ReadSeq {GeneR} | R Documentation |
Read a sequence from a Fasta, Embl or GeneBank file, and put it in a buffer.
readSeq is the generic function, readFasta, readGbk and readEmbl are aliases.
readSeq(file,name=NA, path="", type="E", seqno=0, from=1, to=0,upper=TRUE, index="ix") readFasta(file,name=NA, path="", seqno=0, from=1, to=0,upper = TRUE, index="ix") strReadFasta (file, name = NA, path = "", from = 1, to = 0, index = "ix") readGbk(file,name=NA, path="", seqno=0, from=1, to=0, index="ix") strReadGbk (file, name = NA, path = "", from = 1, to = 0, index = "ix") readEmbl(file,name=NA, path="", seqno=0, from=1, to=0, index="ix") strReadEmbl (file, name = NA, path = "", from = 1, to = 0, index = "ix")
file |
file of the bank |
name |
Name of the sequence in the bank (default: first sequence) |
path |
Path to the bank |
upper |
if TRUE: all sequence is converted to upper case (default), else sequence is read directly (only implemented for Fasta). |
type |
One of: "F" -> fasta. "E" -> embl. |
seqno |
Integer. Number of bufseq where the sequence will be stored |
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. |
integer: 1 if if get the sequence; -1 if error. strReadEmbl return 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",path=".",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')