| WriteEmblSeq {GeneR} | R Documentation |
Write a sequence, with description into a EMBL file. writeEmblSeq write the sequence; writeEmblLine write a feature line, writeEmblComment write a comment line. CompleteStringWithSpace: internal function
writeEmblSeq (file, seqno = 0)
writeEmblLine (file, code = "", header = "", text = "",
nextfield = TRUE, append=TRUE)
writeEmblComment(file, code = "", text = "",
nextfield = TRUE, append=TRUE)
file |
EMBL File name |
code |
2 letters: to be written at line beginning |
header |
First part of line |
text |
a text to be written |
seqno |
Integer, sequence number (bufno) |
nextfield |
TRUE: write XX after line, FALSE: don't write XX. |
append |
Scalar boolean. TRUE -> line(s) is added at the end of the file. FALSE -> file is written over. |
A. Lucas and Vincent Lefort
s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa"
placeString(s)
# Add lines with "CC bla bla bla" and a line "XX"
writeEmblComment(file="toto.embl",code="CC",text="This is a comment for \
this dummy sequence... I try to be long enough to show that this comment \
will be written on several lines",append=FALSE)
# Add a line with "FT CDS bla bla bla"
writeEmblLine(file="toto.embl",code="FT",header="CDS",text="<1..12",
nextfield = FALSE)
# Add lines with "FT bla bla bla"
writeEmblLine(file="toto.embl",code="FT",header="",text="/codon_start=2",
nextfield = FALSE)
writeEmblLine(file="toto.embl",code="FT",header="",text="/gene=\"toto\"",
nextfield = FALSE)
writeEmblLine(file="toto.embl",code="FT",header="",text="/note=\"Here is \
what I think about this gene\"",nextfield = TRUE)
# Add sequence
writeEmblSeq(file="toto.embl")