| bio-0.4.6: A bioinformatics library | Source code | Contents | Index
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`
Instances
Show BlastRecord
blastprogram :: BlastResult -> ByteString | Source
blastversion :: BlastResult -> ByteString | Source
blastdate :: BlastResult -> ByteString | Source
blastreferences :: BlastResult -> ByteString | Source
database :: BlastResult -> ByteString | Source
dbsequences :: BlastResult -> Integer | Source
dbchars :: BlastResult -> Integer | Source
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 !Strand | blastn
Frame !Strand !Int | blastx
Instances
Eq Aux
Show Aux
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
Produced by Haddock version 2.4.2