BIOMTaxonomy

Full name SMRUCC.genomics.Metagenomics.BIOMTaxonomy Assembly SMRUCC.genomics.Core Members 9

01 Syntax

SMRUCC.genomics.Metagenomics.BIOMTaxonomy

02 Methods

Name	Overloads	Summary
TaxonomyString	1	Contact the taxonomy lineage tokens as a taxonomy lineage string uin BIOM format.
TaxonomyFromString	1	这个函数不像BIOMTaxonomy.TaxonomyParser())和BIOMTaxonomy.TaxonomyParserAlt())这两个是专门针对具有分类信息前缀的字符串的解析。这个函数是主要针对于没有分类层次信息前缀的字符串的解析函数，由于没有分类信息的前缀字符串，故而这个函数也主要是依靠tokens之间的前后顺序来赋值分类的rank信息
AsTaxonomy	1	New Taxonomy(lineage)
TaxonomyParser	2	For BIOMTaxonomy.BIOMPrefix
TaxonomyParserAlt	1	For BIOMTaxonomy.BIOMPrefixAlt
FillLineageEmpty	1	fill empty to the missing taxonomy rank level

03 Properties

Name	Overloads	Summary
BIOMPrefix	1	k{x.superkingdom};p{x.phylum};c{x.class};o{x.order};f{x.family};g{x.genus};s{x.species}
BIOMPrefixAlt	1	["superkingdom", "phylum", "class", "order", "family", "genus", "species"]

04 Members

method TaxonomyString #

TaxonomyString(String())

Contact the taxonomy lineage tokens as a taxonomy lineage string uin BIOM format.

Parameters

Name	Type	Description
`lineage`	`String()`	Lineage tokens text array data from Taxonomy.Select() method. (这里所输入的字符串数组可以是没有BIOM前缀的，也可以是具有分类等级前缀的，这个函数会自动执行归一化)

method TaxonomyFromString #

TaxonomyFromString(String, Char)

这个函数不像BIOMTaxonomy.TaxonomyParser()和BIOMTaxonomy.TaxonomyParserAlt()这两个是专门针对具有分类信息前缀的字符串的解析。这个函数是主要针对于没有分类层次信息前缀的字符串的解析函数，由于没有分类信息的前缀字符串，故而这个函数也主要是依靠tokens之间的前后顺序来赋值分类的rank信息

Parameters

Name	Type	Description
`lineage`	`String`	从大到小排序的

method AsTaxonomy #

AsTaxonomy(Dictionary(Of String, String))

New [Taxonomy](cref:T:SMRUCC.genomics.Metagenomics.Taxonomy)(**lineage**)

Parameters

Name	Type	Description
`lineage`	`Dictionary(Of String, String)`	-

method TaxonomyParser #

TaxonomyParser(String)

For BIOMTaxonomy.BIOMPrefix

Remarks

greengenes数据库之中的taxonomy name会存在[]这类的符号，不清楚是因为什么？在这里替换掉

Parameters

Name	Type	Description
`taxonomy$`	`String`	-

method TaxonomyParser overload 2 #

TaxonomyParser(String())

For BIOMTaxonomy.BIOMPrefix

Remarks

greengenes数据库之中的taxonomy name会存在[]这类的符号，不清楚是因为什么？在这里替换掉

Parameters

Name	Type	Description
`taxonomy$`	`String()`	-

method TaxonomyParserAlt #

TaxonomyParserAlt(String)

For BIOMTaxonomy.BIOMPrefixAlt

Parameters

Name	Type	Description
`taxonomy$`	`String`	-

method FillLineageEmpty #

FillLineageEmpty(Dictionary(Of String, String), String)

fill empty to the missing taxonomy rank level

Parameters

Name	Type	Description
`lineage`	`Dictionary(Of String, String)`	-
`empty`	`String`	empty string for the missing taxonomy rank level

property BIOMPrefix #

BIOMPrefix

k__{x.superkingdom};p__{x.phylum};c__{x.class};o__{x.order};f__{x.family};g__{x.genus};s__{x.species}

property BIOMPrefixAlt #

BIOMPrefixAlt

["superkingdom__", "phylum__", "class__", "order__", "family__", "genus__", "species__"]

Remarks

Example:

 no rank__cellular organisms;superkingdom__Eukaryota;no rank__Opisthokonta;kingdom__Fungi;subkingdom__Dikarya;phylum__Ascomycota;no rank__saccharomyceta;subphylum__Pezizomycotina;no rank__leotiomyceta;no rank__dothideomyceta;class__Dothideomycetes;no rank__Dothideomycetes incertae sedis;order__Botryosphaeriales;family__Botryosphaeriaceae;genus__Macrophomina;species__Macrophomina phaseolina;no rank__Macrophomina phaseolina MS6