Writer

Full name SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Motif.Writer Assembly SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.MotifFinder Members 6

01 Syntax

SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Motif.Writer

02 Methods

Name	Overloads	Summary
writeSequenceInfo	1	Writes all of the files that need to be written
writeSites	1	Use any format for writing down the location of the planted site in each sequence
writeMotif	1	Write down the motif that was generated.
writeMotifLength	1	Write down the motif length
writeResult	1	Writes a benchmark result to the output directory
initOutputDirectory	1	Creates the directory where the files will be written

03 Members

method writeSequenceInfo #

writeSequenceInfo(Double, Int32, Int32, Int32, String, String, String, String, WeightMatrix, IList(Of String), IList(Of KeyValuePair(Of String, Int32)))

Writes all of the files that need to be written

Parameters

Name	Type	Description
`icpc`	`Double`	, information content per column
`ml`	`Int32`	-
`sl`	`Int32`	-
`sc`	`Int32`	-
`fastaFileName`	`String`	-
`sitesFileName`	`String`	-
`motifFileName`	`String`	-
`motifLengthFileName`	`String`	-
`motif`	WeightMatrix	-
`bindingSites`	`IList(Of String)`	-
`plantedSequences`	`IList(Of KeyValuePair(Of String, Int32))`	-

method writeSites #

writeSites(Int32, IList(Of String), IList(Of Int32), String)

Use any format for writing down the location of the planted site in each sequence

Parameters

Name	Type	Description
`motifs`	`Int32`	-
`sitePositions`	`IList(Of String)`	-
`filename`	`IList(Of Int32)`	-

method writeMotif #

writeMotif(Int32, WeightMatrix, String, Double)

Write down the motif that was generated. It should be stored in a format as shown in the miniproj.pdf in step 8

Parameters

Name	Type	Description
`motif`	`Int32`	-
`filename`	WeightMatrix	-

method writeMotifLength #

writeMotifLength(Int32, String)

Write down the motif length

Parameters

Name	Type	Description
`ml`	`Int32`	-
`filename`	`String`	-

method writeResult #

writeResult(String, String, String)

Writes a benchmark result to the output directory

Parameters

Name	Type	Description
`outputDirectory`	`String`	, the directory to print the files in
`benchmark`	`String`	, name of benchmark
`result`	`String`	, result for file

method initOutputDirectory #

initOutputDirectory(String)

Creates the directory where the files will be written

Parameters

Name	Type	Description
`filename`	`String`	, path to a file that needs to be written