Safe Haskell	None

Bio.Core.Sequence

Contents

Data definitions
Class definitions
Helper functions

Description

This module defines common data structures for biosequences, i.e. data that represents nucleotide or protein sequences.

Basically, anything resembling or wrapping a sequence should implement the BioSeq class (and BioSeqQual if quality information is available).

The data types are mostly wrappers from lazy bytestrings from Lazy and Char8, but most users of this module should not need to access the underlying data types directly.

Synopsis

Data definitions

newtype Qual Source

A quality value is in the range 0..255.

Constructors

Qual
Fields unQual :: Word8

Instances

Enum Qual
Eq Qual
Integral Qual
Num Qual
Ord Qual
Real Qual
Show Qual
Typeable Qual

newtype Offset Source

An Offset is a zero-based index into a sequence

Constructors

Offset
Fields unOff :: Int64

Instances

Enum Offset
Eq Offset
Integral Offset
Num Offset
Ord Offset
Real Offset
Show Offset
Typeable Offset

newtype SeqData Source

Sequence data are lazy bytestrings of ASCII characters.

Constructors

SeqData
Fields unSD :: ByteString

Instances

Eq SeqData
Ord SeqData
Show SeqData
Typeable SeqData
IsString SeqData
Monoid SeqData
Stringable SeqData

newtype SeqLabel Source

Sequence data are lazy bytestrings of ASCII characters.

Constructors

SeqLabel
Fields unSL :: ByteString

Instances

Eq SeqLabel
Ord SeqLabel
Show SeqLabel
Typeable SeqLabel
IsString SeqLabel
Monoid SeqLabel
Stringable SeqLabel

newtype QualData Source

Quality data are lazy bytestrings of Quals.

Constructors

QualData
Fields unQD :: ByteString

Instances

Eq QualData
Ord QualData
Show QualData
Typeable QualData
Monoid QualData
Stringable QualData

Class definitions

class BioSeq s whereSource

The BioSeq class models sequence data, and any data object that represents a biological sequence should implement it.

Methods

seqid Source

Arguments

:: s
-> SeqLabel	Sequence identifier (typically first word of the header)

seqheader Source

Arguments

:: s
-> SeqLabel	Sequence header (may contain whitespace), by convention the first word matches the `seqid`

seqdata Source

Arguments

:: s
-> SeqData	Sequence data

seqlength Source

Arguments

:: s
-> Offset	Sequence length

seqlabel Source

Arguments

:: s
-> SeqLabel	Deprecated. Instead, use `seqid` if you want the unique ID, or `seqheader` if you want the FASTA style header with ID and comments.

Deprecated: Warning: 'seqlabel' is deprecated, use 'seqid' or 'seqheader' instead.

class BioSeq sq => BioSeqQual sq whereSource

The BioSeqQual class extends BioSeq with quality data. Any correspondig data object should be an instance, this will allow Fasta formatted quality data toFastaQual, as well as the combined FastQ format (via toFastQ).

Methods

seqqual :: sq -> QualData Source

Helper functions

toFasta :: BioSeq s => s -> ByteString Source

Any BioSeq can be formatted as Fasta, 60-char lines.

toFastaQual :: BioSeqQual s => s -> ByteString Source

Output Fasta-formatted quality data (.qual files), where quality values are output as whitespace-separated integers.

toFastQ :: BioSeqQual s => s -> ByteString Source

Output FastQ-formatted data. For simplicity, only the Sanger quality format is supported, and only four lines per sequence (i.e. no line breaks in sequence or quality data).

module Data.Stringable