[R-pkgs] New version of seqinR released

Simon Penel penel at biomserv.univ-lyon1.fr
Wed Dec 12 15:59:10 CET 2007

Dear useRs,

the seqinR package contains utilities to import and analyze biological
sequence data. For a general introduction see this document:

Please do not use r-help for questions about seqinR or r-bugs
for bug report about seqinR. Use instead the seqinR diffusion list:

A new version of seqinR, seqinR 1.1-4, has been released on CRAN.
Here is a summary of changes:

o There is a new chapter to explain how to set up a
  local ACNUC server on Unix-like platforms.

o Function GC() has gained a new argument NA.GC
  defaulting to NA to say what should be returned when the
  GC content cannot be computed from data (for instance with a
  sequence like NNNNNNNNNNNN). The argument oldGC is now
  deprecated and a warning is issued. Functions GC1(),
  GC2(), GC3() are now simple wrappers for the
  more general GCpos() function. The new argument frame
  allows to take the frame into account for CDS.

o Function read.fasta() now supports comment lines
  starting by a semicolon character in FASTA files. An example
  of such a file is provided in sequences/legacy.fasta.
  The argument File is now deprecated. There is
  a new argument seqonly to import just the sequences
  without names, annotations and coercion attempts. There is
  a new argument strip.desc to remove the leading
  '>' character in annotations (as in function readFASTA
  from the Biostrings package). The FASTA file
  example someORF.fsa from Biostrings is also added
  for comparisons.

o Function read.alignment() has gained a new argument
  forceToLower defaulting to TRUE to force lower case in
  the character of the sequence (this is for a smoother interaction
  with the package ape). The argument File is now
  deprecated and a warning is issued when used instead of file.
  The example in the function kaks() has been corrected
  to avoid this warning when reading the example files.

o The details of the socket connection are no more stored in
  the slot socket for objects of class seqAcnucWeb:
  this slot is now deleted. As a consequence, the argument
  socket in function as.SeqAcnucWeb() has been
  removed and there is now a new
  argument socket = "auto" in functions getAnnot(),
  getFrag(), geyKeyword(), getLocation(),
  and getSequence(). The default value "auto" means
  that the details of the socket connection are taken automatically
  when necessary from the last opened bank. The size of local lists
  of sequences is reduced by about a third now as compared to the
  previous version.

o New dataset m16j and waterabs added.

o Generic functions getAnnot(), getFrag(), getKeyword(),
  getLength(), getLocation(), getName(), getSequence() and
  getTrans() have gained methods to handle objects from class list
  and class qaw.

o Functions getAttributsocket() and getNumber.socket()
  are now deprecated, a warning is issued.

o There is a new appendix in which all the examples protected
  by a dontrun statment are forced to be executed.

o New low level utility functions related to an ACNUC server:
  acnucclose(), quitacnuc(), clientid(), countfreelists(),
  knowndbs(), autosocket(), countsubseqs(), savelist(),
  ghelp(), modifylist(), getlistate(), setlistname(),
  residuecount(), isenum(), prettyseq(), gfrag(),

o Utility function parser.socket() has been optimized and
  is about four times faster now. This decreases the time
  needed by the query() function.


the seqinR team

Simon Penel
Laboratoire de Biometrie et Biologie Evolutive           Bat 711  -   CNRS UMR 5558  -    Universite Lyon 1              43 bd du 11 novembre 1918 69622 Villeurbanne Cedex       Tel:   04 72 43 29 04      Fax:  04 72 43 13 88

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