| bio-0.4.6: A bioinformatics library | Source code | Contents | Index
Bio.Sequence.Fasta
Contents
Reading and writing plain FASTA files Reading and writing quality files Combining FASTA and quality files Counting sequences in a FASTA file Helper function for reading your own sequences Data structures
Description
This module incorporates functionality for reading and writing sequence data in the Fasta format. Each sequence consists of a header (with a `>` prefix) and a set of lines containing the sequence data. As Fasta is used for both amino acids and nucleotides, the resulting `Sequence`s are type-tagged with `Unknown`. If you know the type of sequence you are reading, use `castToAmino` or `castToNuc`.
Synopsis
readFasta :: FilePath -> IO [Sequence Unknown]
writeFasta :: FilePath -> [Sequence a] -> IO ()
hReadFasta :: Handle -> IO [Sequence Unknown]
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]
hWriteFastaQual :: Handle -> Handle -> [Sequence a] -> IO ()
writeFastaQual :: FilePath -> FilePath -> [Sequence a] -> IO ()
countSeqs :: FilePath -> IO Int
mkSeqs :: [ByteString] -> [Sequence Unknown]
type Qual = Word8
Reading and writing plain FASTA files
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.
hReadFasta :: Handle -> IO [Sequence Unknown] | Source
Lazily read sequence from handle
hWriteFasta :: Handle -> [Sequence a] -> IO () | Source
Write sequences in FASTA format to a handle.
Reading and writing quality files
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
Combining FASTA and quality files
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.
hWriteFastaQual :: Handle -> Handle -> [Sequence a] -> IO () | Source
writeFastaQual :: FilePath -> FilePath -> [Sequence a] -> IO () | Source
Write sequence and quality data simulatnously This may be more laziness-friendly.
Counting sequences in a FASTA file
countSeqs :: FilePath -> IO Int | Source
Helper function for reading your own sequences
mkSeqs :: [ByteString] -> [Sequence Unknown] | Source
Convert a list of FASTA-formatted lines into a list of sequences. Blank lines are ignored. Comment lines start with are allowed between sequences (and ignored). Lines starting with > initiate a new sequence.
Data structures
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.
Produced by Haddock version 2.4.2