| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.TwoBit
- module Bio.Base
- data TwoBitFile = TBF {
- tbf_raw :: ByteString
- tbf_seqs :: !(HashMap Seqid TwoBitSequence)
- data TwoBitSequence = TBS {
- tbs_n_blocks :: !(IntMap Int)
- tbs_m_blocks :: !(IntMap Int)
- tbs_dna_offset :: !Int
- tbs_dna_size :: !Int
- openTwoBit :: FilePath -> IO TwoBitFile
- getFwdSubseqWith :: TwoBitFile -> TwoBitSequence -> (Word8 -> Mask -> a) -> Int -> [a]
- getSubseq :: TwoBitFile -> Range -> [Nucleotide]
- getSubseqWith :: (Nucleotide -> Mask -> a) -> TwoBitFile -> Range -> [a]
- getSubseqAscii :: TwoBitFile -> Range -> String
- getSubseqMasked :: TwoBitFile -> Range -> [Nucleotides]
- getLazySubseq :: TwoBitFile -> Position -> [Nucleotide]
- getSeqnames :: TwoBitFile -> [Seqid]
- lookupSequence :: TwoBitFile -> Seqid -> Maybe TwoBitSequence
- getSeqLength :: TwoBitFile -> Seqid -> Int
- clampPosition :: TwoBitFile -> Range -> Range
- getRandomSeq :: RandomGen g => TwoBitFile -> Int -> g -> ((Range, [Nucleotide]), g)
- takeOverlap :: Int -> IntMap Int -> [(Int, Int)]
- mergeBlocks :: [(Int, Int)] -> [(Int, Int)] -> [(Int, Int, Mask)]
- data Mask
Documentation
module Bio.Base
data TwoBitFile Source
Would you believe it? The 2bit format stores blocks of Ns in a table at the beginning of a sequence, then packs four bases into a byte. So it is neither possible nor necessary to store Ns in the main sequence, and you would think they aren't stored there, right? And they aren't. Instead Ts are stored which the reader has to replace with Ns.
The sensible way to treat these is probably to just say there are two
kinds of implied annotation (repeats and large gaps for a typical
genome), which can be interpreted in whatever way fits. And that's why
we have Mask and getSubseqWith.
TODO: use binary search for the Int->Int mappings on the raw data?
Constructors
| TBF | |
Fields
| |
data TwoBitSequence Source
Constructors
| TBS | |
Fields
| |
openTwoBit :: FilePath -> IO TwoBitFile Source
Brings a 2bit file into memory. The file is mmap'ed, so it will not work on streams that are not actual files. It's also unsafe if the file is modified in any way.
getFwdSubseqWith :: TwoBitFile -> TwoBitSequence -> (Word8 -> Mask -> a) -> Int -> [a] Source
getSubseq :: TwoBitFile -> Range -> [Nucleotide] Source
Extract a subsequence without masking.
getSubseqWith :: (Nucleotide -> Mask -> a) -> TwoBitFile -> Range -> [a] Source
Extract a subsequence and apply masking. TwoBit file can represent two kinds of masking (hard and soft), where hard masking is usually realized by replacing everything by Ns and soft masking is done by lowercasing. Here, we take a user supplied function to apply masking.
getSubseqAscii :: TwoBitFile -> Range -> String Source
Extract a subsequence with masking for biologists: soft masking is done by lowercasing, hard masking by printing an N.
getSubseqMasked :: TwoBitFile -> Range -> [Nucleotides] Source
Extract a subsequence with typical masking: soft masking is ignored, hard masked regions are replaced with Ns.
getLazySubseq :: TwoBitFile -> Position -> [Nucleotide] Source
Works only in forward direction.
getSeqnames :: TwoBitFile -> [Seqid] Source
lookupSequence :: TwoBitFile -> Seqid -> Maybe TwoBitSequence Source
getSeqLength :: TwoBitFile -> Seqid -> Int Source
clampPosition :: TwoBitFile -> Range -> Range Source
limits a range to a position within the actual sequence
Arguments
| :: RandomGen g | |
| => TwoBitFile | 2bit file |
| -> Int | desired length |
| -> g | RNG |
| -> ((Range, [Nucleotide]), g) | position, sequence, new RNG |
Sample a piece of random sequence uniformly from the genome. Only pieces that are not hard masked are sampled, soft masking is allowed, but not reported. On a 32bit platform, this will fail for genomes larger than 1G bases. However, if you're running this code on a 32bit platform, you have bigger problems to worry about.