nuget
Extension methods for some common operations
BioAssemblyExtensions
01 Syntax
SMRUCC.genomics.BioAssemblyExtensions
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| ExpressionValue | 1 | Extract of the gene expression value |
| IsUnknown | 1 | Current nt base is a unknown base? |
| IsPure | 1 | Is this nt base is pure |
| GetCOGCategory | 1 | 将COG字符串进行修剪，返回的是大写的COG符号 COG4771P -> P; P -> P; <SPACE> -> -; - -> -; |
| DirectCast | 1 | Generate FastaFile from a specific fasta source collection. |
| GetBriefStrandCode | 1 | Convert the nucleotide seuqnece strand description word as character brief code. |
| GetStrands | 1 | Convert the string value type nucleotide strand information description data into a strand enumerate data. |
| IsReversed | 1 | Is this ORF is in the reversed strand direction?(判断一段ORF核酸序列是否为反向的) |
| Group | 1 | 对位点进行分组操作 |
| ExpressionValue | 1 | |
| AsSegment | 1 | |
| IsNullOrEmpty | 1 | |
| DirectCast | 1 | |
| CreatePTTObject | 1 | |
| Group | 1 |
03 Members
ExpressionValue``1(
IEnumerable(Of ``0))Extract of the gene expression value
Type Parameters
| Name | Description |
|---|---|
T |
Parameters
| Name | Type | Description |
|---|---|---|
genes | IEnumerable(Of ``0) | - |
IsUnknown(
Char)Current nt base is a unknown base?
Parameters
| Name | Type | Description |
|---|---|---|
base | Char | - |
IsPure(
Char)Is this nt base is pure
Parameters
| Name | Type | Description |
|---|---|---|
base | Char | - |
GetCOGCategory(
String)将COG字符串进行修剪，返回的是大写的COG符号 COG4771P -> P; P -> P; <SPACE> -> -;
- -> -;
Parameters
| Name | Type | Description |
|---|---|---|
str | String | - |
DirectCast``1(
IEnumerable(Of ``0))Generate FastaFile from a specific fasta source collection.
Type Parameters
| Name | Description |
|---|---|
TFasta |
Parameters
| Name | Type | Description |
|---|---|---|
data | IEnumerable(Of ``0) | Target fasta source collection which its elements base type is FastaSeq |
GetBriefStrandCode(
String)Convert the nucleotide seuqnece strand description word as character brief code. (获取核酸链链方向的描述简要代码)
Parameters
| Name | Type | Description |
|---|---|---|
strand | String | - |
GetStrands(
Char)Convert the string value type nucleotide strand information description data into a strand enumerate data.
Parameters
| Name | Type | Description |
|---|---|---|
c | Char | 从文本文件之中所读取出来关于链方向的字符串描述数据 |
IsReversed(IPolymerSequenceModel)
Is this ORF is in the reversed strand direction?(判断一段ORF核酸序列是否为反向的)
Parameters
| Name | Type | Description |
|---|---|---|
nt | IPolymerSequenceModel | This function parameter is only allowed nucleotide sequence. (请注意，这个只允许核酸序列) |
Group``1(
IEnumerable(Of ``0), Int32)对位点进行分组操作
Parameters
| Name | Type | Description |
|---|---|---|
contigs | IEnumerable(Of ``0) | - |
offsets | Int32 | - |
ExpressionValue(
IEnumerable(Of T))AsSegment(GeneTable)
IsNullOrEmpty(FastaFile)
DirectCast(
IEnumerable(Of TFasta))CreatePTTObject(
IEnumerable(Of SimpleSegment))Group(
IEnumerable(Of Contig), Int32)