Extensions

Full name SMRUCC.genomics.Assembly.NCBI.GenBank.Extensions Assembly SMRUCC.genomics.Core Members 11

01 Syntax

SMRUCC.genomics.Assembly.NCBI.GenBank.Extensions

02 Methods

Name	Overloads	Summary
LocusMaps	1	[location => locus_tag]
LoadPTT	1	a shortcut of the PTT.Load()) function.
ExportProteins	2	Export protein sequence with custom annotation title with given template.
ExportProteins_Short	1	fasta sequence title header in format: locus_tag product_description
makeProtSeqShort	1	假若是新注释的基因组还没有基因号，则默认使用位置来做唯一标示
GeneList	1	export all gene features: RNA + CDS
_16SribosomalRNA	1	make export of the annotated 16s RNA from the given genbank assembly
loadRepliconTable	1
CreateGenbankObject	1
GetObjects	1

03 Members

method LocusMaps #

LocusMaps(PTT)

[location => locus_tag]

Parameters

Name	Type	Description
`PTT`	PTT	-

method LoadPTT #

LoadPTT(String)

a shortcut of the PTT.Load() function.

Parameters

Name	Type	Description
`path`	`String`	-

method ExportProteins overload 2 #

ExportProteins(File, Boolean)

Export protein sequence with full annotation.

Parameters

Name	Type	Description
`gbk`	File	-

method ExportProteins #

ExportProteins(File, StringTemplate, Boolean)

Export protein sequence with custom annotation title with given template.

Parameters

Name	Type	Description
`gb`	File	-
`headers`	`StringTemplate`	the fasta sequence header template
`filterEmpty`	`Boolean`	-

method ExportProteins_Short #

ExportProteins_Short(File, Boolean, Boolean)

fasta sequence title header in format: locus_tag product_description

Parameters

Name	Type	Description
`gb`	File	-
`duplicateOldLocusTag`	`Boolean`	andalso populate an duplicated sequence data if `old_locus_tag` is existed inside thse CDS feature.

method makeProtSeqShort #

makeProtSeqShort(Feature, Boolean, Boolean)

假若是新注释的基因组还没有基因号，则默认使用位置来做唯一标示

Remarks

locus_id info

Parameters

Name	Type	Description
`feature`	Feature	-
`onlyLocusTag`	`Boolean`	-

method GeneList #

GeneList(File)

export all gene features: RNA + CDS

Returns

{locus_tag, gene}

method _16SribosomalRNA #

_16SribosomalRNA(File)

make export of the annotated 16s RNA from the given genbank assembly

Parameters

Name	Type	Description
`Gbk`	File	-

method loadRepliconTable #

loadRepliconTable(String)

method CreateGenbankObject #

CreateGenbankObject(PTT)

method GetObjects #

GetObjects(IEnumerable(Of TGene), Int32, Strands)