bio-0.4.5: A bioinformatics librarySource codeContentsIndex
Data structure
Accessor functions
Adding information to header
Converting to and from [Char]
Sequence utilities
Nucleotide functionality
Protein functionality
Display a nicely formated sequence.
Default type for sequences

Data structures for manipulating (biological) sequences.

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

data Sequence t = Seq !SeqData !SeqData !(Maybe QualData)
type Offset = Int64
type SeqData = ByteString
type Qual = Word8
type QualData = ByteString
(!) :: Sequence a -> Offset -> Char
seqlength :: Sequence a -> Offset
seqlabel :: Sequence a -> SeqData
seqheader :: Sequence a -> SeqData
seqdata :: Sequence a -> SeqData
(?) :: Sequence a -> Offset -> Qual
hasqual :: Sequence a -> Bool
seqqual :: Sequence a -> QualData
appendHeader :: Sequence a -> String -> Sequence a
setHeader :: Sequence a -> String -> Sequence a
fromStr :: String -> SeqData
toStr :: SeqData -> String
defragSeq :: Sequence t -> Sequence t
seqmap :: ((Char, Qual) -> (Char, Qual)) -> Sequence t -> Sequence t
castSeq :: Sequence a -> Sequence b
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
| Asx
| Glx
| Xle
| Xaa
translate :: Sequence Nuc -> Offset -> [Amino]
fromIUPAC :: SeqData -> [Amino]
toIUPAC :: [Amino] -> SeqData
castToAmino :: Sequence a -> Sequence Amino
putSeqLn :: Sequence a -> Int -> Int -> [(Int, Int)] -> IO ()
seqToStr :: Sequence a -> Int -> Int -> [(Int, Int)] -> [Char]
data Unknown
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.
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
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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.
(?) :: Sequence a -> Offset -> QualSource
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
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]
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)
castToNuc :: Sequence a -> Sequence NucSource
Protein functionality
Proteins are chains of amino acids, represented by the IUPAC alphabet.
data Amino Source
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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.
castToAmino :: Sequence a -> Sequence AminoSource
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
data Unknown Source
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