Up: Component summary Component

SequenceFilter

Filters out nucleotide sequences that do not satisfy the criteria.

Version 1.0
Bundle microarray
Categories Filter
Authors Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker View/Report issues
Requires Asser.jar (jar)
Source files component.xml
Usage Example with default values

Inputs

Name Type Mandatory Description
sequences FASTA Mandatory All candidate sequences

Outputs

Name Type Description
selection FASTA Accepted sequences

Parameters

Name Type Default Description
maxLength int -1 Maximum length of the sequences or a negative number to disable this filter
maxN float 1 Maximum number (relative=false) or ratio (relative=true) of unknown nucleotides
maxNSeq int -1 Maximum number of consecutive missing nucleotides or a negative number to disable this filter
minLength int 0 Minimum length of the sequences
relative boolean true If this parameter is true then maxN tells the maximum of the number of unknown nucleotides divided by the length of the sequence.

Test cases

Test case Parameters IN
sequences
OUT
selection
case1 properties sequences selection

maxN=0.5,
maxNSeq=5,
minLength=10,
maxLength=20


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