nuget
An instance of the Genome class represents a genome and its annotation, including the genome sequence, protein-coding genes, and RNA genes in the genome.
Genome
01 Syntax
SMRUCC.genomics.SequenceModel.RNA_Seq.Rockhopper.Core.Genome
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| .ctor | 2 | Constructs a new Genome object based on the specified files (e.g., genome.fna, genes.ptt, rna.rnt). |
| Size | 1 | Returns the size in nucleotides of the genome sequence. |
| GetSeq | 1 | Returns a subsequence of the (1-indexed) genome as specified by the two coordinates, inclusive. |
| NumGenes | 1 | Return the number of genes in the genome. |
| GetGene | 1 | Return the Gene at the specified index. |
| AddPredictedRNAs | 1 | 将预测得到的新转录本（RNA）合并进基因集合。 |
| GetAnnotations | 1 | Returns a String[] representing the annotation (gene, rRNA, tRNA, RNA, "") for each coordinate in the genome on the specified strand. |
| GenesToString | 1 | Return a String representation of all genes in the genome (即 *_transcripts.txt 的表头与数据行）。 |
| readInGenome | 1 | 从 FASTA 文件读取基因组序列，并解析 ID 与名称。 |
| readInGenes | 1 | Reads in a file of genes (either *.ptt or *.rnt) and returns a list of gene objects. |
| mergeGenes | 1 | Given two lists of Genes, creates a new list of Genes containing all the Genes from the two specified lists combined. |
| create_GFF_file | 1 | Based on a list of genes and a FASTA genome file, create a GFF file that can be read by a genome browser. |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| ID | 1 | Returns the ID of the genome. |
| Name | 1 | Returns the name of the genome. |
| BaseFileName | 1 | Returns the path and name of the genome file sans .fna extension. |
| Sequence | 1 | Returns the raw (1-indexed) genome sequence. |
| FormalGenomeName | 1 | Returns the formal genome name, e.g., gi|49175990|ref|NC_000913.2 |
| CodingGenes | 1 | Return the collection of protein coding genes. |
| RnaGenes | 1 | Return the collection of RNA genes. |
| Genes | 1 | Return the collection of all genes. |
04 Fields
| Name | Overloads | Summary |
|---|---|---|
| genome | 1 | 基因组核酸序列。首位追加一个字符以保证 1-indexed 访问。 |
| _formalGenomeName | 1 | First token of FASTA header line, e.g., gi|49175990|ref|NC_000913.2 |
| _baseFileName | 1 | Path and name of genome file sans .fna extension. |
| _genes | 1 | Merged coding genes and RNAs. |
05 Members
#ctor(
String)Constructs a new Genome object based on files in the specified directory (e.g., genome.fna, genes.ptt, rna.rnt).
#ctor(
String, String, String)Constructs a new Genome object based on the specified files (e.g., genome.fna, genes.ptt, rna.rnt). If any of the file names are empty, then they are simply ignored.
Size
Returns the size in nucleotides of the genome sequence. Note: the returned size will be 1 bigger than the actual genome size since we add a character to the beginning of the genome sequence to ensure 1-indexing.
GetSeq(
Int32, Int32)Returns a subsequence of the (1-indexed) genome as specified by the two coordinates, inclusive.
NumGenes
Return the number of genes in the genome.
GetGene(
Int32)Return the Gene at the specified index.
AddPredictedRNAs(
List(Of Gene))将预测得到的新转录本（RNA）合并进基因集合。
GetAnnotations(
Char)Returns a String[] representing the annotation (gene, rRNA, tRNA, RNA, "") for each coordinate in the genome on the specified strand.
GenesToString(
List(Of Condition), String())Return a String representation of all genes in the genome (即 *_transcripts.txt 的表头与数据行）。
readInGenome(
String)从 FASTA 文件读取基因组序列，并解析 ID 与名称。
readInGenes(
String, String)Reads in a file of genes (either .ptt or .rnt) and returns a list of gene objects.
mergeGenes(
List(Of Gene), List(Of Gene))Given two lists of Genes, creates a new list of Genes containing all the Genes from the two specified lists combined.
create_GFF_file(
List(Of Gene), String, Int32)Based on a list of genes and a FASTA genome file, create a GFF file that can be read by a genome browser. The newly created file is output to the same directory as the FASTA genome file and has the same name except with the extension *.gff.
ID
Returns the ID of the genome.
Name
Returns the name of the genome.
BaseFileName
Returns the path and name of the genome file sans .fna extension.
Sequence
Returns the raw (1-indexed) genome sequence.
FormalGenomeName
Returns the formal genome name, e.g., gi|49175990|ref|NC_000913.2|
CodingGenes
Return the collection of protein coding genes.
RnaGenes
Return the collection of RNA genes.
Genes
Return the collection of all genes.
genome
基因组核酸序列。首位追加一个字符以保证 1-indexed 访问。
_formalGenomeName
First token of FASTA header line, e.g., gi|49175990|ref|NC_000913.2|
_baseFileName
Path and name of genome file sans .fna extension.
_genes
Merged coding genes and RNAs.