From gaou ＠ sfc.keio.ac.jp  Fri Nov 14 05:42:51 2014
From: gaou ＠ sfc.keio.ac.jp (Kazuharu Arakawa)
Date: Fri, 14 Nov 2014 05:42:51 +0900
Subject: [Glang-users] 1.9.0 released!
Message-ID: <65990EA3-9D24-4706-853F-040BBE50A5A4@sfc.keio.ac.jp>

gaou.

前回のリリースから2年半ほどかかってしまいましたが、久々のminor version up となる1.9.0をリリースしました。

changelogは以下の通りです。かなり変更が蓄積しているので主要機能を選べないのですが、統計解析系のメソッドが充実しており、とりあえずデータを放り込めば色々情報を出してくれるsummary()関数や、自然言語やtaxonomyに対応したload()関数など、さまざまなものがあります。



===== v.1.9.0    2014.11.14  =====
  * added -amino option to to_fasta()
  * added -mean option to cumulative()
  * added -output=>"f" to nucleotide_periodicity()
  * added -table option for Alternative Codon Tables for translate()
  * added w_tai() and -tai option to G::Seq::Codon::cai()
  * added G::Seq::GCskew::coding_density()
  * added G::Seq::Codon::Dmean()
  * added G::Seq::Util::refseq2gbk()
  * added $gb->annotate(), a wrapper around Restauro-G v.1.5
  * added Rcmd::Summary::summary(), a smart statistical summary interface for given data or data set
  * added pca, hclust, som, kmeans (subset of Rcmd but exported by default through G) for statistical analysis
  * added G::Tools::EMBOSS::emboss(), which can run both EMBOSS and KBWS applications. seqret() is now deprecated.
  * added an option to insert desired number of 'N's between contigs in new G() and load() with 'multiple locus' option.
  * switched file conversion process from BioPerl to EMBOSS REST Service. Now the output formats supported are dependent on EMBOSS http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#out, but we now have support for GFF, GFF2, GFF3 output from $gb->output()
  * load() can now handle name of the species, its abbreviations, and NCBI taxonomy IDs for bacteria. For example, all of the following examples load E.coli K12 genome (NC_000913).
    * $gb = load("Escherichia coli");
    * $gb = load("e.coli k12");
    * $gb = load("511145");
  * $gb->seq_info() now shows number of CDSs (when annotation is present) and number of LOCUSes (with multiple locus option)
  * updated G::Seq::Util::molecular_weight() to handle ssDNA, dsDNA, peptide, RNA, and chemical formula
  * bug fix for -tag option in w_value()
  * bug fix in G::Seq::PatSearch::signature_dist()
  * bug fix in G::Seq::Codon for REST services compatibility
  * bug fix for reading multi-line, multiple feature tags (ex. multiple long GO_function feature tag within a CDS)
  * bug fix for G::IO::Handler::_interpret_format() for embl extension.
  * many minor fixes for use from REST/SOAP services, like default file names
  * Removed G::Tools::Alignment (clustalw(), _fasta(), _blast(), _formatdb(), blastall(), blat(), which have corresponding KBWS tools)
  * Removed G::Seq::AminoAcid::monoisotopic() which was overlapping with residue()
  * Removed G::Seq::AminoAcid::peptide_mass() and it is now merged to G::Seq::Util::molecular_weight()
  * Removed G::Tools::DotE
  * Removed G::Tools::EMBOSS (merged to G::Tools::WebServices)
  * Removed requirements of SOAP::Lite, Bio::Perl, Graph::Layout::Aesthetic at installation
  * changed default behavior of G::Tools::Statistics::cor() to return Pearson linear correlation instead of R^2