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.
- 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
- 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 {}
- contigous :: Integral k => Int -> HashF k
- rcontig :: Integral k => Int -> HashF k
- rcpacked :: Integral k => Int -> HashF k
- class KWords s where
- entropy :: (Ord str, KWords str) => Int -> str -> Double
Data structures etc (Bio.Sequence.SeqData)
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
type SeqData = ByteStringSource
The basic data type used in Sequence
s
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
seqqual :: Sequence a -> QualDataSource
Return the quality data, or error if none exist. Use hasqual if in doubt.
(!) :: Sequence a -> Offset -> CharSource
Read the character at the specified position in the sequence.
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 String.
Nucleotide functionality.
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.
Protein sequence functionality
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.
castToAmino :: Sequence a -> Sequence AminoSource
Other utility functions
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.
File IO
Generic sequence reading
readNuc :: FilePath -> IO [Sequence Nuc]Source
Read nucleotide sequences in any format - Fasta, SFF, FastQ, 2bit, PHD... Todo: detect Illumina vs Sanger FastQ, transparent compression
readProt :: FilePath -> IO [Sequence Amino]Source
Read protein sequences in any supported format (i.e. Fasta)
The Fasta file format (Bio.Sequence.Fasta)
readFasta :: FilePath -> IO [Sequence Unknown]Source
Lazily read sequences from a FASTA-formatted file
writeFasta :: FilePath -> [Sequence a] -> IO ()Source
Write sequences to a FASTA-formatted file. Line length is 60.
Quality data
Not part of the Fasta format, and treated separately.
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.
The FastQ format (Bio.Sequence.FastQ)
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
TwoBit file format support (Bio.Seqeunce.TwoBit)
Used by BLAT
and related tools.
decode2Bit :: ByteString -> [Sequence Nuc]Source
Parse a (lazy) ByteString as sequences in the 2bit format.
read2Bit :: FilePath -> IO [Sequence Nuc]Source
Read sequences from a file in 2bit format and | unmarshall/deserialize into Sequence format.
hRead2Bit :: Handle -> IO [Sequence Nuc]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
This is a struct for containing a set of hashing functions
contigous :: Integral k => Int -> HashF kSource
Contigous constructs an int/eger from a contigous k-word.
rcontig :: Integral k => Int -> HashF kSource
Like contigous
, but returns the same hash for a word and its reverse complement.
rcpacked :: Integral k => Int -> HashF kSource
Like rcontig
, but ignoring monomers (i.e. arbitrarily long runs of a single nucelotide
are treated the same a single nucleotide.