bio-0.3.5: A bioinformatics librarySource codeContentsIndex
Bio.Alignment.BlastFlat
Contents
The BlastFlat data type
Read XML format
Convert from hierarchical to flat structure
Re-exports from the hierarchical module (Bio.Alignment.BlastData)
Description

This module implements a "flattened" data structure for Blast hits, as opposed to the hierarchical structure in Bio.Alignment.BlastData.

The flat data type is useful in many cases where it is more natural to see the result as a set of rows (e.g. for insertaion in a database).

It would probably be more (memory-) efficient to go the other way (i.e. from flat to hierarchical), as passing the current, partially built BlastFlat object down the stream of results and stamping out a stream of completed ones. (See Bio.Alignment.BlastXML.breaks for this week's most cumbersome use of parallelism to avoid the memory issue.)

Synopsis
data BlastFlat = BlastFlat {
query :: !SeqId
qlength :: !Int
subject :: !SeqId
slength :: !Int
bits :: !Double
e_val :: !Double
identity :: (Int, Int)
q_from :: !Int
q_to :: !Int
h_from :: !Int
h_to :: !Int
aux :: !Aux
}
readXML :: FilePath -> IO [BlastFlat]
flatten :: [BlastRecord] -> [BlastFlat]
data BlastRecord
blastprogram :: BlastResult -> ByteString
blastversion :: BlastResult -> ByteString
blastdate :: BlastResult -> ByteString
blastreferences :: BlastResult -> ByteString
database :: BlastResult -> ByteString
dbsequences :: BlastResult -> Integer
dbchars :: BlastResult -> Integer
results :: BlastResult -> [BlastRecord]
data Aux
= Strands !Strand !Strand
| Frame !Strand !Int
data Strand
= Plus
| Minus
The BlastFlat data type
data BlastFlat Source
The BlastFlat data structure contains information about a single match
Constructors
BlastFlat
query :: !SeqId
qlength :: !Int
subject :: !SeqId
slength :: !Int
bits :: !Double
e_val :: !Double
identity :: (Int, Int)
q_from :: !Int
q_to :: !Int
h_from :: !Int
h_to :: !Int
aux :: !Aux
Read XML format
readXML :: FilePath -> IO [BlastFlat]Source
Convert from hierarchical to flat structure
flatten :: [BlastRecord] -> [BlastFlat]Source
Convert BlastRecords into BlastFlats (representing a depth-first traversal of the BlastRecord structure.)
Re-exports from the hierarchical module (Bio.Alignment.BlastData)
data BlastRecord Source
Each query sequence generates a BlastRecord
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blastprogram :: BlastResult -> ByteStringSource
blastversion :: BlastResult -> ByteStringSource
blastdate :: BlastResult -> ByteStringSource
blastreferences :: BlastResult -> ByteStringSource
database :: BlastResult -> ByteStringSource
dbsequences :: BlastResult -> IntegerSource
dbchars :: BlastResult -> IntegerSource
results :: BlastResult -> [BlastRecord]Source
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 !Strandblastn
Frame !Strand !Intblastx
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data Strand Source
The Strand indicates the direction of the match, i.e. the plain sequence or its reverse complement.
Constructors
Plus
Minus
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