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 = FALSE)

## Translation
prot <- translate(seqno=0,from=getOrfs()[1,1],to=getOrfs()[1,2])
writeEmblLine (file="toto.embl",code='FT',header='',
text=paste('/translation="',prot ,'\"',sep=''),nextfield =TRUE)

# Add sequence
writeEmblSeq(file="toto.embl")

## Show file
cat(paste(readLines("toto.embl"),collapse='\n'))


[Package GeneR version 2.24.0 Index]