Safe Haskell	Safe-Infered

Bio.BlastXML

Description

Parse blast XML output.

If you use a recent version of NCBI BLAST and specify XML output (blastall -m 7), this module should be able to parse the result into a hierarchical BlastResult structure.

While the process may consume a bit of memory, the parsing is lazy, and file sizes of several gigabytes can be parsed (see e.g. the xml2x tool for an example). To parse XML, we use TagSoup.

Synopsis

Documentation

readXML :: FilePath -> IO BlastResult Source

Parse BLAST results in XML format

type SeqId = ByteString Source

The sequence id, i.e. the first word of the header field.

data Strand Source

The Strand indicates the direction of the match, i.e. the plain sequence or its reverse complement.

Constructors

Plus
Minus

Instances

Eq Strand
Read Strand
Show Strand

data Aux Source

The Aux field in the BLAST output includes match information that depends on the BLAST flavor (blastn, blastx, or blastp). This data structure captures those variations.

Constructors

Strands !Strand !Strand	blastn
Frame !Strand !Int	blastx

Instances

Eq Aux
Show Aux

data BlastResult Source

A BlastResult is the root of the hierarchy.

Constructors

BlastResult
Fields blastprogram :: !ByteString blastversion :: !ByteString blastdate :: !ByteString blastreferences :: !ByteString database :: !ByteString dbsequences :: !Integer dbchars :: !Integer results :: [BlastRecord]

Instances

Show BlastResult

data BlastRecord Source

Each query sequence generates a BlastRecord

Constructors

BlastRecord
Fields query :: !SeqId qlength :: !Int hits :: [BlastHit]

Instances

Show BlastRecord

data BlastHit Source

Each match between a query and a target sequence (or subject) is a BlastHit.

Constructors

BlastHit
Fields subject :: !SeqId slength :: !Int matches :: [BlastMatch]

Instances

Show BlastHit

data BlastMatch Source

A BlastHit may contain multiple separate matches (typcially when an indel causes a frameshift that blastx is unable to bridge).

Constructors

BlastMatch
Fields bits :: !Double e_val :: !Double identity :: (Int, Int) q_from :: !Int q_to :: !Int h_from :: !Int h_to :: !Int qseq :: !ByteString hseq :: !ByteString aux :: !Aux

Instances

Show BlastMatch