C# Class LibiadaWeb.Helpers.NcbiHelper

The ncbi helper.

Public Methods

Method	Description
ExtractSequenceName ( Bio.IO.GenBank.GenBankMetadata metadata ) : string	Extracts supposed sequence name from metadata.
GetFastaFileStream ( string id ) : Stream	The get file.
GetFastaSequence ( Stream fastaFileStream ) : ISequence	Downloads sequence as fasta file from ncbi.
GetFeatures ( string id ) : List	Extracts features from genBank file downloaded from ncbi.
GetFeatures ( string ids ) : List[]	Extracts features from genBank files downloaded from ncbi.
GetGenBankSequences ( string ids ) : ISequence[]	Extracts sequences from genbank files.
GetMetadata ( ISequence sequence ) : Bio.IO.GenBank.GenBankMetadata	Extracts metadata from genbank file.

Method	Description
GetEfetchParamsString ( string retType ) : string	Creates efetch params string with given return type.
GetGenBankSequence ( string id ) : ISequence	Extracts sequence from genbank file.
GetResponseStream ( string url ) : Stream	The get response.

Extracts supposed sequence name from metadata.

/// Thrown if all name fields are contradictory. ///

public static ExtractSequenceName ( Bio.IO.GenBank.GenBankMetadata metadata ) : string
metadata	Bio.IO.GenBank.GenBankMetadata	/// The metadata. ///
return	string

The get file.

public static GetFastaFileStream ( string id ) : Stream
id	string	/// Accession id of the sequence in ncbi (remote id). ///
return	Stream

Downloads sequence as fasta file from ncbi.

public static GetFastaSequence ( Stream fastaFileStream ) : ISequence
fastaFileStream	Stream	/// The fasta file stream. ///
return	ISequence

Extracts features from genBank file downloaded from ncbi.

public static GetFeatures ( string id ) : List
id	string	/// Accession id of the sequence in ncbi (remote id). ///
return	List

Extracts features from genBank files downloaded from ncbi.

public static GetFeatures ( string ids ) : List[]
ids	string	/// Accession ids of the sequences in ncbi (remote ids). ///
return	List[]

Extracts sequences from genbank files.

public static GetGenBankSequences ( string ids ) : ISequence[]
ids	string	/// The ids. ///
return	ISequence[]

Extracts metadata from genbank file.

/// Thrown if metadata is abscent. ///

public static GetMetadata ( ISequence sequence ) : Bio.IO.GenBank.GenBankMetadata
sequence	ISequence	/// Sequence extracted from genbank file. ///
return	Bio.IO.GenBank.GenBankMetadata