Bio.Sequence
Data structures etc (
Bio.Sequence.SeqData
)
data
Sequence
t
data
Unknown
type
Offset
type
SeqData
type
Qual
type
QualData
Accessor functions
seqlength
seqlabel
seqheader
seqdata
seqqual
(!)
appendHeader
setHeader
Converting to and from String.
fromStr
toStr
Nucleotide functionality.
compl
revcompl
revcompl'
data
Nuc
castToNuc
Protein sequence functionality
data
Amino
translate
fromIUPAC
toIUPAC
castToAmino
File formats
The Fasta file format (
Bio.Sequence.Fasta
)
readFasta
hReadFasta
writeFasta
hWriteFasta
Quality data
readQual
writeQual
hWriteQual
readFastaQual
writeFastaQual
hWriteFastaQual
The FastQ format (
Bio.Sequence.FastQ
)
readFastQ
writeFastQ
hReadFastQ
hWriteFastQ
The phd file format (
Bio.Sequence.Phd
)
readPhd
hReadPhd
TwoBit file format support (
Bio.Seqeunce.TwoBit
)
decode2Bit
read2Bit
hRead2Bit
Hashing functionality (
Bio.Sequence.HashWord
)
data
HashF
k
contigous
rcontig
rcpacked
Entropy calculations
class
KWords
s
entropy