PatternsAPI

Full name SMRUCC.genomics.SequenceModel.Patterns.PatternsAPI Assembly SMRUCC.genomics.Core Members 8

01 Syntax

SMRUCC.genomics.SequenceModel.Patterns.PatternsAPI

02 Methods

Name	Overloads	Summary
Frequency	3	返回来的数据之中的残基的字符是大写的
NTVariations	2	The conservation percentage (%) Is defined as the number of genomes with the same letter on amultiple sequence alignment normalized to range from 0 to 100% for each site along th…
__variation	1	这个是参考的碱基位点
__frequency	1	Statics of the occurence frequency for the specific alphabet at specific column in the fasta source.
Variation	1

03 Members

method Frequency overload 3 #

Frequency(String, Int32)

简单的统计残基的出现频率

Parameters

Name	Type	Description
`Fasta`	`String`	-

method Frequency #

Frequency(FastaFile)

返回来的数据之中的残基的字符是大写的

Parameters

Name	Type	Description
`Fasta`	FastaFile	-

method Frequency overload 2 #

Frequency(IEnumerable(Of FastaSeq))

Simple function for statics the alphabet frequency in the fasta source. The returns matrix, alphabet key char is Upper case. (返回来的数据之中的残基的字符是大写的)

Parameters

Name	Type	Description
`source`	`IEnumerable(Of FastaSeq)`	Fasta sequence source, and all of the fasta sequence in this source must in the same length.

method NTVariations #

NTVariations(FastaFile, Int32, Double)

The conservation percentage (%) Is defined as the number of genomes with the same letter on amultiple sequence alignment normalized to range from 0 to 100% for each site along the chromosome of a specific index genome.

Parameters

Name	Type	Description
`index`	FastaFile	参考序列在所输入的fasta序列之中的位置，默认使用第一条序列作为参考序列

method NTVariations overload 2 #

NTVariations(FastaSeq, FastaFile, Double)

Parameters

Name	Type	Description
`ref`	FastaSeq	-
`Fasta`	FastaFile	-
`cutoff`	`Double`	-

method __variation #

__variation(Char, Int32, Double, PatternModel)

这个是参考的碱基位点

Parameters

Name	Type	Description
`ch`	`Char`	-
`index`	`Int32`	-
`cutoff`	`Double`	-
`fr`	PatternModel	-

method __frequency #

__frequency(IEnumerable(Of FastaSeq), Int32, Char, Int32)

Statics of the occurence frequency for the specific alphabet at specific column in the fasta source. (因为是大小写敏感的，所以参数FASTA里面的所有的序列数据都必须是大写的)

Parameters

Name	Type	Description
`Fasta`	`IEnumerable(Of FastaSeq)`	-
`p`	`Int32`	The column number.
`C`	`Char`	Alphabet specific for the frequency statics
`numOfFasta`	`Int32`	The total number of the fasta sequence

method Variation #

Variation(IPatternSite, Char, Double)