bio-0.4.5: A bioinformatics librarySource codeContentsIndex
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 Sequences 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 IntSource
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 = Word8Source
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.
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