PatternsAPI

namespace: SMRUCC.genomics.SequenceModel.Patterns

Methods

__frequency

1
SMRUCC.genomics.SequenceModel.Patterns.PatternsAPI.__frequency(System.Collections.Generic.IEnumerable{SMRUCC.genomics.SequenceModel.FASTA.FastaToken},System.Int32,System.Char,System.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@”N:SMRUCC.genomics.SequenceModel.FASTA”里面的所有的序列数据都必须是大写的)

Parameter Name Remarks
Fasta -
p The column number.
C Alphabet specific for the frequency statics
numOfFasta The total number of the fasta sequence

__variation

1
SMRUCC.genomics.SequenceModel.Patterns.PatternsAPI.__variation(System.Char,System.Int32,System.Double,SMRUCC.genomics.SequenceModel.Patterns.PatternModel)

这个是参考的碱基位点

Parameter Name Remarks
ch -
index -
cutoff -
fr -

Frequency

1
SMRUCC.genomics.SequenceModel.Patterns.PatternsAPI.Frequency(System.Collections.Generic.IEnumerable{SMRUCC.genomics.SequenceModel.FASTA.FastaToken})

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)

Parameter Name Remarks
source

Fasta sequence source, and all of the fasta sequence
in this source must in the same length.
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NTVariations

1
SMRUCC.genomics.SequenceModel.Patterns.PatternsAPI.NTVariations(SMRUCC.genomics.SequenceModel.FASTA.FastaFile,System.Int32,System.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.

Parameter Name Remarks
index 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