Bio.ABI.Clean

Documentation

class Cleanable a where

Ability to clean initial data. Returns cleaned variant or Nothing if it can not be cleaned.

Minimal complete definition

cleanWith

Methods

clean :: a -> Maybe a

cleanWith :: Thresholds -> a -> Maybe a

Instances

Cleanable BasecalledSequence

Defined in Bio.ABI.Clean

Methods

clean :: BasecalledSequence -> Maybe BasecalledSequence

cleanWith :: Thresholds -> BasecalledSequence -> Maybe BasecalledSequence

Cleanable BasecalledSequenceWithRawData

Defined in Bio.ABI.Clean

Methods

clean :: BasecalledSequenceWithRawData -> Maybe BasecalledSequenceWithRawData

cleanWith :: Thresholds -> BasecalledSequenceWithRawData -> Maybe BasecalledSequenceWithRawData

data Thresholds

Thresholds to clean the data.

ABI file contains sequence with quality. By design of sanger sequencing method start and end of the sequence have bad quality. Moreover, internal part of the sequence can also has bad quality. To clean the data we make 2 steps.

Step 1. Clean edges:

• take frame with frameSize and go through the sequence;
• on each step evaluate mean value;
• if mean value less than edgeThreshold, go further;
• if mean value more than edgeThreshold stop and cut the sequence from END of this frame;
• repeat this algorithm for the right edge.

Step 2. Evaluate quality:

• for cropped sequence evaluate mean value;
• if mean value less then innerThreshold, sequence is bad;
• if mean value more then innerThreshold, sequence is acceptable.

Logic of this algorithm and defaultThresholds were obtained by taking experiments with read ABI files.

Constructors

Thresholds

Fields

• frameSize :: Int
• edgeThreshold :: Double
• innerThreshold :: Double

Instances

Show Thresholds

Defined in Bio.ABI.Clean

Methods

showsPrec :: Int -> Thresholds -> ShowS

show :: Thresholds -> String

showList :: [Thresholds] -> ShowS

Eq Thresholds

Defined in Bio.ABI.Clean

Methods

(==) :: Thresholds -> Thresholds -> Bool

(/=) :: Thresholds -> Thresholds -> Bool

defaultThresholds :: Thresholds

These thresholds were selected by many experiments on ab1-files.