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changelog [2014/05/01 07:06]
gaou [v.1.8.14 in development]
changelog [2017/03/22 06:54] (current)
gaou [v.1.9.2 in development]
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 [[optimization|Optimization work in progress list]] [[optimization|Optimization work in progress list]]
  
-===== v.1.8.14    in development ​ =====+===== v.1.9.   in development ​===== 
 +  * added .gbff extension to be interpreted as GenBank format 
 +  * added protein_id shortcut in the G::IO structure 
 +  * updated TogoWS URL 
 +===== v.1.9.1 ​   2016.01.04 ===== 
 +  * bug fix in base_counter 
 +  * fixed a serious bug in the previous revision, where the default codon table was set to be number 25 instead of 1 
 +===== v.1.9.0 ​   2014.11.14 ​ =====
   * added -amino option to to_fasta()   * added -amino option to to_fasta()
   * added -mean option to cumulative()   * added -mean option to cumulative()
   * added -output=>"​f"​ to nucleotide_periodicity()   * 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::​GCskew::​coding_density()
   * added G::​Seq::​Codon::​Dmean()   * added G::​Seq::​Codon::​Dmean()
 +  * added G::​Seq::​Util::​refseq2gbk()
   * added $gb->​annotate(),​ a wrapper around Restauro-G v.1.5   * 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 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.   * added an option to insert desired number of '​N'​s between contigs in new G() and load() with '​multiple locus' option.
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     * $gb = load("​e.coli k12");     * $gb = load("​e.coli k12");
     * $gb = load("​511145"​);​     * $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   * 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 for -tag option in w_value()
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   * bug fix in G::​Seq::​Codon for REST services compatibility   * 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 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   * 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::​Tools::​Alignment (clustalw(),​ _fasta(), _blast(), _formatdb(),​ blastall(), blat(), which have corresponding KBWS tools)
changelog.1398928008.txt.gz · Last modified: 2014/05/01 07:06 by gaou