| readSeq {GeneR} | R Documentation |
These functions load a sequence from a Fasta, Embl or GeneBank sequence bank file into a GeneR sequence buffer or as a character string..
readSeq is the generic function, readFasta, readGbk and readEmbl are aliases.
readSeq(file,name=NA, type="F", seqno=0,
from=1, to=0,upper=TRUE, index="ix")
readFasta(file,name=NA, seqno=0,
from=1, to=0,upper = TRUE, index="ix")
strReadFasta (file, name = NA, from = 1,
to = 0,upper = TRUE)
readGbk(file,name=NA, seqno=0, from=1, to=0,upper = TRUE,index="ix")
strReadGbk (file, name = NA, from = 1,
to = 0,upper = TRUE)
readEmbl(file,name=NA, seqno=0, from=1, to=0,upper = TRUE,index="ix")
strReadEmbl (file, name = NA, from = 1,
to = 0,upper = TRUE, index = "ix")
file |
String/scalar, File name of the bank |
name |
String/scalar, Sequence name (default : first sequence) |
upper |
upper case letters conversion (TRUE: The whole sequence is converted to upper case letters, FALSE : no conversion (only implemented for Fasta sequence)). |
type |
String/scalar, Bank format ("F" -> fasta. "E" -> embl, "G" -> GenBank) |
seqno |
Integer/scalar, Sequence number (buffer number) |
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) |
index |
String/scalar, type of index ( "ix" -> sequence name is the accession number "id" -> sequence name is the identifier) |
integer: 1 if OK; -1 if error. strReadFasta, strReadGbk and strReadEmbl returns the sequence as character string.
L.Cottret, A. Lucas.
GeneR,
globals,
readEmblLocation,
readGbkLocation,
getSeq,
sizeSeqEmbl,
sizeSeqFasta
## Get a sequence from Ncbi
seqNcbi("BY608190",file="BY608190.gbk",type="G")
## Read Gbk file to buffer 0
readGbk("BY608190.gbk")
## Or to a character string
strReadGbk("BY608190.gbk")
## Write to Fasta file
writeFasta(file='toto.fa')
## Make an index to this file
indexFasta('toto.fa')
readFasta (file="toto.fa",seqno=0,from=1,to=159)
## Show seqence on buffer 0
getSeq()
## Make a Fake file
writeEmblLine(file='toto.embl',code='AC',header='tmp',append=FALSE)
writeEmblSeq(file='toto.embl')
## Make index on file toto.embl
indexEmbl('toto.embl')
## Read Embl file to buffer 0
readEmbl('toto.embl')
## Or read "directly"
strReadEmbl('toto.embl')