downloadFasta: Download FASTA for a list of canonical (P04637) and isoform...

In vitkl/ProtDomSeq: Work with InterPro Protein Domains and FASTA Sequences (UniProt)

Description

Download FASTA for a list of canonical (P04637) and isoform (P04637-2) UniprotAC

Load all FASTA from single UniProt file and filter by uniprot_ac

Usage

downloadFasta(uniprot_ac, file_name)


  loadAllFASTA(uniprot_url = "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz",
  uniprot_ac, file = "sp.fasta.gz")

Arguments

uniprot_ac	character vector containg canonical and isoform UniprotAC
file_name	file name and directory to save the result ("./dir/filename")
uniprot_url	file name and directory to save the result ("./dir/filename")
uniprot_ac	character vector containg canonical and isoform UniprotAC

Details

downloadFasta is intended to download from Uniprot and write fasta sequence file (renaming the name of the sequence given by UniProt to UniprotAC only) given generic (P04637) or isoform (P04637-2) UniprotAC. If the file already contains the sequences for given UniprotAC you get a message, if some sequences are missing all sequences will be reloaded.

Value

nothing

AAStringSet

Author(s)

Vitalii Kleshchevnikov

Vitalii Kleshchevnikov

See Also

downloadFasta_postproc

Examples

downloadFasta(uniprot_ac = c("P04637", "P04637-2"), file_name = "my_canonical_and_isoform.fasta")

vitkl/ProtDomSeq documentation built on May 3, 2019, 8:08 p.m.