultiLineComment :: Text -> Int -> Parser String

Parses multiline comment as one string.

parseMultiLine :: Text -> Int -> Parser [String]

Parses multiline comment from new line.

parseBreak :: Text -> Parser ()

Parses line break for multiline section.

parseDefItem :: Text -> Parser Text

Parses one item like "Something=Something else;"

parseTillChar :: Char -> Parser String

Parses line till specific char (e.g. semicolon or dot) before spaceendOfLineendOfInput.

hyphenConcat :: [String] -> String

Delete needless space after hyphen on concat.