Core 1.0.2 1.1.0 delta

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These are detailed notes on changes made between bioperl-release-1-0-2 and bioperl-release-1-1-0.

Bio::Align::DNAStatistics
Descriptions and more importantly words of warning
Bio::Align::Utilities
Doc fix
Bio::AlignIO::phylip
Provide linebreaks for molphy format
Bio::Cluster::UniGene
Methods now return undef instead of stringified hash ref when no value is present
Added MGI method for use with mouse unigene data files.
Bio::Cluster::UniGeneI
Added MGI method for use with mouse unigene data files.
Bio::ClusterIO::dbsnp
Fixed an AUTOLOAD bug
Bio::ClusterIO::unigene
Fixed bug which caused regexes to be precompiled twice.
Bio::DB::Fasta
PrimarySeq::Fasta needs to implement the method 'desc'
Bio::DB::GFF
Changed redundant definition of display_name() to description() so that code matches docs
Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?
Updates & improvements to the glyphs. Added missing methods to Bio::DasI.
Migrating fix 1.52.2.5 to trunk.
Bio::DB::GFF::Adaptor::dbi
Changed redundant definition of display_name() to description() so that code matches docs
Handle case of password but no username
Bio::DB::GFF::Adaptor::dbi::mysql
Changed redundant definition of display_name() to description() so that code matches docs
Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?
Bio::DB::GFF::Adaptor::dbi::mysqlopt
Fixed problems with merged_segments() subroutine which became apparent when EST alignments got messier; added a pleasantly simple histogram routine to the GFF database
Bio::DB::GFF::Aggregator
Changed redundant definition of display_name() to description() so that code matches docs
Bio::DB::GFF::Aggregator::alignment
Changed redundant definition of display_name() to description() so that code matches docs
Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?
Bio::DB::GFF::Aggregator::clone
Changed redundant definition of display_name() to description() so that code matches docs
Bio::DB::GFF::Aggregator::transcript
Changed redundant definition of display_name() to description() so that code matches docs
Bio::DB::GFF::Feature
Fixed problems with merged_segments() subroutine which became apparent when EST alignments got messier; added a pleasantly simple histogram routine to the GFF database
Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?
Updates & improvements to the glyphs. Added missing methods to Bio::DasI.
Bio::DB::GFF::RelSegment
Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?
Improved semantics of abs_start() and abs_end() calls for gadfly compatibility
Bio::DB::GFF::Segment
Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?
Improved semantics of abs_start() and abs_end() calls for gadfly compatibility
Cleaned up biographics keyhandling; added a -desc argument to the bio::graphics::feature object
Bio::DasI
This will go away eventuall - SeqFeature::CollectionI to replace eventually
Updates & improvements to the glyphs. Added missing methods to Bio::DasI.
Bio::DescribableI
First commits of describable and identifiable interfaces - primaryseqI modified
Small mostly cosmetic changes (like, added $ID$ line etc).
Changed redundant definition of display_name() to description() so that code matches docs
Bio::Factory::EMBOSS
Double quote to see the variable's value
Bio::Factory::FTLocationFactory
Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.
Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.
Bio::Factory::LocationFactoryI
Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.
Bio::Factory::SequenceFactoryI
Documentation fixes
Bio::Graphics::Feature
Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?
Updates & improvements to the glyphs. Added missing methods to Bio::DasI.
Cleaned up biographics keyhandling; added a -desc argument to the bio::graphics::feature object
Bio::Graphics::FeatureFile
Cleaned up biographics keyhandling; added a -desc argument to the bio::graphics::feature object
Bio::Graphics::Glyph
Changed redundant definition of display_name() to description() so that code matches docs
Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?
Bio::Graphics::Glyph::cds
Updates & improvements to the glyphs. Added missing methods to Bio::DasI.
Bio::Graphics::Glyph::diamond
Changed redundant definition of display_name() to description() so that code matches docs
Bio::Graphics::Glyph::dna
Updates & improvements to the glyphs. Added missing methods to Bio::DasI.
Bio::Graphics::Glyph::generic
Changed label() code so that display_id() is preferred over the seqname()
Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?
Updates & improvements to the glyphs. Added missing methods to Bio::DasI.
Bio::Graphics::Glyph::graded_segments
Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?
Bio::Graphics::Glyph::translation
Updates & improvements to the glyphs. Added missing methods to Bio::DasI.
Bio::Graphics::Glyph::triangle
Changed redundant definition of display_name() to description() so that code matches docs
Bio::Graphics::Panel
Fixed stupid error in which pad_left was used instead of pad_right, rendering pad_right unusable
Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?
Updates & improvements to the glyphs. Added missing methods to Bio::DasI.
Cleaned up biographics keyhandling; added a -desc argument to the bio::graphics::feature object
Bio::IdCollectionI
The IdCollectionI interface supports objects with multiple ids
Bio::IdentifiableI
First commits of describable and identifiable interfaces - primaryseqI modified
Small mostly cosmetic changes (like, added $ID$ line etc).
Changed redundant definition of display_name() to description() so that code matches docs
Bio::Location::Fuzzy
Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.
Bio::Location::Simple
Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.
Bio::Location::Split
Undo commented region so that we fix reported FThelper writing problem
Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.
Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.
Need to check is_remote() before propagating strand to a subloc.
Bio::LocationI
Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.
Bio::PrimarySeq
First commits of describable and identifiable interfaces - primaryseqI modified
Bio::PrimarySeqI
First commits of describable and identifiable interfaces - primaryseqI modified
Support desc and description per the identifier interface
Bio::Root::Err
Http://bio.perl.org/Core/Examples no longer exists, the scripts are in examples/
Bio::Root::IO
No msgs on undefined CLEANUP
Bio::Root::Root
Added _load_module().
Propagated Lincoln's untainting fix to SeqIO module loading. _load_module() now throws an exception if name not legal.
Bio::Root::RootI
Migrating commit 1.47.2.7 on branch-1-0-0 to trunk
Bio::Root::Vector
Http://bio.perl.org/Core/Examples no longer exists, the scripts are in examples/
Bio::Search::HSP::BlastHSP
The regexp in _set_seq inserted an extra space on the end of each alignment line. In _set_residues(), these lines get concatenated together but the blank space still remains between each line. This screws up the generation of the $identicalList_query, $identicalList_sbjct, etc., because the characters in the query and sbjct sequences (with spaces) don't line up with the match line sequence (which, because it's parsed differently doesn't have the spaces). I was getting incorrect seq_inds() coordinates because of this.
The regexp in _set_seq inserted an extra space on the end of each alignment line. In _set_residues(), these lines get concatenated together but the blank space still remains between each line. This screws up the generation of the $identicalList_query, $identicalList_sbjct, etc., because the characters in the query and sbjct sequences (with spaces) don't line up with the match line sequence (which, because it's parsed differently doesn't have the spaces). I was getting incorrect seq_inds() coordinates because of this.
Bio::Search::HSP::GenericHSP
Changes for WABA parsing and inheritance fixes with SeqFeature::SimilarityPair
Moved some BlastXX methods over
Bio::Search::HSP::WABAHSP
Changes so that WABAs output more-or-less informatively
Bio::Search::Hit::BlastHit
After discussion with steve chervitz, decided that frac_identical and frac_conserved would be better off returning a fraction with 3 digits of precision (rather than 2). I also changed these functions so that the never round up to 100%, in other words, .9997 gets rounded off to .999 rather than 1.000
Bio::Search::Hit::GenericHit
Moved some BlastXX methods over
Bio::SearchIO
Doc bug fixed
Doc bug fixed
Bio::SearchIO::FastHitEventBuilder
Fast Event processor which does not handle HSPs for fast skims
Set query length in the Hit for the sake of logical length code
Bio::SearchIO::SearchResultEventBuilder
Set query length in the Hit for the sake of logical length code
Bio::SearchIO::blast
Support parsing of RPS-BLAST
Remove test for /Score/ in query description parsing to deal with people putting weird things in their blast db descriptions
Bio::SearchIO::blastxml
Set query length in the Hit for the sake of logical length code
Bio::SearchIO::waba
Set reporttype
Bio::Seq
Added mention of LocationI and Location::SplitLocationI
Bio::Seq::PrimedSeq
These are the early versions of this. I am actively working on these at the moment and will be continuing over the next several days.
Substantial revisions in the way things are behaving. This thing is shaping up nicely. Far too many changes to document here. Things that are yet to be done: 1. Implement RangeI methods in SeqFeature::Primer 2. complete tests 3. implement negative testing. "only tests that throw are successful, grasshopper." 4. fix primer3 test so that the stream itself is tested. 5. decide on a proper ID scheme.
Bio::Seq::SeqFactory
Test that type which factory is asked to instantiate is-a Bio::PrimarySeqI
For now allow SeqFactory to accept Bio::Seq::QualI objects as well as Bio::PrimarySeqI types for creation
Bio::SeqFeature::CollectionI
Initial collection interface -- will change
Bio::SeqFeature::Computation
Inheritance fixes -- improvements to computation
Bio::SeqFeature::Generic
Inheritance fixes -- improvements to computation
Repaired spelling error in documentation.
Bio::SeqFeature::Primer
These are the early versions of this. I am actively working on these at the moment and will be continuing over the next several days.
Substantial revisions in the way things are behaving. This thing is shaping up nicely. Far too many changes to document here. Things that are yet to be done: 1. Implement RangeI methods in SeqFeature::Primer 2. complete tests 3. implement negative testing. "only tests that throw are successful, grasshopper." 4. fix primer3 test so that the stream itself is tested. 5. decide on a proper ID scheme.
More fun implementing interfaces. Whoooey, is this a good time.
Altered some of the RangeI-implementing methods in Primer.pm. Discovered a hideous fault in Consed and fixed it. (set_contig_quality doubles quality values if called) Mangled Trim.pm in slight ways to figure out what was broken in Consed. Working on nicer tests for primer3.
Bio::SeqFeature::Similarity
Inheritance fixes -- improvements to computation
Bio::SeqFeature::SimilarityPair
Inheritance fixes -- improvements to computation
Bio::SeqFeatureI
Added a display_id() method to Bio::SeqFeatureI (needs it) and enhanced Aggregator API to accept complex aggregator notation -- perhaps we should call it an aggravator?
Repaired spelling error in documentation. ('implementation')
Bio::SeqIO
Small mostly cosmetic changes (like, added $ID$ line etc).
Link to fh
Updates & improvements to the glyphs. Added missing methods to Bio::DasI.
Adapted to use _load_module() in Root.pm.
Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.
Bio::SeqIO::FTHelper
Added $location->strand setting for sublocations in a split location
Undo chris's changes
Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.
Bio::SeqIO::bsml
Updates & improvements to the glyphs. Added missing methods to Bio::DasI.
_initialize() got duplicated a while back when SeqFactory methods were added - moved the appropriate code to the right version of _initialize.
Bio::SeqIO::embl
Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.
Bio::SeqIO::fasta
Programatically set the sequence width
Bio::SeqIO::genbank
Fixed missing GI bug for buggy records without versions tested on 20,000 sequences
Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.
Bio::SeqIO::phd
phd.pm was not getting the proper $id. trim.pm was not returning proper trimpoints from trim_singlet() both are 'fixed' now.
These are the early versions of this. I am actively working on these at the moment and will be continuing over the next several days.
Bio::SeqIO::primer3
These are really rough starts for a module that will read primer3 outfiles and return Bio::SeqFeature::Primer objects. I will commit Bio::SeqFeature::Primer later today, I hope. This tests successfully and generally works but really is a work in progress.
These are the early versions of this. I am actively working on these at the moment and will be continuing over the next several days.
Substantial revisions in the way things are behaving. This thing is shaping up nicely. Far too many changes to document here. Things that are yet to be done: 1. Implement RangeI methods in SeqFeature::Primer 2. complete tests 3. implement negative testing. "only tests that throw are successful, grasshopper." 4. fix primer3 test so that the stream itself is tested. 5. decide on a proper ID scheme.
Bio::SeqIO::swiss
The annotation object wasn't being correctly attached to the new seqs.
Adapted FTHelper and the parsers for genbank, embl, and swissprot to utilize the new LocationFactoryI framework for location parsing. All tests pass, which is no guarantee for complete coverage of location string space.
Bio::SimpleAlign
Moved comments to notes so they show up in perldoc
Bio::Structure::Atom
Added methods for segID and saner atomname writing
Bio::Structure::IO::pdb
- segID reading / writing added - better (correct ?) ATOM name writing - sane placement of TER record - fixed bug when writing continuation lines
Bio::Tools::Alignment::Consed
Altered some of the RangeI-implementing methods in Primer.pm. Discovered a hideous fault in Consed and fixed it. (set_contig_quality doubles quality values if called) Mangled Trim.pm in slight ways to figure out what was broken in Consed. Working on nicer tests for primer3.
Bio::Tools::Alignment::Trim
phd.pm was not getting the proper $id. trim.pm was not returning proper trimpoints from trim_singlet() both are 'fixed' now.
Altered some of the RangeI-implementing methods in Primer.pm. Discovered a hideous fault in Consed and fixed it. (set_contig_quality doubles quality values if called) Mangled Trim.pm in slight ways to figure out what was broken in Consed. Working on nicer tests for primer3.
Bio::Tools::BPpsilite
Some updates so the CPAN rendered modules have the correct name
Bio::Tools::Blast
Http://bio.perl.org/Core/Examples no longer exists, the scripts are in examples/
Some updates so the CPAN rendered modules have the correct name
Bio::Tools::GFF
Indented some code
Bio::Tools::Phylo::Molphy
Added Molphy parser (only tested on protml)
Need IO::String
Bio::Tools::Phylo::Molphy::Result
Added Molphy parser (only tested on protml)
Bio::Tools::Phylo::PAML
Implement seqtype CODONML parsing
NG parser more intelligent
Bio::Tools::Phylo::PAML::Result
Implement seqtype CODONML parsing
Bio::Tools::Primer3
Put this in the new place as discussed on Bioperl-l. Added things that broke when it moved from under the umbrella of SeqIO.
Bio::Tools::RestrictionEnzyme
Migrating fix 1.19.2.2 to trunk.
Added Ryan's enzymes
Bio::Tools::Run::WrapperBase
Base for runnable wrappers
Doc fix, default value of for error_string, leading underscore for private data
Cleanup of tempfiles works
Bio::Tools::SeqAnal
Some updates so the CPAN rendered modules have the correct name
Bio::Tools::Sigcleave
Some updates so the CPAN rendered modules have the correct name
Bio::Tools::Sim4::Results
Estisfirst -> estfirst
Bio::Tools::WWW
Some updates so the CPAN rendered modules have the correct name
Bio::Tree::Node
Fixes to ancestor (couldn't set value) and description (_desription -> _desc) subs
Completed depth/breadth 'order' option for get_nodes(); added 'sortby' option for get_Descendents and each_Descendent: takes 'height', 'creation' or coderef to be used for sorting
Bio::Tree::NodeI
Tree builder event handler made aware of nodetype/treetype arguments (to implement a node/tree factory); NHX tree format added; Tree::NodeNHX node type added (for nhx tag storage); TreeEventBuilder made NHX tag aware, and able to handle nonbinary trees; basic testing added.
Completed depth/breadth 'order' option for get_nodes(); added 'sortby' option for get_Descendents and each_Descendent: takes 'height', 'creation' or coderef to be used for sorting
Placeholder warnings about height() method yielding incorrect answers for anything but binary trees ... will fixup after discussions at BOSC
Bio::Tree::NodeNHX
Add to repository
Quote hash keys for backward compatibility
Bio::Tree::Tree
Tree builder event handler made aware of nodetype/treetype arguments (to implement a node/tree factory); NHX tree format added; Tree::NodeNHX node type added (for nhx tag storage); TreeEventBuilder made NHX tag aware, and able to handle nonbinary trees; basic testing added.
Completed depth/breadth 'order' option for get_nodes(); added 'sortby' option for get_Descendents and each_Descendent: takes 'height', 'creation' or coderef to be used for sorting
New functions - split to new module (monophyly test and find_node)
Added score and id capability
Placeholder warnings about height() method yielding incorrect answers for anything but binary trees ... will fixup after discussions at BOSC
Bio::Tree::TreeFunctionsI
New functions - split to new module (monophyly test and find_node)
Fixed is_monophyletic thx to Justin Reese
Test of paraphyly added
Bio::Tree::TreeI
Added score and id capability
Placeholder warnings about height() method yielding incorrect answers for anything but binary trees ... will fixup after discussions at BOSC
Bio::TreeIO
Tree builder event handler made aware of nodetype/treetype arguments (to implement a node/tree factory); NHX tree format added; Tree::NodeNHX node type added (for nhx tag storage); TreeEventBuilder made NHX tag aware, and able to handle nonbinary trees; basic testing added.
Bio::TreeIO::TreeEventBuilder
Tree builder event handler made aware of nodetype/treetype arguments (to implement a node/tree factory); NHX tree format added; Tree::NodeNHX node type added (for nhx tag storage); TreeEventBuilder made NHX tag aware, and able to handle nonbinary trees; basic testing added.
Bio::TreeIO::nhx
Tree builder event handler made aware of nodetype/treetype arguments (to implement a node/tree factory); NHX tree format added; Tree::NodeNHX node type added (for nhx tag storage); TreeEventBuilder made NHX tag aware, and able to handle nonbinary trees; basic testing added.
Bio::TreeIO::tabtree
Made tabtree.pm know about nonbinary trees ...
Bio::Variation::SNP
Fixed an AUTOLOAD bug
FAQ
How do I parse CDS join() statements in Genbank or EMBL...
Motifs and agrep, minor changes
Makefile.PL
ExtUtils::MakeMaker provides a prompt function
1.1 release version for makefile
biodesign.pod
Mention howto, minor changes
bioperl.lisp
Small mostly cosmetic changes (like, added $ID$ line etc).
Added Bio::Factory::LocationFactoryI with one method (so far) from_string(). Added implementation for Genbank-compatible feature table location strings, which is a complete rewrite of the location parsing code. Also, added test LocationFactory.t. Tests pass.
bioperl.pod
Added waba2gff.pl
Added script parse_codeml.pl
Dan's script...
Added description of longorf.pl
New revcom_dir location
bptutorial.pl
SearchIO supports RPS-BLAST, minor changes
Added mention of LocationI and Location::SplitLocationI
Added example for changing CGI parameter using RemoteBlast
Space before comma allows URL to work
examples/gb2features.pl
Dan's script...
examples/longorf.pl
Dan's script...
Minor changes
Minor change
scripts/feature_draw.pl
Cleaned up biographics keyhandling; added a -desc argument to the bio::graphics::feature object
scripts/parse_codeml.pl
Example of parsing codeml results
Print some more info
scripts/render_sequence.pl
Cleaned up biographics keyhandling; added a -desc argument to the bio::graphics::feature object
scripts/revcom_dir.pl
New location
scripts/waba2gff.pl
Convert raw waba to one type of GFF (not necessarily sanger output from WABA storage)
Support infile passing on cmd line with no argument
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