Read location {GeneR} | R Documentation |
Extracts by keywords, from a GeneBank or an EMBL sequence entry, annotations from the features field
readGbkLocation (file, name = NA, from = 1, to = 0, key = "CDS", subkey = "") readEmblLocation (file, name = NA, from = 1, to = 0, key = "CDS", subkey = "")
file |
String/scalar, File name of the bank |
name |
String/scalar, Sequence name (default : first sequence) |
from, to |
Integer/scalar, Absolute addresses of the begin and the end of the fragment, (1 means the first nucleotide and 0 conventionally the last one; from must not be larger than to) |
key |
String/scalar,. Feature to retrieve. (ex: GENE, CDS...) |
subkey |
String/scalar, Label to retrieve (ex: locus\_tag, note, codon\_start...). |
A data frame
P.Durosay(C), L.Cottret(R), A. Lucas
## Not run: # Get SARS Sequence seqNcbi("NC_004718",file="NC_004718.gbk",type="G") # Get CDS Positions readGbkLocation(file="NC_004718.gbk") # Get peptides... readGbkLocation(file="NC_004718.gbk",key="mat_peptide",subkey="product") ## End(Not run) # The same with EMBL... # # Get SARS Sequence ## Not run: download.file("http://bioinfo.hku.hk/sars/AY291451.seq", destfile="AY291451.seq") # Get CDS Positions readEmblLocation(file="AY291451.seq") # Get peptides... readEmblLocation(file="AY291451.seq",key="mat_peptide",subkey="product") ## End(Not run)