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 |
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')