SizeSeqFasta {GeneR}R Documentation

Size of a sequence from a fasta/embl/gbk file

Description

Give the size of a sequence from a fasta/embl/gbk file.

Usage

sizeSeqFasta(file,name=NA)
sizeSeqEmbl(file,name=NA, index="ix")
sizeSeqGbk(file,name=NA)

Arguments

file

File name of the bank

name

Name of the sequence in the bank (default: first sequence)

index

character. "ix": Name is accn of sequence.
"id" : Le name is id of sequence.

Value

Size of sequence, NULL if error.

Author(s)

P.Durosay(C). L.Cottret(R)

See Also

readSeq

Examples

seqNcbi("NC_004718",file="NC_004718.gbk",type="G")
sizeSeqGbk("NC_004718.gbk")
# Or:
sizeSeqGbk("NC_004718.gbk","NC_004718")



# Idem with fasta format
seqNcbi("NC_004718",file="NC_004718.fa",type="F")
sizeSeqFasta("NC_004718.fa")
# Or:
sizeSeqFasta("NC_004718.fa","gi|30271926|ref|NC_004718.3|")

## Not run: 
# With Embl
download.file("http://bioinfo.hku.hk/sars/AY291451.seq",
destfile="AY291451.seq")
sizeSeqEmbl("AY291451.seq")

## End(Not run)


[Package GeneR version 2.24.0 Index]