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---------------------------------------------------------
Revision history for BioPerl core modules
---------------------------------------------------------
The comprehensive history and ongoing development of BioPerl:
http://github.com/bioperl/bioperl-live
Some of that history is also highlighted on our wiki:
http://www.bioperl.org/wiki/Change_log
http://www.bioperl.org/wiki/History_of_BioPerl
Bugs and requested features list:
https://redmine.open-bio.org/projects/bioperl
CPAN releases are branched from 'master'.
---------------------------------------------------------
1.?.?
[New features]
* Bio::Seq::SimulatedRead
- New module to represent reads taken from other sequences [fangly]
* Bio::Tools::IUPAC
- New regexp() method to create regular expressions from IUPAC sequences
[fangly]
* Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
- Code refresh [fangly]
* Bio::DB::Taxonomy
- Added support for the Greengenes and Silva taxonomies [fangly]
* Bio::Tree::TreeFunctionsI
- get_lineage_string() represents a lineage as a string [fangly]
- add_trait() returns instead of reporting an error when the column
number is exceeded in add_trait() [fangly]
- Option to support tree leaves without trait [fangly]
- Allow ID of 0 in trait files [fangly]
* Bio::DB::Taxonomy::list
- Misc optimizations [fangly]
- Option -names of get_taxon() to help with ambiguous taxa [fangly]
* Bio::DB::Taxonomy::*
- get_num_taxa() returns the number of taxa in the database [fangly]
* Bio::DB::Fasta and Bio::DB::Qual
- support indexing an arbitrary list of files [fangly]
- user can supply an arbitrary index file name [fangly]
- new option to remove index file at the end [fangly]
* Bio::DB::Fasta
- now handles IUPAC degenerate residues [fangly]
* Bio::PrimarySeq and Bio::PrimarySeqI
- speed improvements for large sequences [Ben Woodcroft, fangly]
* Bio::PrimaryQual
- tightened and optimized quality string validation [fangly]
* Bio::SeqIO::fasta
- new method and option 'block', to create FASTA output with space
intervaled blocks (similar to genbank or EMBL) has been implemented.
- package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
in favour of the methods 'width' and 'preferred_id_type` respectively.
* Bio::FeatureIO::*
- moved from bioperl-live into the separate distribution Bio-FeatureIO
* Bio::SeqFeature::Annotated
- moved from bioperl-live into the separate distribution Bio-FeatureIO
* Bio::Cluster::SequenceFamily
- improved performance when using get_members with overlapping multiple
criteria
[Bug fixes]
* [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
* [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
* [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
information was lost in a multi-result blast file [Paul Cantalupo]
* [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
total gaps [Paul Cantalupo]
* [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
* [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
when end of domain indicator is split across lines [Paul Cantalupo]
* [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
cjfields]
* [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
instances where blank lines are within sequences [cjfields]
* Bio::DB::Fasta reports correct alphabet for files with multiple sequence
types [fangly]
* Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
* [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
cjfields]
* Various fixes for Stockholm file indexing and processing [bosborne]
* Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
breaks parsing [cjfields]
* Fix case where Bio::Seq::Meta* objects with no meta information could not
be reverse-complemented [fangly]
* Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
* Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
when unsure that values will be numerical [fangly]
* Fix undef warnings in Bio::SeqIO::embl [fangly]
* Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
* Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
* Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
Sallou]
* Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
source_tag and display_name must return a string, not undef [fangly]
* Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
add_SeqFeature takes a single argument [fangly]
* Use cross-platform filenames and temporary directory in
Bio::DB::Taxonomy::flatfile [fangly]
* Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
properly identified as existing taxa in the database [fangly]
* Fix issue where a Bio::DB::Taxonomy::list object could not be created
without also passing a lineage to store [fangly]
* Prevent passing a directory to the gi2taxid option (-g) of
bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
[fangly]
* Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
* Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
* Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
object before trying to access, and no longer returns repeated sequences.
1.6.901 May 18, 2011
[Notes]
* Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
modules using Ace will also be deprecated [lds, cjfields]
* Minor bug fix release
* Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
* Address Build.PL issues when DBI is not present [hartzell]
* Skip gbxml.t and Interpro tests when modules not installed [cjfields]
* Remove deprecated code for perl 5.14.0 compat [cjfields]
* Due to schema changes and lack of support for older versions, support
for NeXML 0.9 is only (very) partially implemented.
See: https://redmine.open-bio.org/issues/3207
[Bug fixes]
* [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
docs [genehack, cjfields]
* $VERSION for CPAN/cpanm-based installs was broken; force setting of
module version from dist_version (probably not the best way to do this,
but it seems to work) [rbuels, cjfields]
1.6.900 April 14, 201
[Notes]
* This will probably be the last release to add significant features to
core modules; subsequent releases will be for bug fixes alone.
We are planning on a restructuring of core for summer 2011, potentially
as part of the Google Summer of Code. This may become BioPerl 2.0.
* Version bump represents 'just prior to v 1.7'. We may have point
releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
This code essentially is what is on the github master branch.
[New features]
* Core code updated for perl 5.12.x [cjfields, Charle Tilford]
* Bio::Tree refactor
- major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
- removal of Scalar::Util::weaken code, which was causing odd headaches
with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
* Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
many others]
* Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
[Warren Kretzschmar]
* Bio::SeqIO::gbxml
- bug 2515 - new contribution [Ryan Golhar, jhannah]
* Bio::Assembly::IO
- support for reading Maq, Sam and Bowtie files [maj]
- support for reading 454 GS Assembler (Newbler) ACE files [fangly]
- bug 2483: support for writing ACE files [Joshua Udall, fangly]
- bug 2599: support DBLINK annotation in GenBank files [cjfields]
- bug 2726: reading/writing granularity: whole scaffold or one contig
at a time [Joshua Udall, fangly]
* Bio::OntologyIO
- Added parsing of xrefs to OBO files, which are stored as secondary
dbxrefs of the cvterm [Naama Menda]
- General Interpro-related code refactors [dukeleto, rbuels, cjfields]
* PAML code updated to work with PAML 4.4d [DaveMessina]
[Bug fixes]
* [3198] - sort tabular BLAST hits by score [DaveMessina]
* [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
* [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
* [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
[cjfields]
* [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
* [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
* [3164] - TreeFunctionsI syntax bug [gjuggler]
* [3163] - AssemblyIO speedup [fangly]
* [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
hyphaltip]
* [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
* [3158] - fix EMBL file mis-parsing [cjfields]
* [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
cjfields]
* [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
* [3148] - URL change for UniProt [cjfields]
* [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
* [3136] - HMMer3 parser fixes [kblin]
* [3126] - catch description [Toshihiko Akiba]
* [3122] - Catch instances where non-seekable filehandles were being
seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
* [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
[dukeleto, rbuels, cjfields]
* [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
jhannah]
* [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
* [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
cjfields]
* [3107] - BLAST alignment column_from_residue_number() [cjfields]
* [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
* [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
* [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
* [3086] - EMBL misparsing long tags [kblin, cjfields]
* [3085] - CommandExts and array of files [maj, hyphaltip]
* [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
for alignment slices [Ha X. Dang, cjfields]
* [3076] - XMFA alignment strand wrong [Ha X., cjfields]
* [3073] - fix parsing of GenBank files from RDP [cjfields]
* [3068] - FASTQ parse failure with trailing 0 [cjfields]
* [3064] - All-gap midline BLAST report issues [cjfields]
* [3063] - BLASt report RID [Razi Khaja, cjfields]
* [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
* [3053] - LOCUS line formatting [M. Wayne, cjfields]
* [3039] - correct Newick output root node branch length [gjuggler,
DaveMessina]
* [3038] - SELEX alignment error [Bernd, cjfields]
* [3033] - PrimarySeq ID setting [Bernd, maj]
* [3032] - Fgenesh errors [Wes Barris, hyphaltip]
* [3034] - AlignIO::clustal output [Bernd, DaveMessina]
* [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
* [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
* [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
* [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
PAML 4.4d [DaveMessina]
* [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
DaveMessina]
* [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
* [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
* [3017] - using threads with Bio::DB::GenBank [cjfields]
* [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
* [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
* [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
* [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
* [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
cjfields]
* [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
* [2977] - TreeIO issues [DaveMessina]
* [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
* [2944] - Bio::Tools::GFF score [cjfields]
* [2942] - correct MapTiling output [maj]
* [2939] - PDB residue insertion codes [John May, maj]
* [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
* [2928] - GuessSeqFormat raw [maj]
* [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
* [2922] - open() directive issue [cjfields]
* [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
* [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
* [2899] - SeqFeature::Store host issues [lstein, dbolser]
* [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
cjfields]
* [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
* [2876] - CDD search with RemoteBlast [Malcolm Cook]
* [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
* [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
* [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
* [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
* [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
* [2758] - Bio::AssemblyIO ace problems [fangly]
* [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
* [2726] - ace file IO [Josh, fangly]
* [2700] - Refactor Build.PL [cjfields]
* [2673] - addition of simple Root-based clone() method [cjfields]
* [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
* [2599] - support for DBLINK annotation in GenBank files [cjfields]
* [2594] - Bio::Species memory leak [cjfields]
* [2515] - GenBank XML parser [jhannah]
* [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
* [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
* [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
cjfields]
* [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
[Deprecated]
* Bio::Expression modules - these were originally designed to go with the
bioperl-microarray suite of tools, however they have never been completed
and so have been removed from the distribution. The original code has
been moved into the inactive bioperl-microarray suite. [cjfields]
[Other]
* Repository moved from Subversion (SVN) to
http://github.com/bioperl/bioperl-live [cjfields]
* Bug database has moved to Redmine (https://redmine.open-bio.org)
* Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
Thieme have been moved to their own distribution (Bio-Microarray).
[cjfields]
1.6.1 Sept. 29, 2009 (point release)
* No change from last alpha except VERSION and doc updates [cjfields]
1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
* Fix for silent OBDA bug related to FASTA validation [cjfields]
1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
* Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
* [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
[cjfields]
* BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
* WinXP test fixes [cjfields, maj]
* BioPerl.pod added for descriptive information, fixes CPAN indexing
[cjfields]
* Minor doc fixes [cjfields]
1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
* Fix tests failing due to merging issues [cjfields]
* More documentation updates for POD parsing [cjfields]
1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
* Bio::Root::Build
- fix YAML meta data generation [cjfields]
1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
* Bio::Align::DNAStatistics
- fix divide by zero problem [jason]
* Bio::AlignIO::*
- bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
* Bio::AlignIO::stockholm
- bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
* Bio::Assembly::Tools::ContigSpectrum
- function to score contig spectrum [fangly]
* Bio::DB::EUtilities
- small updates [cjfields]
* Bio::DB::Fasta
- berkeleydb database now autoindexes wig files and locks correctly
[lstein]
* Bio::DB::HIV
- various small updates for stability; tracking changes to LANL
database interface [maj]
* Bio::DB::SeqFeature (lots of updates and changes)
- add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
- bug 2835 - patch [Dan Bolser]
- bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
* Bio::DB::SwissProt
- bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
* Bio::Factory::FTLocationFactory
- mailing list bug fix [cjfields]
* Bio::LocatableSeq
- performance work on column_from_residue_number [hartzell]
* Bio::Matrix::IO::phylip
- bug 2800 - patch to fix phylip parsing [Wei Zou]
* Bio::Nexml
- Google Summer of Code project from Chase Miller - parsers for Nexml
file format [maj, chmille4]
* Bio::PopGen
- Make Individual, Population, Marker objects AnnotatableI [maj]
- simplify LD code [jason]
* Bio::RangeI
- deal with empty intersection [jason]
* Bio::Restriction
- significant overhaul of Bio::Restriction system: complete support for
external and non-palindromic cutters. [maj]
* Bio::Root::Build
- CPANPLUS support, no automatic installation [sendu]
* Bio::Root::IO
- allow IO::String (regression fix) [cjfields]
- catch unintentional undef values [cjfields]
- throw if non-fh is passed to -fh [maj]
* Bio::Root::Root/RootI
- small debugging and core fixes [cjfields]
* Bio::Root::Test
- bug RT 48813 - fix for Strawberry Perl bug [kmx]
* Bio::Root::Utilities
- bug 2737 - better warnings [cjfields]
* Bio::Search
- tiling completely refactored, HOWTO added [maj]
NOTE : Bio::Search::Hit::* classes do not use this code directly; we
will deprecate usage of the older tiling code in the next BioPerl
release
- small fixes [cjfields]
* Bio::SearchIO
- Infernal 1.0 output now parsed [cjfields]
- new parser for gmap -f9 output [hartzell]
- bug 2852 - fix infinite loop in some output [cjfields]
- blastxml output now passes all TODO tests [cjfields]
- bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
- RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
- bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
* Bio::Seq::LargePrimarySeq
- delete tempdirs [cjfields]
- bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
* Bio::Seq::Quality
- extract regions based on quality threshold value [Dan Bolser, heikki]
- bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
* Bio::SeqFeature::Lite
- various Bio::DB::SeqFeature-related fixes [lstein]
* Bio::SeqFeature::Tools::TypeMapper
- additional terms for GenBank to SO map [scain]
* Bio::SeqIO::chadoxml
- bug 2785 - patch to get this working for bp_seqconvert [cjfields]
* Bio::SeqIO::embl
- support for CDS records [dave_messina, Sylvia]
* Bio::SeqIO::fastq
- complete refactoring to handle all FASTQ variants, perform validation,
write output. API now conforms with other Bio* parsers and the rest of
Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
[cjfields]
* Bio::SeqIO::genbank
- bug 2784 - fix DBSOURCE issue [Phillip Garland]
- bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
* Bio::SeqIO::largefasta
- parser returns a Bio::Seq::LargePrimarySeq [jhannah]
* Bio::SeqIO::raw
- add option for 'single' and 'multiple'
* Bio::SeqIO::scf
- bug 2881 - fix scf round-tripping [Adam Søgren]
* Bio::SeqUtils
- bug 2766, 2810 - copy over tags from features, doc fixes [David
Jackson]
* Bio::SimpleAlign
- bug 2793 - patch for add_seq index issue [jhannah, maj]
- bug 2801 - throw if args are required [cjfields]
- bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
[Tristan Lefebure, maj]
- bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
- fix POD and add get_SeqFeatures filter [maj]
* Bio::Tools::dpAlign
- add support for LocatableSeq [ymc]
- to be moved to a separate distribution [cjfields, rbuels]
* Bio::Tools::EUtilities
- fix for two bugs from mail list [Adam Whitney, cjfields]
- add generic ItemContainerI interface for containing same methods
[cjfields]
* Bio::Tools::HMM
- fix up code, add more warnings [cjfields]
- to be moved to a separate distribution [cjfields, rbuels]
* Bio::Tools::Primer3
- bug 2862 - fenceposting issue fixed [maj]
* Bio::Tools::Run::RemoteBlast
- tests for remote RPS-BLAST [mcook]
* Bio::Tools::SeqPattern
- bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
* Bio::Tools::tRNAscanSE
- use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
* Bio::Tree::*
- bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
* Bio::Tree::Statistics
- several methods for calculating Fitch-based score, internal trait
values, statratio(), sum of leaf distances [heikki]
* Bio::Tree::Tree
- bug 2869 - add docs indicating edge case where nodes can be
prematurely garbage-collected [cjfields]
- add as_text() function to create Tree as a string in specified format
[maj]
* Bio::Tree::TreeFunctionsI
- bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
Lefebure, maj]
* Bio::TreeIO::newick
- fix small semicolon issue [cjfields]
* scripts
- update to bp_seqfeature_load for SQLite [lstein]
- hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
- fastam9_to_table - fix for MPI output [jason]
- gccalc - total stats [jason]
* General Stuff
- POD cleanup re: FEEDBACK section [maj, cjfields]
- cleanup or fix dead links [cjfields]
- Use of no_* methods (indicating 'number of something') is deprecated
in favor of num_* [cjfields]
- lots of new tests for the above bugs and refactors [everyone!]
- new template for Komodo text editor [cjfields]
1.6.0 Winter 2009
* Feature/Annotation rollback
- Problematic changes introduced prior to the 1.5 release have been
rolled back. These changes led to subtle bugs involving operator
overloading and interface methods.
- Behavior is very similar to that for BioPerl 1.4, with tag values
being stored generically as simple scalars. Results in a modest
speedup.
* Bio::Graphics
- Split into a separate distribution on CPAN, primarily so development
isn't reliant on a complete BioPerl release.
- Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
is only available via Subversion (via bioperl-live main trunk)
* Bio::Root::Test
- Common test bed for all BioPerl modules
* Bio::Root::Build
- Common Module::Build-based subclass for all BioPerl modules
* Bio::DB::EUtilities
- Complete refactoring to split up parsing (Bio::Tools::EUtilities),
parameter handling (Bio::Tools::EUtilities::EUtilParameters),
and user agent request posting and retrieval
* Test implementation and reorganization
- Tests have been reorganized into groups based on classes or use
cases.
- Automated test coverage is now online:
http://www.bioperl.org/wiki/Test_Coverage
- After this release, untested modules will be moved into a
separate developer distribution until tests can be derived.
Also, new modules to be added are expected to have a test suite
and adequate test coverage.
1.5.2 Developer release
Full details of changes since 1.5.1 are available online at:
http://www.bioperl.org/wiki/Change_log
The following represents a brief overview of the most important changes.
o Bio::Map
- Overhaul. Brand new system fully allows markers to have multiple
positions on multiple maps, and to have relative positions. Should be
backward compatible.
o Bio::Taxonomy
- This module and all the modules in the Taxonomy directory now
deprecated in favour of Bio::Taxon and Bio::Tree::Tree
o Bio::DB::Taxonomy
- Taxonomy.pm
* get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
* New methods ancestor(), each_Descendent() and _handle_internal_id().
* Allows for different database modules to create Bio::Taxon objects
with the same internal id when the same taxon is requested from each.
- flatfile.pm
* get_Children_Taxids() is deprecated, superceded by each_Descendent().
* No longer includes the fake root node 'root'; there are multiple roots
now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
- entrez.pm
* get_node() has new option -full
* Caches data retrieved from website
o Bio::Species
- Now a Bio::Taxon. Carries out the species name -> specific name munging
that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
backward compatability in species() method.
o Bio::Search and Bio::SearchIO
- Overhaul. The existing system has been sped up via some minor changes
(mostly gain-of-function to the API). Bio::PullParserI is introduced
as a potential eventual replacment for the existing system, though as
yet only a Hmmpfam parser exists written using it.
1.5.1 Developer release
o Major problem with how Annotations were written out with
Bio::Seq is fixed by reverting to old behavior for
Bio::Annotation objects.
o Bio::SeqIO
- genbank.pm
* bug #1871; REFLOOP' parsing loop, I changed the pattern to
expect at l east 9 spaces at the beginning of a line to
indicate line wrapping.
* Treat multi-line SOURCE sections correctly, this defect broke
both common_name() and classification()
* parse swissprot fields in genpept file
* parse WGS genbank records
- embl.pm
* Changed regexp for ID line. The capturing parentheses are
the same, the difference is an optional repeated-not-semi-
colon expression following the captured \S+. This means the
regexp works when the division looks like /PRO;/ or when the
division looks like /ANG ;/ - the latter is from EMBL
repbase
* fix ID line parsing: the molecule string can have spaces in
it. Like: "genomic DNA"
- swiss.pm: bugs #1727, #1734
- entrezgene.pm
* Added parser for entrezgene ASN1 (text format) files.
Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
o Bio::AlignIO
- maf.pm coordinate problem fixed
o Bio::Taxonomy and Bio::DB::Taxonomy
- Parse NCBI XML now so that nearly all the taxonomy up-and-down
can be done via Web without downloading all the sequence.
o Bio::Tools::Run::RemoteBlast supports more options and complies
to changes to the NCBI interface. It is reccomended that you
retrieve the data in XML instead of plain-text BLAST report to
insure proper parsing and retrieval of all information as NCBI
fully expects to change things in the future.
o Bio::Tree and Bio::TreeIO
- Fixes so that re-rooting a tree works properly
- Writing out nhx format from a newick/nexus file will properly output
bootstrap information. The use must move the internal node labels over
to bootstraps.
for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
$node->bootstrap($node->id);
$node->id('');
}
- Nexus parsing is much more flexible now, does not care about
LF.
- Cladogram drawing module in Bio::Tree::Draw
- Node height and depth now properly calculated
- fix tree pruning algorithm so that node with 1 child gets merged
o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
bugs and improvements were added, see Gbrowse mailing list for most of
these.
o Bio::DB::GFF partially supports GFF3. See information about
gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
o Better location parsing in Bio::Factory::FTLocationFactory -
this is part of the engine for parsing EMBL/GenBank feature table
locations. Nested join/order-by/complement are allowed now
o Bio::PrimarySeqI->translate now takes named parameters
o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
reconstruction) is now supported. Parsing different models and
branch specific parametes are now supported.
o Bio::Factory::FTLocationFactory - parse hierarchical locations
(joins of joins)
o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
for getter/setter functions
o Bio::SearchIO
- blast bug #1739; match scientific notation in score
and possible e+ values
- blast.pm reads more WU-BLAST parameters and parameters, match
a full database pathname,
- Handle NCBI WEB and newer BLAST formats specifically
(Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
- psl off-by-one error fixed
- exonerate parsing much improved, CIGAR and VULGAR can be parsed
and HSPs can be constructed from them.
- HSPs query/hit now have a seqdesc field filled out (this was
always available via $hit->description and
$result->query_description
- hmmer.pm can parse -A0 hmmpfam files
- Writer::GbrowseGFF more customizeable.
o Bio::Tools::Hmmpfam
make e-value default score displayed in gff, rather than raw score
allow parse of multiple records
1.5 Developer release
o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
provide Jukes-Cantor and Kimura pairwise distance methods,
respectively.
o Bio::AlignIO support for "po" format of POA, and "maf";
Bio::AlignIO::largemultifasta is a new alternative to
Bio::AlignIO::fasta for temporary file-based manipulation of
particularly large multiple sequence alignments.
o Bio::Assembly::Singlet allows orphan, unassembled sequences to
be treated similarly as an assembled contig.
o Bio::CodonUsage provides new rare_codon() and probable_codons()
methods for identifying particular codons that encode a given
amino acid.
o Bio::Coordinate::Utils provides new from_align() method to build
a Bio::Coordinate pair directly from a
Bio::Align::AlignI-conforming object.
o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
web service using standard Pubmed query syntax, and retrieve
results as XML.
o Bio::DB::GFF has various sundry bug fixes.
o Bio::FeatureIO is a new SeqIO-style subsystem for
writing/reading genomic features to/from files. I/O classes
exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
classes only read/write Bio::SeqFeature::Annotated objects.
Notably, the GFF v3 class requires features to be typed into the
Sequence Ontology.
o Bio::Graph namespace contains new modules for manipulation and
analysis of protein interaction graphs.
o Bio::Graphics has many bug fixes and shiny new glyphs.
o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
indexing for HMMER reports and FASTA qual files, respectively.
o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
new objects that can be placed within a Bio::Map::MapI-compliant
genetic/physical map; Bio::Map::Physical provides a new physical
map type; Bio::MapIO::fpc provides finger-printed clone mapping
import.
o Bio::Matrix::PSM provide new support for postion-specific
(scoring) matrices (e.g. profiles, or "possums").
o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
be instantiated without explicitly using Bio::OntologyIO. This
is possible through changes to Bio::Ontology::OntologyStore to
download ontology files from the web as necessary. Locations of
ontology files are hard-coded into
Bio::Ontology::DocumentRegistry.
o Bio::PopGen includes many new methods and data types for
population genetics analyses.
o New constructor to Bio::Range, unions(). Given a list of
ranges, returns another list of "flattened" ranges --
overlapping ranges are merged into a single range with the
mininum and maximum coordinates of the entire overlapping group.
o Bio::Root::IO now supports -url, in addition to -file and -fh.
The new -url argument allows one to specify the network address
of a file for input. -url currently only works for GET
requests, and thus is read-only.
o Bio::SearchIO::hmmer now returns individual Hit objects for each
domain alignment (thus containing only one HSP); previously
separate alignments would be merged into one hit if the domain
involved in the alignments was the same, but this only worked
when the repeated domain occured without interruption by any
other domain, leading to a confusing mixture of Hit and HSP
objects.
o Bio::Search::Result::ResultI-compliant report objects now
implement the "get_statistics" method to access
Bio::Search::StatisticsI objects that encapsulate any
statistical parameters associated with the search (e.g. Karlin's
lambda for BLAST/FASTA).
o Bio::Seq::LargeLocatableSeq combines the functionality already
found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
o Bio::SeqFeature::Annotated is a replacement for
Bio::SeqFeature::Generic. It breaks compliance with the
Bio::SeqFeatureI interface because the author was sick of
dealing with untyped annotation tags. All
Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
compliant, and accessible through Bio::Annotation::Collection.
o Bio::SeqFeature::Primer implements a Tm() method for primer
melting point predictions.
o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
o Bio::Taxonomy::Node now implements the methods necessary for
Bio::Species interoperability.
o Bio::Tools::CodonTable has new reverse_translate_all() and
make_iupac_string() methods.
o Bio::Tools::dpAlign now provides sequence profile alignments.
o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
parsers.
o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
for designing small inhibitory RNA.
o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
methods based on a distance matrix.
o Bio::Tree::Statistics provides an assess_bootstrap() method to
calculate bootstrap support values on a guide tree topology,
based on provided bootstrap tree topologies.
o Bio::TreeIO now supports the Pagel (PAG) tree format.
1.4 branch
1.4.1
o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
o Bio::Graphics will work with gd1 or gd2
o Bio::SearchIO
- hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
(RF lines alone)
- blast.pm Parse multi-line query fields properly
- small speed improvements to blasttable.pm and others
o Bio::DB::Taxonomy has better support for hierarchy traversal so that
Bio::Taxonomy::Node can be as simple as Bio::Species object while still
supporting more complex queries
1.4. Stable major release
Since initial 1.2.0, 3000 separate changes have been made to make this release.
o installable scripts
o global module version from Bio::Root:Version
o Bio::Graphics
- major improvements; SVG support
o Bio::Popgen
- population genetics
- support several population genetics types of questions.
- Tests for statistical neutrality of mutations
(Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
Tests of population structure (Wright's F-statistic: Fst) is in
Bio::PopGen::PopStats. Calculating composite linkage
disequilibrium (LD) is available in Bio::PopGen::Statistics as
well.
- Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
and csv (comma delimited formatted) data.
- a directory for implementing population simulations has
been added Bio::PopGen::Simulation and 2 simulations - a
Coalescent and a simple single-locus multi-allele genetic drift
simulation have been provided. This replaces the code in
Bio::Tree::RandomTree which has been deprecated until proper
methods for generating random phylogenetic trees are
implemented.
o Bio::Restriction
- new restrion analysis modules
o Bio::Tools::Analysis
- web based DNA and Protein analysis framework and several
implementations
o Bio::Seq::Meta
- per residue annotable sequences
o Bio::Matrix
- Bio::Matrix::PSM - Position Scoring Matrix
- Bio::Matrix::IO has been added for generalized parsing of
matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
initial implementations for parsing BLOSUM/PAM and Phylip
Distance matricies respectively. A generic matrix
implementation for general use was added in
Bio::Matrix::Generic.
o Bio::Ontology
- major changes
o Bio:Tree
o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
- small inhibitory RNA
o Bio::SeqFeature::Tools
- seqFeature mapping tools
- Bio::SeqFeature::Tools::Unflattener.pm
-- deal with mapping GenBank feature collections into
Chado/GFF3 processable feature sets (with SO term mappings)
o Bio::Tools::dpAlign
- pure perl dynamic programming sequence alignment
- needs Bioperl-ext
o new Bio::SearchIO formats
- axt and psl: UCSC formats.
- blasttable: NCBI -m 8 or -m 9 format from blastall
o new Bio::SeqIO formats
- chado, tab, kegg, tigr, game
- important fixes for old modules
o Bio::AlignIO: maf
o improved Bio::Tools::Genewise
o Bio::SeqIO now can recongnize sequence formats automatically from
stream
o new parsers in Bio::Tools:
Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
o Bio::DB::Registry bugs fixed
- BerkeleyDB-indexed flat files can be used by the OBDA system
- Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
used by the OBDA system
o several new HOWTOs
- SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
Databases
o hundreds of new and improved files
o
o Bio::Tree::AlleleNode has been updated to be a container of
an Bio::PopGen::Individual object for use in the Coalescent simulations.
1.2 Branch
1.2.3 Stable release update
o Bug #1475 - Fix and add speedup to spliced_seq for remote location
handling.
o Bug #1477 - Sel --> Sec abbreviation fixed
o Fix bug #1487 where paring in-between locations when
end < start caused the FTLocationFactory logic to fail.
o Fix bug #1489 which was not dealing with keywords as an
arrayref properly (this is fixed on the main trunk because
keywords returns a string and the array is accessible via
get_keywords).
o Bio::Tree::Tree memory leak (bug #1480) fixed
Added a new initialization option -nodelete which
won't try and cleanup the containing nodes if this
is true.
o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
this was only present on the branch for the 1.2.1 and 1.2.2 series
- Also merged main trunk changes to the branch which make
newick -> nhx round tripping more effective (storing branch length
and bootstrap values in same locate for NodeNHX and Node
implementations.) Fixes to TreeIO parsing for labeled internal
also required small changes to TreeIO::nhx. Improved
tests for this module as well.
o Bio::SearchIO
- Fixed bugs in BLAST parsing which couldn't parse NCBI
gapped blast properly (was losing hit significance values due to
the extra unexpeted column).
- Parsing of blastcl3 (netblast from NCBI) now can handle case of
integer overflow (# of letters in nt seq dbs is > MAX_INT)
although doesn't try to correct it - will get the negative
number for you. Added a test for this as well.
- Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
has no top-level family classification scores but does have scores and
alignments for individual domains.
- Parsing FASTA reports where ungapped percent ID is < 10 and the
regular expression to match the line was missing the possibility of
an extra space. This is rare, which is why we probably did not
catch it before.
- BLAST parsing picks up more of the statistics/parameter fields
at the bottom of reports. Still not fully complete.
- SearchIO::Writer::HTMLResultWriter and TextResultWriter
were fixed to include many improvements and added flexiblity
in outputting the files. Bug #1495 was also fixed in the process.
o Bio::DB::GFF
- Update for GFF3 compatibility.
- Added scripts for importing from UCSC and GenBank.
- Added a 1.2003 version number.
o Bio::Graphics
- Updated tutorial.
- Added a 1.2003 version number.
o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
properly writing keywords out.
o Bio::SeqIO::genbank
- Fixed bug/enhancement #1513 where dates of
the form D-MMM-YYYY were not parsed. Even though this is
invalid format we can handle it - and also cleanup the date
string so it is properly formatted.
- Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
and written with Genbank format. Similarly bug #1515 is fixed to
parse in the ORIGIN text.
o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
to specify the ID type, one of (accession accession.version
display primary). See Bio::SeqIO::preferred_id_type method
documentation for more information.
o Unigene parsing updated to handle file format changes by NCBI
1.2.2 Stable release update