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$Id: Changes,v 1.39 2003/12/22 20:00:34 heikki Exp $
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$Id: Changes,v 1.49.4.1 2006/10/02 23:10:11 sendu Exp $
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Revision history for Bioperl core modules
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1.5 series - these releases represent the pre-1.6 releases, the 1.6 series
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will be branches from the last 1.5.x release.
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1.5.2 Developer release
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Full details of changes since 1.5.1 are available online at:
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http://www.bioperl.org/wiki/Change_log
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The following represents a brief overview of the most important changes.
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- Overhaul. Brand new system fully allows markers to have multiple
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positions on multiple maps, and to have relative positions. Should be
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- This module and all the modules in the Taxonomy directory now
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deprecated in favour of Bio::Taxon and Bio::Tree::Tree
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* get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
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* New methods ancestor(), each_Descendent() and _handle_internal_id().
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* Allows for different database modules to create Bio::Taxon objects
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with the same internal id when the same taxon is requested from each.
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* get_Children_Taxids() is deprecated, superceded by each_Descendent().
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* No longer includes the fake root node 'root'; there are multiple roots
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now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
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* get_node() has new option -full
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* Caches data retrieved from website
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- Now a Bio::Taxon. Carries out the species name -> specific name munging
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that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
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backward compatability in species() method.
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o Bio::Search and Bio::SearchIO
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- Overhaul. The existing system has been sped up via some minor changes
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(mostly gain-of-function to the API). Bio::PullParserI is introduced
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as a potential eventual replacment for the existing system, though as
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yet only a Hmmpfam parser exists written using it.
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1.5.1 Developer release
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o Major problem with how Annotations were written out with
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Bio::Seq is fixed by reverting to old behavior for
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Bio::Annotation objects.
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* bug #1871; REFLOOP' parsing loop, I changed the pattern to
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expect at l east 9 spaces at the beginning of a line to
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indicate line wrapping.
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* Treat multi-line SOURCE sections correctly, this defect broke
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both common_name() and classification()
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* parse swissprot fields in genpept file
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* parse WGS genbank records
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* Changed regexp for ID line. The capturing parentheses are
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the same, the difference is an optional repeated-not-semi-
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colon expression following the captured \S+. This means the
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regexp works when the division looks like /PRO;/ or when the
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division looks like /ANG ;/ - the latter is from EMBL
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* fix ID line parsing: the molecule string can have spaces in
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it. Like: "genomic DNA"
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- swiss.pm: bugs #1727, #1734
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* Added parser for entrezgene ASN1 (text format) files.
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Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
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- maf.pm coordinate problem fixed
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o Bio::Taxonomy and Bio::DB::Taxonomy
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- Parse NCBI XML now so that nearly all the taxonomy up-and-down
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can be done via Web without downloading all the sequence.
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o Bio::Tools::Run::RemoteBlast supports more options and complies
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to changes to the NCBI interface. It is reccomended that you
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retrieve the data in XML instead of plain-text BLAST report to
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insure proper parsing and retrieval of all information as NCBI
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fully expects to change things in the future.
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o Bio::Tree and Bio::TreeIO
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- Fixes so that re-rooting a tree works properly
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- Writing out nhx format from a newick/nexus file will properly output
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bootstrap information. The use must move the internal node labels over
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for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
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$node->bootstrap($node->id);
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- Nexus parsing is much more flexible now, does not care about
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- Cladogram drawing module in Bio::Tree::Draw
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- Node height and depth now properly calculated
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- fix tree pruning algorithm so that node with 1 child gets merged
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o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
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bugs and improvements were added, see Gbrowse mailing list for most of
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o Bio::DB::GFF partially supports GFF3. See information about
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gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
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o Better location parsing in Bio::Factory::FTLocationFactory -
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this is part of the engine for parsing EMBL/GenBank feature table
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locations. Nested join/order-by/complement are allowed now
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o Bio::PrimarySeqI->translate now takes named parameters
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o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
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reconstruction) is now supported. Parsing different models and
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branch specific parametes are now supported.
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o Bio::Factory::FTLocationFactory - parse hierarchical locations
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o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
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for getter/setter functions
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- blast bug #1739; match scientific notation in score
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and possible e+ values
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- blast.pm reads more WU-BLAST parameters and parameters, match
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a full database pathname,
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- Handle NCBI WEB and newer BLAST formats specifically
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(Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
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- psl off-by-one error fixed
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- exonerate parsing much improved, CIGAR and VULGAR can be parsed
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and HSPs can be constructed from them.
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- HSPs query/hit now have a seqdesc field filled out (this was
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always available via $hit->description and
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$result->query_description
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- hmmer.pm can parse -A0 hmmpfam files
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- Writer::GbrowseGFF more customizeable.
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o Bio::Tools::Hmmpfam
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make e-value default score displayed in gff, rather than raw score
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allow parse of multiple records
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1.5 Developer release
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o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
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provide Jukes-Cantor and Kimura pairwise distance methods,
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o Bio::AlignIO support for "po" format of POA, and "maf";
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Bio::AlignIO::largemultifasta is a new alternative to
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Bio::AlignIO::fasta for temporary file-based manipulation of
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particularly large multiple sequence alignments.
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o Bio::Assembly::Singlet allows orphan, unassembled sequences to
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be treated similarly as an assembled contig.
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o Bio::CodonUsage provides new rare_codon() and probable_codons()
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methods for identifying particular codons that encode a given
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o Bio::Coordinate::Utils provides new from_align() method to build
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a Bio::Coordinate pair directly from a
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Bio::Align::AlignI-conforming object.
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o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
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Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
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web service using standard Pubmed query syntax, and retrieve
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o Bio::DB::GFF has various sundry bug fixes.
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o Bio::FeatureIO is a new SeqIO-style subsystem for
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writing/reading genomic features to/from files. I/O classes
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exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
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classes only read/write Bio::SeqFeature::Annotated objects.
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Notably, the GFF v3 class requires features to be typed into the
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o Bio::Graph namespace contains new modules for manipulation and
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analysis of protein interaction graphs.
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o Bio::Graphics has many bug fixes and shiny new glyphs.
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o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
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indexing for HMMER reports and FASTA qual files, respectively.
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o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
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new objects that can be placed within a Bio::Map::MapI-compliant
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genetic/physical map; Bio::Map::Physical provides a new physical
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map type; Bio::MapIO::fpc provides finger-printed clone mapping
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o Bio::Matrix::PSM provide new support for postion-specific
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(scoring) matrices (e.g. profiles, or "possums").
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o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
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be instantiated without explicitly using Bio::OntologyIO. This
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is possible through changes to Bio::Ontology::OntologyStore to
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download ontology files from the web as necessary. Locations of
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ontology files are hard-coded into
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Bio::Ontology::DocumentRegistry.
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o Bio::PopGen includes many new methods and data types for
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population genetics analyses.
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o New constructor to Bio::Range, unions(). Given a list of
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ranges, returns another list of "flattened" ranges --
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overlapping ranges are merged into a single range with the
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mininum and maximum coordinates of the entire overlapping group.
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o Bio::Root::IO now supports -url, in addition to -file and -fh.
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The new -url argument allows one to specify the network address
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of a file for input. -url currently only works for GET
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requests, and thus is read-only.
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o Bio::SearchIO::hmmer now returns individual Hit objects for each
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domain alignment (thus containing only one HSP); previously
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separate alignments would be merged into one hit if the domain
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involved in the alignments was the same, but this only worked
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when the repeated domain occured without interruption by any
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other domain, leading to a confusing mixture of Hit and HSP
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o Bio::Search::Result::ResultI-compliant report objects now
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implement the "get_statistics" method to access
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Bio::Search::StatisticsI objects that encapsulate any
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statistical parameters associated with the search (e.g. Karlin's
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lambda for BLAST/FASTA).
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o Bio::Seq::LargeLocatableSeq combines the functionality already
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found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
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o Bio::SeqFeature::Annotated is a replacement for
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Bio::SeqFeature::Generic. It breaks compliance with the
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Bio::SeqFeatureI interface because the author was sick of
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dealing with untyped annotation tags. All
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Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
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compliant, and accessible through Bio::Annotation::Collection.
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o Bio::SeqFeature::Primer implements a Tm() method for primer
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melting point predictions.
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o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
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InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
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o Bio::Taxonomy::Node now implements the methods necessary for
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Bio::Species interoperability.
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o Bio::Tools::CodonTable has new reverse_translate_all() and
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make_iupac_string() methods.
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o Bio::Tools::dpAlign now provides sequence profile alignments.
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o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
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o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
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o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
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for designing small inhibitory RNA.
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o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
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methods based on a distance matrix.
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o Bio::Tree::Statistics provides an assess_bootstrap() method to
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calculate bootstrap support values on a guide tree topology,
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based on provided bootstrap tree topologies.
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o Bio::TreeIO now supports the Pagel (PAG) tree format.
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o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
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o Bio::Graphics will work with gd1 or gd2
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- hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
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- blast.pm Parse multi-line query fields properly
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- small speed improvements to blasttable.pm and others
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o Bio::DB::Taxonomy has better support for hierarchy traversal so that
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Bio::Taxonomy::Node can be as simple as Bio::Species object while still
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supporting more complex queries
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1.4. Stable major release
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Since initial 1.2.0, 3000 separate changes have been made to make this release.
added
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Changes
