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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 formats 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
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 a] -> IO ()
hReadFastQ :: Handle -> IO [Sequence Nuc]
hWriteFastQ :: Handle -> [Sequence a] -> IO ()
readPhd :: FilePath -> IO (Sequence Nuc)
hReadPhd :: Handle -> IO (Sequence Nuc)
decode2Bit :: ByteString -> [Sequence Unknown]
read2Bit :: FilePath -> IO [Sequence Unknown]
hRead2Bit :: Handle -> IO [Sequence Unknown]
data HashF k = HF {
hash :: SeqData -> Offset -> Maybe k
hashes :: SeqData -> [(k, Offset)]
ksort :: [k] -> [k]
}
contigous :: Integral k => Int -> HashF k
rcontig :: Integral k => Int -> HashF k
rcpacked :: Integral 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 | 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
Constructors
Seq !SeqData !SeqData !(Maybe QualData) | header and actual sequence
Instances
Eq (Sequence t)
Show (Sequence a)
data Unknown | Source
type Offset = Int64 | Source
An offset, index, or length of a `SeqData`
type SeqData = ByteString | Source
The basic data type used in `Sequence`s
type Qual = Word8 | Source
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 | Source
Quality data is a `Qual` vector, currently implemented as a ByteString.
Accessor functions
seqlength :: Sequence a -> Offset | Source
Return sequence length.
seqlabel :: Sequence a -> SeqData | Source
Return sequence label (first word of header)
seqheader :: Sequence a -> SeqData | Source
Return full header.
seqdata :: Sequence a -> SeqData | Source
Return the sequence data.
seqqual :: Sequence a -> QualData | Source
Return the quality data, or error if none exist. Use hasqual if in doubt.
(!) :: Sequence a -> Offset -> Char | Source
Read the character at the specified position in the sequence.
appendHeader :: Sequence a -> String -> Sequence a | Source
setHeader :: Sequence a -> String -> Sequence a | Source
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 | Source
Convert a String to `SeqData`
toStr :: SeqData -> String | Source
Convert a `SeqData` to a String
Nucleotide functionality.
compl :: Char -> Char | Source
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 | Source
Calculate the reverse complement. This is only relevant for the nucleotide alphabet, and it leaves other characters unmodified.
revcompl' :: SeqData -> SeqData | Source
Calculate the reverse complent for SeqData only.
data Nuc | Source
For type tagging sequences (protein sequences use `Amino` below)
castToNuc :: Sequence a -> Sequence Nuc | Source
Protein sequence functionality
data Amino | Source
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] | 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] -> SeqData | Source
Convert a list of amino acids to a sequence in IUPAC format.
castToAmino :: Sequence a -> Sequence Amino | Source
Other utility functions
defragSeq :: Sequence t -> Sequence t | Source
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 | Source
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 formats
The Fasta file format (Bio.Sequence.Fasta)
readFasta :: FilePath -> IO [Sequence Unknown] | Source
Lazily read sequences from a FASTA-formatted file
hReadFasta :: Handle -> IO [Sequence Unknown] | Source
Lazily read sequence from handle
writeFasta :: FilePath -> [Sequence a] -> IO () | Source
Write sequences to a FASTA-formatted file. Line length is 60.
hWriteFasta :: Handle -> [Sequence a] -> IO () | Source
Write sequences in FASTA format to a handle.
Quality data
Not part of the Fasta format, and treated separately.
readQual :: FilePath -> IO [Sequence Unknown] | Source
Read quality data for sequences to a file.
writeQual :: FilePath -> [Sequence a] -> IO () | Source
Write quality data for sequences to a file.
hWriteQual :: Handle -> [Sequence a] -> IO () | Source
readFastaQual :: FilePath -> FilePath -> IO [Sequence Unknown] | Source
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 () | Source
Write sequence and quality data simulatnously This may be more laziness-friendly.
hWriteFastaQual :: Handle -> Handle -> [Sequence a] -> IO () | Source
The FastQ format (Bio.Sequence.FastQ)
readFastQ :: FilePath -> IO [Sequence Nuc] | Source
writeFastQ :: FilePath -> [Sequence a] -> IO () | Source
hReadFastQ :: Handle -> IO [Sequence Nuc] | Source
hWriteFastQ :: Handle -> [Sequence a] -> IO () | Source
The phd file format (Bio.Sequence.Phd)
These contain base (nucleotide) calling information, and are generated by `phred`.
readPhd :: FilePath -> IO (Sequence Nuc) | Source
Parse a .phd file, extracting the contents as a Sequence
hReadPhd :: Handle -> IO (Sequence Nuc) | Source
Parse .phd contents from a handle
TwoBit file format support (Bio.Seqeunce.TwoBit)
Used by `BLAT` and related tools.
decode2Bit :: ByteString -> [Sequence Unknown] | Source
Parse a (lazy) ByteString as sequences in the 2bit format.
read2Bit :: FilePath -> IO [Sequence Unknown] | Source
Read sequences from a file in 2bit format and | unmarshall/deserialize into Sequence format.
hRead2Bit :: Handle -> IO [Sequence Unknown] | Source
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 | Source
This is a struct for containing a set of hashing functions
Constructors
HF |
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 => Int -> HashF k | Source
Contigous constructs an int/eger from a contigous k-word.
rcontig :: Integral k => Int -> HashF k | Source
Like `contigous`, but returns the same hash for a word and its reverse complement.
rcpacked :: Integral k => Int -> HashF k | Source
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 | Source
Methods
kwords :: Int -> s -> [s] | Source
Instances
KWords ([] a)
entropy :: (Ord str, KWords str) => Int -> str -> Double | Source
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