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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

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