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

Generic GenBankSequence

Defined in Bio.GB.Type

Associated Types

type Rep GenBankSequence :: Type -> Type

Methods

from :: GenBankSequence -> Rep GenBankSequence x

to :: Rep GenBankSequence x -> GenBankSequence

NFData GenBankSequence

Defined in Bio.GB.Type

Methods

rnf :: GenBankSequence -> ()

type Rep GenBankSequence

Defined in Bio.GB.Type

type Rep GenBankSequence = D1 ('MetaData "GenBankSequence" "Bio.GB.Type" "cobot-io-0.1.4.4-CqLQJQSI3e86Tkry2VYHOf" 'False) (C1 ('MetaCons "GenBankSequence" 'PrefixI 'True) (S1 ('MetaSel ('Just "meta") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Meta) :*: S1 ('MetaSel ('Just "gbSeq") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (MarkedSequence Feature Char))))

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

Generic Meta

Defined in Bio.GB.Type

Associated Types

type Rep Meta :: Type -> Type

Methods

from :: Meta -> Rep Meta x

to :: Rep Meta x -> Meta

NFData Meta

Defined in Bio.GB.Type

Methods

rnf :: Meta -> ()

type Rep Meta

Defined in Bio.GB.Type

type Rep Meta = D1 ('MetaData "Meta" "Bio.GB.Type" "cobot-io-0.1.4.4-CqLQJQSI3e86Tkry2VYHOf" 'False) (C1 ('MetaCons "Meta" 'PrefixI 'True) (((S1 ('MetaSel ('Just "locus") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Locus) :*: S1 ('MetaSel ('Just "definition") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text))) :*: (S1 ('MetaSel ('Just "accession") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text)) :*: S1 ('MetaSel ('Just "version") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Version)))) :*: ((S1 ('MetaSel ('Just "keywords") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text)) :*: S1 ('MetaSel ('Just "source") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Source))) :*: (S1 ('MetaSel ('Just "references") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [Reference]) :*: S1 ('MetaSel ('Just "comments") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [Text])))))

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

Generic Form

Defined in Bio.GB.Type

Associated Types

type Rep Form :: Type -> Type

Methods

from :: Form -> Rep Form x

to :: Rep Form x -> Form

NFData Form

Defined in Bio.GB.Type

Methods

rnf :: Form -> ()

type Rep Form

Defined in Bio.GB.Type

type Rep Form = D1 ('MetaData "Form" "Bio.GB.Type" "cobot-io-0.1.4.4-CqLQJQSI3e86Tkry2VYHOf" 'False) (C1 ('MetaCons "Linear" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Circular" 'PrefixI 'False) (U1 :: Type -> Type))

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

Generic Locus

Defined in Bio.GB.Type

Associated Types

type Rep Locus :: Type -> Type

Methods

from :: Locus -> Rep Locus x

to :: Rep Locus x -> Locus

NFData Locus

Defined in Bio.GB.Type

Methods

rnf :: Locus -> ()

type Rep Locus

Defined in Bio.GB.Type

type Rep Locus = D1 ('MetaData "Locus" "Bio.GB.Type" "cobot-io-0.1.4.4-CqLQJQSI3e86Tkry2VYHOf" 'False) (C1 ('MetaCons "Locus" 'PrefixI 'True) ((S1 ('MetaSel ('Just "name") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :*: (S1 ('MetaSel ('Just "len") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :*: S1 ('MetaSel ('Just "molType") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text))) :*: (S1 ('MetaSel ('Just "form") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Form)) :*: (S1 ('MetaSel ('Just "gbDivision") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text)) :*: S1 ('MetaSel ('Just "modificationDate") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text)))))

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

Generic Version

Defined in Bio.GB.Type

Associated Types

type Rep Version :: Type -> Type

Methods

from :: Version -> Rep Version x

to :: Rep Version x -> Version

NFData Version

Defined in Bio.GB.Type

Methods

rnf :: Version -> ()

type Rep Version

Defined in Bio.GB.Type

type Rep Version = D1 ('MetaData "Version" "Bio.GB.Type" "cobot-io-0.1.4.4-CqLQJQSI3e86Tkry2VYHOf" 'False) (C1 ('MetaCons "Version" 'PrefixI 'True) (S1 ('MetaSel ('Just "versionT") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :*: S1 ('MetaSel ('Just "gbId") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text))))

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

Generic Source

Defined in Bio.GB.Type

Associated Types

type Rep Source :: Type -> Type

Methods

from :: Source -> Rep Source x

to :: Rep Source x -> Source

NFData Source

Defined in Bio.GB.Type

Methods

rnf :: Source -> ()

type Rep Source

Defined in Bio.GB.Type

type Rep Source = D1 ('MetaData "Source" "Bio.GB.Type" "cobot-io-0.1.4.4-CqLQJQSI3e86Tkry2VYHOf" 'False) (C1 ('MetaCons "Source" 'PrefixI 'True) (S1 ('MetaSel ('Just "sourceT") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :*: S1 ('MetaSel ('Just "organism") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text))))

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

Generic Reference

Defined in Bio.GB.Type

Associated Types

type Rep Reference :: Type -> Type

Methods

from :: Reference -> Rep Reference x

to :: Rep Reference x -> Reference

NFData Reference

Defined in Bio.GB.Type

Methods

rnf :: Reference -> ()

type Rep Reference

Defined in Bio.GB.Type

type Rep Reference = D1 ('MetaData "Reference" "Bio.GB.Type" "cobot-io-0.1.4.4-CqLQJQSI3e86Tkry2VYHOf" 'False) (C1 ('MetaCons "Reference" 'PrefixI 'True) ((S1 ('MetaSel ('Just "referenceT") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :*: S1 ('MetaSel ('Just "authors") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text))) :*: (S1 ('MetaSel ('Just "title") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text)) :*: (S1 ('MetaSel ('Just "journal") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text)) :*: S1 ('MetaSel ('Just "pubmed") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Text))))))

data Feature

One single feature.

Constructors

Feature

Fields

• fName :: Text

  main information about feature

• 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

Generic Feature

Defined in Bio.GB.Type

Associated Types

type Rep Feature :: Type -> Type

Methods

from :: Feature -> Rep Feature x

to :: Rep Feature x -> Feature

NFData Feature

Defined in Bio.GB.Type

Methods

rnf :: Feature -> ()

IsMarking Feature

Defined in Bio.GB.Type

type Rep Feature

Defined in Bio.GB.Type

type Rep Feature = D1 ('MetaData "Feature" "Bio.GB.Type" "cobot-io-0.1.4.4-CqLQJQSI3e86Tkry2VYHOf" 'False) (C1 ('MetaCons "Feature" 'PrefixI 'True) (S1 ('MetaSel ('Just "fName") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Text) :*: S1 ('MetaSel ('Just "fProps") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 [(Text, Text)])))

type Parser = Parsec Void Text