Read location {GeneR}R Documentation

Get features from a GeneBank file

Description

Extract from a GeneBank file some features

Usage

readGbkLocation(file,name=NA, path="", from = 1, to = 0, index = "ix",
key = "CDS",key2="locus_tag")

readEmblLocation(file,name=NA, path="", from=1, to=0, index="ix",
key="CDS",key2="locus_tag")

Arguments

file File of the bank
name Name of the sequence in the bank (default: first sequence)
path Path to the bank
from,to Begining and ending of sequence, can be vectors. 0 represent the last nucleotide and 1 the first one.
index "ix": name is accn of sequence.
"id" : name is id of sequence.
key String. Feature that we want positions. (ex: GENE, CDS...)
key2 String. label that we want precisions (ex: locus_tag, note, codon_start...).

Value

A list with:

locations.begins Begining positions of feature "key"
locations.ends Ending positions of feature "key"
locations.begins.limits Foreach begining position , get if it is exact (0) or fuzzy (1)
locations.ends.limits Foreach ending position , get if it is exact (0) or fuzzy (1)
locations.strand Foreach position, get if it strand si 5'-3' (0) or 3'-5' (1)
locations.key2 Label corresponding to "key2".

Note

Use this function carefully: bug found...

Author(s)

P.Durosay(C), L.Cottret(R), A. Lucas

See Also

readEmblLocation,readSeq

Examples


## 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",key2="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",key2="product")
## End(Not run)


[Package GeneR version 1.4.2 Index]