Extensions

Full name SMRUCC.genomics.Assembly.Uniprot.XML.Extensions Assembly SMRUCC.genomics.Core Members 8

01 Syntax

SMRUCC.genomics.Assembly.Uniprot.XML.Extensions

02 Methods

Name	Overloads	Summary
ProteinSequence	1	Get protein sequence
KO	1	Get KO number of this protein
GO	1	Get KO number of this protein
EnumerateAllIDs	1	includes uniprot accession id and db entry in other database
ORF	1	try get ORF locus_tag value
SubCellularLocations	1	获取蛋白质在细胞内的亚细胞定位结果
GetDomainData	1	获取蛋白质的功能结构信息
Term2Gene	1	生成KEGG或者GO注释分类的mapping表

03 Members

method ProteinSequence #

ProteinSequence(entry)

Get protein sequence

Parameters

Name	Type	Description
`prot`	entry	-

method KO #

KO(entry)

Get KO number of this protein

Parameters

Name	Type	Description
`protein`	entry	-

Returns

returns nothing if not found

method GO #

GO(entry)

Get KO number of this protein

Parameters

Name	Type	Description
`protein`	entry	-

method EnumerateAllIDs #

EnumerateAllIDs(entry)

includes uniprot accession id and db entry in other database

Parameters

Name	Type	Description
`entry`	entry	-

method ORF #

ORF(entry)

try get ORF locus_tag value

Parameters

Name	Type	Description
`protein`	entry	-

method SubCellularLocations #

SubCellularLocations(entry)

获取蛋白质在细胞内的亚细胞定位结果

Parameters

Name	Type	Description
`protein`	entry	-

method GetDomainData #

GetDomainData(entry)

获取蛋白质的功能结构信息

Parameters

Name	Type	Description
`prot`	entry	-

Returns

get domain type feature information

method Term2Gene #

Term2Gene(UniProtXML, String, IDTypes)

生成KEGG或者GO注释分类的mapping表

Parameters

Name	Type	Description
`uniprotXML`	UniProtXML	-
`type$`	`String`	-
`idType`	IDTypes	-

Returns

term --> geneID