retrieve_seqs: function to automatically retrieve sequences from a databank...
In geantonicelli/firstPackage: set of wrapper functions for phylogenetic analysis

Description Usage Arguments Value Author(s) See Also Examples

this is a function to retrieve sequences of DNA, RNA or protein from databases structured under ACNUC and located on the web, the retrieval is limited to accession numbers as selection criteria, remote access to ACNUC databases works by opening a socket connection on a port (for example on port number 5558 at pbil.univ-lyon1.fr) and by communicating on this socket following the protocol described here

1	retrieve_seqs(seqnames, acnucdb)

`seqnames`	a character vector specifying the accession numbers of the sequences to be retrieved
`acnucdb`	a character string specifying the name of the ACNUC database to be searched. Use `'choosebank'` without arguments to see a list of available databases

this function returns a named list with the sequences matching the sequence names of class SeqAcnucWeb retrieved by 'query' based on the provided accession numbers the name of each list item is composed of the accession number and the length of the sequence

gerardo esteban antonicelli

'print_alignment' 'clean_alignment' 'load_alignment' 'make_tree' 'max_parsimony'

seqs <- retrieve_seqs(c('P06747', 'P0C569', 'O56773', 'Q5VKP1'), 'swissprot')
## Not run: viruses_annot <- read.csv(system.file('extdata',
                                               'CoV_genomes_annot.csv',
                                               package='firstPackage'))
## End(Not run)
## Not run: accessions <- viruses_annot$accession
## Not run: seqs <- retrieve_seqs(accessions, 'genbank')
## Not run: str(seqs)