Bio.GB.Type

Documentation

data GenBankSequence

Type that represents contents of .gb file that is used to store information about genetic constructions.

Constructors

GenBankSequence

Fields

• meta :: Meta

  meta-information about the sequence

• gbSeq :: MarkedSequence Feature Char

  sequence that is marked by Features

Instances

Eq GenBankSequence

Defined in Bio.GB.Type

Methods

(==) :: GenBankSequence -> GenBankSequence -> Bool

(/=) :: GenBankSequence -> GenBankSequence -> Bool

Show GenBankSequence

Defined in Bio.GB.Type

Methods

showsPrec :: Int -> GenBankSequence -> ShowS

show :: GenBankSequence -> String

showList :: [GenBankSequence] -> ShowS

data Meta

Meta-information about sequence.

Constructors

Meta

Fields

• locus :: Locus

  general info about sequence

• definition :: Maybe Text

  brief description of sequence

• accession :: Maybe Text

  the unique identifier for a sequence record

• version :: Maybe Version

  id of sequence in GenBank database

• keywords :: Maybe Text

  word or phrase describing the sequence

• source :: Maybe Source

  free-format information including an abbreviated form of the organism name, sometimes followed by a molecule type

• references :: [Reference]

  publications by the authors of the sequence that discuss the data reported in the record

• comments :: [Text]

  comments about the sequence (note that there can be (!!!) empty comments)

Instances

Eq Meta

Defined in Bio.GB.Type

Methods

(==) :: Meta -> Meta -> Bool

(/=) :: Meta -> Meta -> Bool

Show Meta

Defined in Bio.GB.Type

Methods

showsPrec :: Int -> Meta -> ShowS

show :: Meta -> String

showList :: [Meta] -> ShowS

data Form

At this moment there are two known (to me) forms of seuqences that can be present in .gb file.

Constructors

Linear

Circular

Instances

Eq Form

Defined in Bio.GB.Type

Methods

(==) :: Form -> Form -> Bool

(/=) :: Form -> Form -> Bool

Show Form

Defined in Bio.GB.Type

Methods

showsPrec :: Int -> Form -> ShowS

show :: Form -> String

showList :: [Form] -> ShowS

data Locus

First line that should be present in every .gb file. Contains general info about sequence.

Constructors

Locus

Fields

• name :: Text

  name of sequence

• len :: Int

  length of sequence

• molType :: Text

  type of molecule that is sequenced

• form :: Maybe Form

  form of sequence

• gbDivision :: Maybe Text

  GenBank division to which a record belongs

• modificationDate :: Text

  date of last modification of sequence

Instances

Eq Locus

Defined in Bio.GB.Type

Methods

(==) :: Locus -> Locus -> Bool

(/=) :: Locus -> Locus -> Bool

Show Locus

Defined in Bio.GB.Type

Methods

showsPrec :: Int -> Locus -> ShowS

show :: Locus -> String

showList :: [Locus] -> ShowS

data Version

Id of sequence in GenBank database.

Constructors

Version

Fields

• versionT :: Text

  id itself

• gbId :: Maybe Text

  GenInfo Identifier that is assigned when sequence changes

Instances

Eq Version

Defined in Bio.GB.Type

Methods

(==) :: Version -> Version -> Bool

(/=) :: Version -> Version -> Bool

Show Version

Defined in Bio.GB.Type

Methods

showsPrec :: Int -> Version -> ShowS

show :: Version -> String

showList :: [Version] -> ShowS

data Source

Information about source of this sequence.

Constructors

Source

Fields

• sourceT :: Text

  free-format (as if all this format is not too much "free format") information including an abbreviated form of the organism name, sometimes followed by a molecule type

• organism :: Maybe Text

  the formal scientific name for the source organism

Instances

Eq Source

Defined in Bio.GB.Type

Methods

(==) :: Source -> Source -> Bool

(/=) :: Source -> Source -> Bool

Show Source

Defined in Bio.GB.Type

Methods

showsPrec :: Int -> Source -> ShowS

show :: Source -> String

showList :: [Source] -> ShowS

data Reference

Publications by the authors of the sequence that discuss the data reported in the record.

Constructors

Reference

Fields

• referenceT :: Text

  reference itself

• authors :: Maybe Text

  list of authors in the order in which they appear in the cited article

• title :: Maybe Text

  title of the published work

• journal :: Maybe Text

  MEDLINE abbreviation of the journal name

• pubmed :: Maybe Text

  PubMed Identifier

Instances

Eq Reference

Defined in Bio.GB.Type

Methods

(==) :: Reference -> Reference -> Bool

(/=) :: Reference -> Reference -> Bool

Show Reference

Defined in Bio.GB.Type

Methods

showsPrec :: Int -> Reference -> ShowS

show :: Reference -> String

showList :: [Reference] -> ShowS

data Feature

One single feature.

Constructors

Feature

Fields

• fName :: Text

  main information about feature

• fStrand53 :: Bool

  set to True if sequence is contained on 5'-3' strand. Set to False otherwise

• fProps :: [(Text, Text)]

  properties of feature (such as "label", "gene", "note" etc.)

Instances

Eq Feature

Defined in Bio.GB.Type

Methods

(==) :: Feature -> Feature -> Bool

(/=) :: Feature -> Feature -> Bool

Ord Feature

Defined in Bio.GB.Type

Methods

compare :: Feature -> Feature -> Ordering

(<) :: Feature -> Feature -> Bool

(<=) :: Feature -> Feature -> Bool

(>) :: Feature -> Feature -> Bool

(>=) :: Feature -> Feature -> Bool

max :: Feature -> Feature -> Feature

min :: Feature -> Feature -> Feature

Show Feature

Defined in Bio.GB.Type

Methods

showsPrec :: Int -> Feature -> ShowS

show :: Feature -> String

showList :: [Feature] -> ShowS

IsMarking Feature

Defined in Bio.GB.Type