WriteEmblSeq {GeneR}R Documentation

Write to Embl file

Description

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

Usage

writeEmblSeq (file, seqno = 0)
writeEmblLine (file, code = "", header = "", text = "",
                           nextfield = TRUE, append=TRUE)
writeEmblComment(file, code = "", text = "",
                           nextfield = TRUE, append=TRUE)

Arguments

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.

Author(s)

A. Lucas and Vincent Lefort

Examples


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")

[Package GeneR version 1.4.2 Index]