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GFF (General Feature Format) specifications document
GFFTable
01 Syntax
SMRUCC.genomics.Annotation.Assembly.NCBI.GenBank.TabularFormat.GFF.GFFTable
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| .ctor | 1 | Copy specific type |
| GetByName | 1 | |
| LoadDocument | 1 | Load a GFF (General Feature Format) specifications document file from a plant text file. |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| GffVersion | 1 | gff-version (##gff-version 2) GFF version - In Case it Is a real success And we want To change it. |
| SrcVersion | 1 | source-version (##source-version <source> <version text>) So that people can record what version Of a program Or package was used To make the data In this file. |
| date | 1 | date (##date <date>) The date the file was made, Or perhaps that the prediction programs were run. |
| type | 1 | type (##Type <type> [<seqname>]) The type Of host sequence described by the features. |
| processor | 1 | 生成这个文件的应用程序 |
| DNA | 1 | DNA (##DNA <seqname> ##acggctcggattggcgctggatgatagatcagacgac ##... |
| RNA | 1 | RNA (##RNA <seqname> ##acggcucggauuggcgcuggaugauagaucagacgac ##... |
| Protein | 1 | Protein (##Protein <seqname> ##MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSF ##... |
| SeqRegion | 1 | sequence-region (##sequence-region <seqname> <start> <end>) To indicate that this file only contains entries for the specified subregion of a sequence. |
| Size | 1 | Genome size in bp |
| features | 1 | 基因组上面的特性位点 |
| species | 1 |
04 Members
#ctor(GFFTable,
Features)Copy specific type
Parameters
| Name | Type | Description |
|---|---|---|
gff | GFFTable | - |
type | Features | - |
GetByName(
String)Parameters
| Name | Type | Description |
|---|---|---|
Name | String | Feature.attributes -> name |
LoadDocument(
String, Int32)Load a GFF (General Feature Format) specifications document file from a plant text file. (从一个指定的文本文件之中加载基因组特性片段的数据)
Parameters
| Name | Type | Description |
|---|---|---|
path | String | - |
defaultVersion | Int32 | 当GFF的文件头部之中没有包含有版本字样的时候，所使用的的默认版本号，默认是版本3 |
GffVersion
gff-version (##gff-version 2)
GFF version - In Case it Is a real success And we want To change it. The current Default version Is 2, so If this line Is Not present version 2 Is assumed.
SrcVersion
source-version (##source-version <source> <version text>)
So that people can record what version Of a program Or package was used To make the data In this file. I suggest the version Is text without whitespace. That allows things Like 1.3, 4a etc. There should be at most one source-version line per source.
date
date (##date <date>)
The date the file was made, Or perhaps that the prediction programs were run. We suggest to use astronomical format 1997-11-08 for 8th November 1997, first because these sort properly, And second to avoid any US/European bias.
type
type (##Type <type> [<seqname>])
The type Of host sequence described by the features. Standard types are 'DNA', 'Protein' and 'RNA'. The optional <seqname> allows multiple ##Type definitions describing multiple GFF sets in one file, each of which have a distinct type. If the name is not provided, then all the features in the file are of the given type. Thus, with this meta-comment, a single file could contain DNA, RNA and Protein features, for example, representing a single genomic locus or 'gene', alongside type-specific features of its transcribed mRNA and translated protein sequences. If no ##Type meta-comment is provided for a given GFF file, then the type is assumed to be DNA.
processor
生成这个文件的应用程序
DNA
DNA
(##DNA <seqname> ##acggctcggattggcgctggatgatagatcagacgac ##... ##End-DNA)
To give a DNA sequence. Several people have pointed out that it may be convenient to include the sequence in the file. It should Not become mandatory to do so, And in our experience this has been very little used. Often the seqname will be a well-known identifier, And the sequence can easily be retrieved from a database, Or an accompanying file.
RNA
RNA
(##RNA <seqname> ##acggcucggauuggcgcuggaugauagaucagacgac ##... ##End-RNA)
Similar to DNA. Creates an implicit ##Type RNA <seqname> directive.
Protein
Protein
(##Protein <seqname>
##MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSF ##... ##End-Protein)
Similar to DNA. Creates an implicit ##Type Protein <seqname> directive.
SeqRegion
sequence-region (##sequence-region <seqname> <start> <end>)
To indicate that this file only contains entries for the specified subregion of a sequence.
Size
Genome size in bp
features
基因组上面的特性位点
species