annotation.genomics

require(GCModeller); #' Genomics context data annotation toolkit imports "annotation.genomics" from "seqtoolkit";

Genomics context data annotation toolkit

This R# package module provides the api for read/write and manipulate the genomics context annotation data:

read the genomics context annotation table file: read.gff, read.gtf, read.nucmer;

export the genomics context annotation data: write.gff3, as.tabular, write.PTT_tabular;

query the genomics context features: gff_features, source_features, type_features, genes_features, upstream;

extract the sequence region data: extract_gff_seqs.

.NET clr type export
gene_info: GeneBrief	The gene brief information data in a ncbi PTT document.(PTT文件之中的一行，即一个基因的对象摘要信息)

.NET clr function exports
as.data.frame.feature	Feature: A feature is here an interval (i.e., a range of positions) on a chromosome or a union of such intervals. In the case of RNA-Seq, the features are typically genes, where each gene is considered here as the union of all its exons. One may also consider each exon as a feature, e.g., in order to check for alternative splicing. For comparative ChIP-Seq, the features might be binding region from a pre-determined list.
read.gtf	read the gtf format genomics context annotation table file
read.gff	read the gff3 file
write.gff3	save the genomics feature annotation table object as a gff3 format table file
source_features	get the genomics features from the given gff table by its source name
type_features	get the genomics features from the given gff table by its feature type
gff_features	get gff features by id reference
as.tabular	export the gene annotation data as the tabular format table object
as.geneTable	export the PTT tabular table object as a collection of the gene table records
as.PTT	export the genbank database file object as a PTT tabular table object
upstream	Create the upstream location
genes_features	Extract all gene features from a given genomics context assembly data
write.PTT_tabular	write the genomics context annotation data as the PTT tabular format table file
read.nucmer	read the nucmer alignment delta format file
extract_gff_seqs	extract the sequence region data of the genomics features in the given gff3 table from the reference sequence data

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