[Seqinr-forum] FASTA output splits into all headers then all sequences

[Oliver Clay]

   - [Seqinr-forum] suggested SeqinR function for printing a list of
   sequences to a fasta file
   <http://lists.r-forge.r-project.org/pipermail/seqinr-forum/2009q4/000057.html>
     *Coghlan, Avril  **Thu Dec 10 17:51:11 CET 2009*

Dear Jean and Simon,

I took Jean's example from the above thread,

> library(seqinr)
> choosebank("genbank")
> query("humtRNAs", "SP=homo sapiens AND M=TRNA")
> myseqs <- getSequence(humtRNAs)
> mynames <- getName(humtRNAs)
> write.fasta(myseqs,mynames, file = "myseqs.fasta") ######

and made a few changes, but after those changes my output was no
longer a normal FASTA file: instead, it first had all header lines
bunched together, then all the DNA sequences concatenated in one
block. Here are the commands I used:

library(seqinr)
choosebank("genbank")
query("mydat", "AU=Matute")
modifylist("mydat",operation=">613")
modifylist("mydat",operation="<615")
myseqs <- getSequence(mydat)
mynames <- getName(mydat)
write.fasta(myseqs,mynames, file = "myseqs.fasta")

I've tried repeating this example many times under the same conditions
(new R console, on Mac OSX). The problem seem to be intermittent,
because very rarely I do get the normal FASTA output, but then the
next time everything segregates again. Do you have an idea what might
be causing this?

Many thanks for your help,

Best regards,

Oliver Clay
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