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Bio.Sequence.SFF

Description

Read (and write?) the SFF file format used by Roche/454 sequencing to store flowgram data.

A flowgram is a series of values (intensities) representing homopolymer runs of A,G,C, and T in a fixed cycle, and usually displayed as a histogram.

The Staden Package contains an io_lib, with a C routine for parsing this format. According to comments in the sources, the io_lib implementation is based on a file called getsff.c, which I've been unable to track down.

It is believed that all values are stored big endian.

Synopsis

data SFF = SFF !CommonHeader [ReadBlock]

data CommonHeader = CommonHeader {

index_offset :: Int64
index_length :: Int32
num_reads :: Int32
key_length :: Int16
flow_length :: Int16
flowgram_fmt :: Word8
flow :: ByteString
key :: ByteString

}

data ReadHeader = ReadHeader {

name_length :: Int16
num_bases :: Int32
clip_qual_left :: Int16
clip_qual_right :: Int16
clip_adapter_left :: Int16
clip_adapter_right :: Int16
read_name :: ByteString

}

data ReadBlock = ReadBlock {

read_header :: !ReadHeader
flow_data :: !ByteString
flow_index :: !ByteString
bases :: !SeqData
quality :: !QualData

}

readSFF :: FilePath -> IO SFF
writeSFF :: FilePath -> SFF -> IO ()
writeSFF' :: FilePath -> SFF -> IO Int
recoverSFF :: FilePath -> IO SFF
sffToSequence :: SFF -> [Sequence Nuc]
trim :: ReadBlock -> ReadBlock
trimFromTo :: Integral i => i -> i -> ReadBlock -> ReadBlock
trimKey :: CommonHeader -> Sequence Nuc -> Maybe (Sequence Nuc)
baseToFlowPos :: Integral i => ReadBlock -> i -> Int
flowToBasePos :: Integral i => ReadBlock -> i -> Int
test :: FilePath -> IO ()
convert :: FilePath -> IO ()
flowgram :: ReadBlock -> [Flow]
packFlows :: [Flow] -> ByteString
unpackFlows :: ByteString -> [Flow]
type Flow = Int16
type Qual = Word8
type Index = Word8
type SeqData = ByteString
type QualData = ByteString

data ReadName = ReadName {

date :: (Int, Int, Int)
time :: (Int, Int, Int)
region :: Int
x_loc :: Int
y_loc :: Int

}

decodeReadName :: ByteString -> Maybe ReadName
encodeReadName :: ReadName -> ByteString

Documentation

data SFF | Source

The data structure storing the contents of an SFF file (modulo the index)
Constructors

SFF !CommonHeader [ReadBlock] |

Instances

Show SFF
Binary SFF

data CommonHeader | Source

SFF has a 31-byte common header Todo: remove items that are derivable (counters, magic, etc) cheader_lenght points to the first read header. Also, the format is open to having the index anywhere between reads, we should really keep count and check for each read. In practice, it seems to be places after the reads.

The following two fields are considered part of the header, but as they are static, they are not part of the data structure magic :: Word32 -- ^ 0x2e736666, i.e. the string .sff version :: Word32 -- ^ 0x00000001

Constructors

CommonHeader |

index_offset :: Int64 | Points to a text(?) section
index_length :: Int32 |
num_reads :: Int32 |
key_length :: Int16 |
flow_length :: Int16 |
flowgram_fmt :: Word8 |
flow :: ByteString |
key :: ByteString |

Instances

Show CommonHeader
Binary CommonHeader

data ReadHeader | Source

Each Read has a fixed read header
Constructors

ReadHeader |

name_length :: Int16 |
num_bases :: Int32 |
clip_qual_left :: Int16 |
clip_qual_right :: Int16 |
clip_adapter_left :: Int16 |
clip_adapter_right :: Int16 |
read_name :: ByteString |

Instances

Show ReadHeader
Binary ReadHeader

data ReadBlock | Source

This contains the actual flowgram for a single read.
Constructors

ReadBlock |

read_header :: !ReadHeader |
flow_data :: !ByteString |
flow_index :: !ByteString |
bases :: !SeqData |
quality :: !QualData |

Instances

Show ReadBlock

readSFF :: FilePath -> IO SFF | Source

writeSFF :: FilePath -> SFF -> IO () | Source

Write an `SFF` to the specified file name

writeSFF' :: FilePath -> SFF -> IO Int | Source

Write an `SFF` to the specified file name, but go back and update the read count. Useful if you want to output a lazy stream of `ReadBlock`s. Returns the number of reads written.

recoverSFF :: FilePath -> IO SFF | Source

sffToSequence :: SFF -> [Sequence Nuc] | Source

trim :: ReadBlock -> ReadBlock | Source

Trim a read according to clipping information

trimFromTo :: Integral i => i -> i -> ReadBlock -> ReadBlock | Source

Trim a read to specific sequence position. The current implementation has the unintended side effect of always trimming the flowgram down to a basecalled position.

trimKey :: CommonHeader -> Sequence Nuc -> Maybe (Sequence Nuc) | Source

baseToFlowPos :: Integral i => ReadBlock -> i -> Int | Source

Convert a sequence position to the corresponding flow position

flowToBasePos :: Integral i => ReadBlock -> i -> Int | Source

Convert a flow position to the corresponding sequence position

test :: FilePath -> IO () | Source

test serialization by output'ing the header and first two reads in an SFF, and the same after a decode + encode cycle.

convert :: FilePath -> IO () | Source

Convert a file by decoding it and re-encoding it This will lose the index (which isn't really necessary)

flowgram :: ReadBlock -> [Flow] | Source

packFlows :: [Flow] -> ByteString | Source

Pack a list of flows into the corresponding binary structure (the flow_data field)

unpackFlows :: ByteString -> [Flow] | Source

Unpack the flow_data field into a list of flow values

type Flow = Int16 | Source

The type of flowgram value

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 Index = Word8 | Source

type SeqData = ByteString | Source

The basic data type used in `Sequence`s

type QualData = ByteString | Source

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

data ReadName | Source

Read names encode various information, as per this struct.
Constructors

ReadName |

date :: (Int, Int, Int) |
time :: (Int, Int, Int) |
region :: Int |
x_loc :: Int |
y_loc :: Int |

Instances

Show ReadName

decodeReadName :: ByteString -> Maybe ReadName | Source

encodeReadName :: ReadName -> ByteString | Source

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