getDasSequence: Query nucleotide or amino acid sequence to session's DAS...
In gthar/DASiR: Distributed Annotation System in R

Description Usage Arguments Details Value Author(s) See Also Examples

This function retrieves the nucleotide or amino acid sequence for the given ranges using the corresponding data source id (or title) in the session's DAS server

1	getDasSequence(source,ranges, class=c("character", "DNAStringSet", "RNAStringSet", "AAStringSet"))

`source`	Data source id (or title). See `getDasSource`.
`ranges`	`GRanges` object containing the seqname(s) and range(s) to query. Make sure this information is consistent with those returned by `getDasEntries`.
`class`	Instance of the class to be used in the output. By default it returns a regular `character` vector, but we recomend using Biostring classes for retrieving large sequences. Most usual Biosting classes are `DNAStringSet` for genomic sequences, `RNAStringSet` for transcripts and `AAStringSet` for aminoacids.

This function allows to query the DAS server and returns the nucleotide or amino acid sequence available at the given ranges.

Please, be sure to pass the identifiers EXACTLY as the values returned by the functions available here (DAS is case-sensitive). It is also recommended that you check the capabilities for each of the data sources.

Please, notice that this function codes the parameters in a URL to query the server. This function could fail if you ask for many ranges. Also, notice that the speed of the query depends on the number of elements and the load in the server.

Please, use this function smartly and do not overload servers.

Nucleotide or amino acid sequences that match the content of the annotation for the given ranges in the server.

If there are not matching results, output is NULL.

Oscar Flores <oflores@mmb.pcb.ub.es>

Anna Mantsoki <anna.mantsoki@bsc.es>

getDas-functions

    # Set session server to the UniProt DAS Reference Server

    setDasServer(server="http://www.ebi.ac.uk/das-srv/uniprot/das")       

    print(getDasServer())

    source <- "uniprot" #Uniprot

    ranges <- GRanges(c("A0A000","A0A001"), IRanges(start=c(1,1), end=c(394,591)))

    sequences <- getDasSequence(source, ranges)

    print(sequences)