Dear useRs,
the seqinR package contains utilities to import and analyze biological
sequence data. For a general introduction see this document:
http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf
Please do not use r-help for questions about seqinR or r-bugs
for bug report about seqinR. Use instead the seqinR diffusion list:
http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng
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(),
print.seqAcnucWeb()
o Utility function parser.socket() has been optimized and
is about four times faster now. This decreases the time
needed by the query() function.
Best,
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
http://lbbe.univ-lyon1.fr/-Penel-Simon-.html?lang=fr
http://pbil.univ-lyon1.fr/members/penel
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