bio-0.5.3: A bioinformatics library

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Data structures for manipulating (biological) sequences.

Generally supports both nucleotide and protein sequences, some functions, like revcompl, only makes sense for nucleotides.


Data structure

A sequence is a header, sequence data itself, and optional quality data. Sequences are type-tagged to identify them as nucleotide, amino acids, or unknown type. All items are lazy bytestrings. The Offset type can be used for indexing.

If you use overloaded strings (e.g., ghc -XOverloadedString), you can easily construct sequences from string literals.

data Sequence t Source

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


Seq !SeqData !SeqData !(Maybe QualData)

header and actual sequence


Eq (Sequence t) 
Show (Sequence a)

A more arranged show instance for Sequences reassembling the display of the fasta-format

type Offset = Int64Source

An offset, index, or length of a SeqData

type SeqData = ByteStringSource

The basic data type used in Sequences

Quality data is normally associated with nucleotide sequences

type Qual = Word8Source

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 = ByteStringSource

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

Accessor functions

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

Read the character at the specified position in the sequence.

seqlength :: Sequence a -> OffsetSource

Return sequence length.

seqlabel :: Sequence a -> SeqDataSource

Return sequence label (first word of header)

seqheader :: Sequence a -> SeqDataSource

Return full header.

seqdata :: Sequence a -> SeqDataSource

Return the sequence data.

hasqual :: Sequence a -> BoolSource

Check whether the sequence has associated quality data.

seqqual :: Sequence a -> QualDataSource

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

Adding information to header

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

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

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

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

Converting to and from [Char]

It is probably better to use the IsString class from String for this.

fromStr :: String -> SeqDataSource

Convert a String to SeqData

toStr :: SeqData -> StringSource

Convert a SeqData to a String

Sequence utilities

defragSeq :: Sequence t -> Sequence tSource

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 tSource

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.

castSeq :: Sequence a -> Sequence bSource

Phantom type functionality, unchecked conversion between sequence types

Nucleotide functionality

Nucleotide sequences contain the alphabet [A,C,G,T]. IUPAC specifies an extended nucleotide alphabet with wildcards, but it is not supported at this point.

compl :: Char -> CharSource

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 NucSource

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

revcompl' :: SeqData -> SeqDataSource

Calculate the reverse complent for SeqData only.

data Nuc Source

For type tagging sequences (protein sequences use Amino below)

Protein functionality

Proteins are chains of amino acids, represented by the IUPAC alphabet.

data Amino Source




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

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]Source

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

toIUPAC :: [Amino] -> SeqDataSource

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

Display a nicely formated sequence.

putSeqLn :: Sequence a -> Int -> Int -> [(Int, Int)] -> IO ()Source

A simple function to display a sequence: we generate the sequence string and | call putStrLn

seqToStr :: Sequence a -> Int -> Int -> [(Int, Int)] -> [Char]Source

Returns a properly formatted and probably highlighted string | representation of a sequence. Highlighting is done using ANSI-Escape | sequences.

Default type for sequences