nuget
A FASTA file that contains multiple sequence data. (一个包含有多条序列数据的FASTA文件)
FastaFile
01 Syntax
SMRUCC.genomics.SequenceModel.FASTA.FastaFile
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| .ctor | 1 | 构造函数会自动移除空值对象 |
| Distinct | 1 | Get a new fasta2 object which is been clear the duplicated records in the collection. |
| Read | 1 | Load the fasta file from the local filesystem. |
| LoadNucleotideData | 1 | 加载一个FASTA序列文件并检查其中是否全部为核酸序列数据，假若不是，则会将该序列移除 |
| DocParser | 1 | 当lines参数为空的时候，会返回一个空集合而非返回空值 |
| ParseDocument | 1 | Try parsing a fasta file object from the text file content doc |
| QueryAny | 1 | |
| Query | 2 | |
| Select | 1 | Where Selector |
| Save | 3 | Save the fasta file into the local filesystem. |
| Generate | 1 | 在写入数据到文本文件之前需要将目标对象转换为文本字符串 |
| AppendToFile | 1 | |
| Match | 1 | 使用正则表达式来搜索在序列中含有特定模式的序列对象 |
| SaveData | 1 | 可以使用这个方法来作为通用的继承与fasta对象的集合的序列的数据保存工作 |
| Clone | 1 | 完完全全的按值複製 |
| SingleSequence | 1 | 文件之中是否只包含有一条序列？ |
| op_Implicit | 1 | |
| AsKSource | 1 | |
| AddRange | 1 | |
| ToUpper | 1 | |
| ToLower | 1 | |
| Split | 1 | |
| Take | 1 | |
| Write | 1 | |
| ToString | 1 | |
| GetEnumerator | 1 | |
| GetEnumerator1 | 1 | |
| Add | 1 | |
| Clear | 1 | |
| Contains | 1 | |
| CopyTo | 1 | |
| Remove | 1 | |
| IndexOf | 1 | |
| Insert | 1 | |
| RemoveAt | 1 | |
| SaveData | 1 | |
| op_Addition | 1 | |
| op_GreaterThan | 1 | |
| op_LessThan | 1 | |
| IsValidFastaFile | 1 |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| FilePath | 1 | 本FASTA数据文件对象的文件位置 |
| Count | 1 | |
| IsReadOnly | 1 | |
| Item | 1 | |
| MimeType | 1 |
04 Members
#ctor(
IEnumerable(Of FastaSeq))构造函数会自动移除空值对象
Parameters
| Name | Type | Description |
|---|---|---|
data | IEnumerable(Of FastaSeq) | - |
Distinct
Get a new fasta2 object which is been clear the duplicated records in the collection. (获取去除集合中的重复的记录新列表，原有列表中数据未被改变)
Read(
String, Boolean, Char)Load the fasta file from the local filesystem.
Parameters
| Name | Type | Description |
|---|---|---|
file | String | - |
strict | Boolean | 当参数为真的时候，目标文件不存在则会抛出错误，反之则会返回一个空文件 |
deli | Char | Delimiter character for tokens in fasta sequence header. |
LoadNucleotideData(
String, Boolean)加载一个FASTA序列文件并检查其中是否全部为核酸序列数据，假若不是，则会将该序列移除
Parameters
| Name | Type | Description |
|---|---|---|
path | String | - |
DocParser(
IEnumerable(Of String), String)当lines参数为空的时候，会返回一个空集合而非返回空值
Parameters
| Name | Type | Description |
|---|---|---|
lines | IEnumerable(Of String) | - |
deli | String | - |
ParseDocument(
String, Char())Try parsing a fasta file object from the text file content doc
Parameters
| Name | Type | Description |
|---|---|---|
doc | String | The file data content in the fasta file, not the path of the fasta file! |
QueryAny(
String, CompareMethod)Parameters
| Name | Type | Description |
|---|---|---|
KeyWord | String | A key string that to search in this fasta file. |
CaseSensitive | CompareMethod | For text compaired method that not case sensitive, otherwise in the method od binary than case sensitive. |
Query(
String, CompareMethod)Parameters
| Name | Type | Description |
|---|---|---|
KeyWord | String | A key string that to search in this fasta file. |
CaseSensitive | CompareMethod | For text compaired method that not case sensitive, otherwise in the method od binary than case sensitive. |
Select(
Func(Of FastaSeq, Boolean))Where Selector
Parameters
| Name | Type | Description |
|---|---|---|
prediction | Func(Of FastaSeq, Boolean) | - |
Save(
String, Encoding)Save the fasta file into the local filesystem.
Remarks
this function will split sequence data by 60 chars per line
Parameters
| Name | Type | Description |
|---|---|---|
Path | String | - |
encoding | Encoding | 不同的程序会对这个由要求，例如meme程序在linux系统之中要求序列文件为unicode编码格式而windows版本的meme程序则要求ascii格式 |
Save(
Int32, String, String, Encodings)Save the fasta file into the local filesystem.
Parameters
| Name | Type | Description |
|---|---|---|
Path | Int32 | - |
encoding | String | 不同的程序会对这个由要求，例如
|
Save(
Int32, String, String, Encoding)Save the fasta file into the local filesystem.
Parameters
| Name | Type | Description |
|---|---|---|
path | Int32 | the file path for save the fasta sequence data |
encoding | String | 不同的程序会对这个由要求，例如meme程序在linux系统之中要求序列文件为unicode编码格式而windows版本的meme程序则要求ascii格式 |
Generate(
Int32, String)在写入数据到文本文件之前需要将目标对象转换为文本字符串
AppendToFile(
String)Parameters
| Name | Type | Description |
|---|---|---|
file | String | The target FASTA file that to append this FASTA sequences.(将要拓展这些FASTA序列的目标FASTA文件) |
Match(
String, RegexOptions)使用正则表达式来搜索在序列中含有特定模式的序列对象
Parameters
| Name | Type | Description |
|---|---|---|
regxText | String | the regular expression pattern for matches of the fasta sequence data |
SaveData``1(
IEnumerable(Of ``0), String, Encodings)可以使用这个方法来作为通用的继承与fasta对象的集合的序列的数据保存工作
Type Parameters
| Name | Description |
|---|---|
T |
Parameters
| Name | Type | Description |
|---|---|---|
data | IEnumerable(Of ``0) | - |
path | String | - |
encoding | Encodings | - |
Clone
完完全全的按值複製
SingleSequence(
String)文件之中是否只包含有一条序列？
Parameters
| Name | Type | Description |
|---|---|---|
path$ | String | - |
FilePath
本FASTA数据文件对象的文件位置
Count
Remarks
Count和Item属性可以兼容R#脚本的索引语法
IsReadOnly
Item
MimeType
op_Implicit(
String)AsKSource()
AddRange(
IEnumerable(Of FastaSeq))ToUpper()
ToLower()
Split(
String)Query(
String, Int32, CompareMethod)Take(
IEnumerable(Of String), CompareMethod)Write(
TextWriter, Int32, String)ToString()
GetEnumerator()
GetEnumerator1()
Add(FastaSeq)
Clear()
Contains(FastaSeq)
CopyTo(FastaSeq(),
Int32)Remove(FastaSeq)
IndexOf(FastaSeq)
Insert(
Int32, FastaSeq)RemoveAt(
Int32)SaveData(
IEnumerable(Of T), String, Encodings)op_GreaterThan(FastaFile,
String)op_LessThan(FastaFile,
String)IsValidFastaFile(
String)