bio-0.5.2: A bioinformatics library

Safe Haskell | Safe-Inferred

Bio.Sequence

Contents

- Data structures etc (Bio.Sequence.SeqData)
  - Accessor functions
  - Converting to and from String.
  - Nucleotide functionality.
  - Protein sequence functionality
  - Other utility functions
- File IO
  - Generic sequence reading
  - The Fasta file format (Bio.Sequence.Fasta)
  - Quality data
  - The FastQ format (Bio.Sequence.FastQ)
  - The phd file format (Bio.Sequence.Phd)
  - TwoBit file format support (Bio.Seqeunce.TwoBit)
- Hashing functionality (Bio.Sequence.HashWord)
- Entropy calculations

Description

This is a meta-module importing and re-exporting sequence-related stuff.

It encompasses the Bio.Sequence.SeqData, Bio.Sequence.Fasta, and Bio.Sequence.TwoBit modules.

Synopsis

- data Sequence t = Seq !SeqData !SeqData !(Maybe QualData)
- data Unknown
- type Offset = Int64
- type SeqData = ByteString
- type Qual = Word8
- type QualData = ByteString
- seqlength :: Sequence a -> Offset
- seqlabel :: Sequence a -> SeqData
- seqheader :: Sequence a -> SeqData
- seqdata :: Sequence a -> SeqData
- seqqual :: Sequence a -> QualData
- (!) :: Sequence a -> Offset -> Char
- appendHeader :: Sequence a -> String -> Sequence a
- setHeader :: Sequence a -> String -> Sequence a
- fromStr :: String -> SeqData
- toStr :: SeqData -> String
- compl :: Char -> Char
- revcompl :: Sequence Nuc -> Sequence Nuc
- revcompl' :: SeqData -> SeqData
- data Nuc
- castToNuc :: Sequence a -> Sequence Nuc
- data Amino
  - = Ala
  - | Arg
  - | Asn
  - | Asp
  - | Cys
  - | Gln
  - | Glu
  - | Gly
  - | His
  - | Ile
  - | Leu
  - | Lys
  - | Met
  - | Phe
  - | Pro
  - | Ser
  - | Thr
  - | Tyr
  - | Trp
  - | Val
  - | STP
  - | Asx
  - | Glx
  - | Xle
  - | Xaa
- translate :: Sequence Nuc -> Offset -> [Amino]
- fromIUPAC :: SeqData -> [Amino]
- toIUPAC :: [Amino] -> SeqData
- castToAmino :: Sequence a -> Sequence Amino
- defragSeq :: Sequence t -> Sequence t
- seqmap :: ((Char, Qual) -> (Char, Qual)) -> Sequence t -> Sequence t
- readNuc :: FilePath -> IO [Sequence Nuc]
- readProt :: FilePath -> IO [Sequence Amino]
- readFasta :: FilePath -> IO [Sequence Unknown]
- hReadFasta :: Handle -> IO [Sequence Unknown]
- writeFasta :: FilePath -> [Sequence a] -> IO ()
- hWriteFasta :: Handle -> [Sequence a] -> IO ()
- readQual :: FilePath -> IO [Sequence Unknown]
- writeQual :: FilePath -> [Sequence a] -> IO ()
- hWriteQual :: Handle -> [Sequence a] -> IO ()
- readFastaQual :: FilePath -> FilePath -> IO [Sequence Unknown]
- writeFastaQual :: FilePath -> FilePath -> [Sequence a] -> IO ()
- hWriteFastaQual :: Handle -> Handle -> [Sequence a] -> IO ()
- readFastQ :: FilePath -> IO [Sequence Nuc]
- writeFastQ :: FilePath -> [Sequence Nuc] -> IO ()
- hReadFastQ :: Handle -> IO [Sequence Nuc]
- hWriteFastQ :: Handle -> [Sequence Nuc] -> IO ()
- readSangerQ :: FilePath -> IO [Sequence Nuc]
- writeSangerQ :: FilePath -> [Sequence Nuc] -> IO ()
- hReadSangerQ :: Handle -> IO [Sequence Nuc]
- hWriteSangerQ :: Handle -> [Sequence Nuc] -> IO ()
- readIllumina :: FilePath -> IO [Sequence Nuc]
- writeIllumina :: FilePath -> [Sequence Nuc] -> IO ()
- hReadIllumina :: Handle -> IO [Sequence Nuc]
- hWriteIllumina :: Handle -> [Sequence Nuc] -> IO ()
- readPhd :: FilePath -> IO (Sequence Nuc)
- hReadPhd :: Handle -> IO (Sequence Nuc)
- decode2Bit :: ByteString -> [Sequence Nuc]
- read2Bit :: FilePath -> IO [Sequence Nuc]
- hRead2Bit :: Handle -> IO [Sequence Nuc]
- data HashF k = HF {
  - hash :: SeqData -> Offset -> Maybe k
  - hashes :: SeqData -> [(k, Offset)]
  - ksort :: [k] -> [k]
  }
- contigous :: (Integral k, Show k, Eq k) => Int -> HashF k
- rcontig :: (Integral k, Show k, Eq k) => Int -> HashF k
- rcpacked :: (Integral k, Show k, Eq k) => Int -> HashF k
- class KWords s where
  - kwords :: Int -> s -> [s]
- entropy :: (Ord str, KWords str) => Int -> str -> Double

# Data structures etc (Bio.Sequence.SeqData)

data Sequence t

A sequence consists of a header, the sequence data itself, and optional quality data. The type parameter is a phantom type to separate nucleotide and amino acid sequences

Constructors

Seq !SeqData !SeqData !(Maybe QualData) | header and actual sequence

Instances

Eq (Sequence t) |
Show (Sequence a) | A more arranged show instance for Sequences reassembling the display of the fasta-format

data Unknown

type Offset = Int64

An offset, index, or length of a `SeqData`

type SeqData = ByteString

The basic data type used in `Sequence`s

type Qual = Word8

Basic type for quality data. Range 0..255. Typical Phred output is in the range 6..50, with 20 as the line in the sand separating good from bad.

type QualData = ByteString

Quality data is a `Qual` vector, currently implemented as a `ByteString`.

## Accessor functions

seqlength :: Sequence a -> Offset

Return sequence length.

seqlabel :: Sequence a -> SeqData

Return sequence label (first word of header)

seqheader :: Sequence a -> SeqData

Return full header.

seqdata :: Sequence a -> SeqData

Return the sequence data.

seqqual :: Sequence a -> QualData

Return the quality data, or error if none exist. Use hasqual if in doubt.

(!) :: Sequence a -> Offset -> Char

Read the character at the specified position in the sequence.

appendHeader :: Sequence a -> String -> Sequence a

Modify the header by appending text, or by replacing all but the sequence label (i.e. first word).

setHeader :: Sequence a -> String -> Sequence a

Modify the header by appending text, or by replacing all but the sequence label (i.e. first word).

## Converting to and from String.

fromStr :: String -> SeqData

Convert a String to `SeqData`

toStr :: SeqData -> String

Convert a `SeqData` to a String

## Nucleotide functionality.

compl :: Char -> Char

Complement a single character. I.e. identify the nucleotide it can hybridize with. Note that for multiple nucleotides, you usually want the reverse complement (see `revcompl` for that).

revcompl :: Sequence Nuc -> Sequence Nuc

Calculate the reverse complement. This is only relevant for the nucleotide alphabet, and it leaves other characters unmodified.

revcompl' :: SeqData -> SeqData

Calculate the reverse complent for SeqData only.

data Nuc

For type tagging sequences (protein sequences use `Amino` below)

castToNuc :: Sequence a -> Sequence Nuc

## Protein sequence functionality

data Amino

Constructors

Ala |
Arg |
Asn |
Asp |
Cys |
Gln |
Glu |
Gly |
His |
Ile |
Leu |
Lys |
Met |
Phe |
Pro |
Ser |
Thr |
Tyr |
Trp |
Val |
STP |
Asx |
Glx |
Xle |
Xaa |

Instances

Eq Amino |
Show Amino |

translate :: Sequence Nuc -> Offset -> [Amino]

Translate a nucleotide sequence into the corresponding protein sequence. This works rather blindly, with no attempt to identify ORFs or otherwise QA the result.

fromIUPAC :: SeqData -> [Amino]

Convert a sequence in IUPAC format to a list of amino acids.

toIUPAC :: [Amino] -> SeqData

Convert a list of amino acids to a sequence in IUPAC format.

castToAmino :: Sequence a -> Sequence Amino

## Other utility functions

defragSeq :: Sequence t -> Sequence t

Returns a sequence with all internal storage freshly copied and with sequence and quality data present as a single chunk.

By freshly copying internal storage, `defragSeq` allows garbage collection of the original data source whence the sequence was read; otherwise, use of just a short sequence name can cause an entire sequence file buffer to be retained.

By compacting sequence data into a single chunk, `defragSeq` avoids linear-time traversal of sequence chunks during random access into sequence data.

seqmap :: ((Char, Qual) -> (Char, Qual)) -> Sequence t -> Sequence t

map over sequences, treating them as a sequence of (char,word8) pairs. This will work on sequences without quality, as long as the function doesn't try to examine it. The current implementation is not very efficient.

# File IO

## Generic sequence reading

readNuc :: FilePath -> IO [Sequence Nuc]

Read nucleotide sequences in any format - Fasta, SFF, FastQ, 2bit, PHD... Todo: detect Illumina vs Sanger FastQ, transparent compression

readProt :: FilePath -> IO [Sequence Amino]

Read protein sequences in any supported format (i.e. Fasta)

## The Fasta file format (Bio.Sequence.Fasta)

readFasta :: FilePath -> IO [Sequence Unknown]

Lazily read sequences from a FASTA-formatted file

hReadFasta :: Handle -> IO [Sequence Unknown]

Lazily read sequence from handle

writeFasta :: FilePath -> [Sequence a] -> IO ()

Write sequences to a FASTA-formatted file. Line length is 60.

hWriteFasta :: Handle -> [Sequence a] -> IO ()

Write sequences in FASTA format to a handle.

## Quality data

Not part of the Fasta format, and treated separately.

readQual :: FilePath -> IO [Sequence Unknown]

Read quality data for sequences to a file.

writeQual :: FilePath -> [Sequence a] -> IO ()

Write quality data for sequences to a file.

hWriteQual :: Handle -> [Sequence a] -> IO ()

readFastaQual :: FilePath -> FilePath -> IO [Sequence Unknown]

Read sequence and associated quality. Will error if the sequences and qualites do not match one-to-one in sequence.

writeFastaQual :: FilePath -> FilePath -> [Sequence a] -> IO ()

Write sequence and quality data simulatnously This may be more laziness-friendly.

hWriteFastaQual :: Handle -> Handle -> [Sequence a] -> IO ()

## The FastQ format (Bio.Sequence.FastQ)

readFastQ :: FilePath -> IO [Sequence Nuc]

Deprecated: FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead

writeFastQ :: FilePath -> [Sequence Nuc] -> IO ()

Deprecated: FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead

hReadFastQ :: Handle -> IO [Sequence Nuc]

Deprecated: FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead

hWriteFastQ :: Handle -> [Sequence Nuc] -> IO ()

Deprecated: FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead

readSangerQ :: FilePath -> IO [Sequence Nuc]

writeSangerQ :: FilePath -> [Sequence Nuc] -> IO ()

hReadSangerQ :: Handle -> IO [Sequence Nuc]

hWriteSangerQ :: Handle -> [Sequence Nuc] -> IO ()

readIllumina :: FilePath -> IO [Sequence Nuc]

writeIllumina :: FilePath -> [Sequence Nuc] -> IO ()

hReadIllumina :: Handle -> IO [Sequence Nuc]

hWriteIllumina :: Handle -> [Sequence Nuc] -> IO ()

## The phd file format (Bio.Sequence.Phd)

These contain base (nucleotide) calling information, and are generated by `phred`.

readPhd :: FilePath -> IO (Sequence Nuc)

Parse a .phd file, extracting the contents as a Sequence

hReadPhd :: Handle -> IO (Sequence Nuc)

Parse .phd contents from a handle

## TwoBit file format support (Bio.Seqeunce.TwoBit)

Used by `BLAT` and related tools.

decode2Bit :: ByteString -> [Sequence Nuc]

Parse a (lazy) ByteString as sequences in the 2bit format.

read2Bit :: FilePath -> IO [Sequence Nuc]

Read sequences from a file in 2bit format and | unmarshall/deserialize into Sequence format.

hRead2Bit :: Handle -> IO [Sequence Nuc]

Read sequences from a file handle in the 2bit format and | unmarshall/deserialze into Sequence format.

# Hashing functionality (Bio.Sequence.HashWord)

Packing words from sequences into integral data types

data HashF k

This is a struct for containing a set of hashing functions

Constructors

HF |

Fields

hash :: SeqData -> Offset -> Maybe k

  calculates the hash at a given offset in the sequence

hashes :: SeqData -> [(k, Offset)]

  calculate all hashes from a sequence, and their indices

ksort :: [k] -> [k]

  for sorting hashes

contigous :: (Integral k, Show k, Eq k) => Int -> HashF k

Contigous constructs an int/eger from a contigous k-word.

rcontig :: (Integral k, Show k, Eq k) => Int -> HashF k

Like `contigous`, but returns the same hash for a word and its reverse complement.

rcpacked :: (Integral k, Show k, Eq k) => Int -> HashF k

Like `rcontig`, but ignoring monomers (i.e. arbitrarily long runs of a single nucelotide are treated the same a single nucleotide.

# Entropy calculations

class KWords s where

Methods

kwords :: Int -> s -> [s]

Instances

KWords [a] |

entropy :: (Ord str, KWords str) => Int -> str -> Double