nuget
对blastn和blastx的比对结果进行可视化操作
BlastVisualize
01 Syntax
SMRUCC.genomics.Visualize.NCBIBlastResult.BlastVisualize
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| ShortID | 1 | 对Entry信息进行简化 |
| ExportTableOrderByGI | 1 | Export the drawing order of the species hits on the graphics. |
| ApplyDescription | 1 | 将编号信息转换为描述信息 |
| ApplyDescription2 | 1 | 将编号信息转换为描述信息 |
| LoadResult | 1 | Read the blast output table result text file which was download from the NCBI blast website. |
| CreateTableFromBlastOutput | 1 | 这个函数主要是针对blastp的结果的 |
| __createHits | 1 | 只需要找出有hits的query，然后将位置列举出来即可 |
| __COGsBrush | 1 | 这个函数使用的是GeneBrief.COG属性来获取分类值 |
| PlotMap | 1 | 对blast结果进行可视化 |
03 Fields
| Name | Overloads | Summary |
|---|---|---|
| ConvertFactor | 1 | 一个碱基或者一个氨基酸所对应的像素 |
04 Members
ShortID(
FastaFile, String)对Entry信息进行简化
Remarks
if the export parameter is not empty then the function will export the entry information into the target directory.
Parameters
| Name | Type | Description |
|---|---|---|
data | FastaFile | - |
ExportTableOrderByGI(
AlignmentTable)Export the drawing order of the species hits on the graphics.
Parameters
| Name | Type | Description |
|---|---|---|
Tab | AlignmentTable | - |
ApplyDescription(
AlignmentTable, IEnumerable(Of gbEntryBrief), Int32)将编号信息转换为描述信息
Parameters
| Name | Type | Description |
|---|---|---|
table | AlignmentTable | - |
info | IEnumerable(Of gbEntryBrief) | - |
ApplyDescription2(
AlignmentTable, IEnumerable(Of gbEntryBrief), Int32)将编号信息转换为描述信息
Remarks
Please notices that this function requires the target hit its subjectids property is just the locus tag value.
Parameters
| Name | Type | Description |
|---|---|---|
table | AlignmentTable | - |
info | IEnumerable(Of gbEntryBrief) | - |
LoadResult(
String)Read the blast output table result text file which was download from the NCBI blast website.
Parameters
| Name | Type | Description |
|---|---|---|
path | String | - |
CreateTableFromBlastOutput(
String, String, IEnumerable(Of GeneTable))这个函数主要是针对blastp的结果的
Parameters
| Name | Type | Description |
|---|---|---|
source | String | blast输出日志文件夹 |
__createHits(
Dictionary(Of String, GeneTable), v228)只需要找出有hits的query，然后将位置列举出来即可
Parameters
| Name | Type | Description |
|---|---|---|
ORF | Dictionary(Of String, GeneTable) | - |
Blastoutput | v228 | - |
__COGsBrush(
Boolean, PTT, Boolean, String, Boolean, IGraphics, Int32)这个函数使用的是GeneBrief.COG属性来获取分类值
Parameters
| Name | Type | Description |
|---|---|---|
queryNoColor | Boolean | - |
refQuery | PTT | - |
COGTextureMappings | Boolean | - |
TextureSource$ | String | - |
ResourceIDMapping | Boolean | - |
g | IGraphics | - |
MaxIDLength% | Int32 | - |
PlotMap(
AlignmentTable, PTT, String(), Int32, Boolean, String, FastaSeq, Boolean, Boolean, Boolean, Boolean, Boolean, String, Boolean, Double, ICOGsBrush, Int32)对blast结果进行可视化
Remarks
You can using the custom_order parameter to specific the order of the genome drawing on the visualized image. idType: 1 -> locusID; 2 -> geneName + id_number
Parameters
| Name | Type | Description |
|---|---|---|
alignment | AlignmentTable | - |
refQuery | PTT | - |
AlignmentColorSchema | String() | bit_scores, identities |
queryBrush | Int32 | query基因组上面的基因的颜色画刷的来源，默认是使用内部的COG颜色 |
QueryNoColor | Boolean | 如果这个参数为真，那么query的基因箭头矩形对象将不会有任何颜色 |
ConvertFactor
一个碱基或者一个氨基酸所对应的像素