Core 1.2.0 1.2.1 delta

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

Bio::AlignIO::bl2seq
Pass in report_type to bl2seq -- for now, until we get patches to auto-detect
Bio::AlignIO::clustalw
Pass the verbosity down
Bio::AlignIO::phylip
Sunday morning Issue #1373
Merge changes for Issue #1373 onto branch
Parse interleaved files where id and first sequence bit run into one another
Bio::AlignIO::psi
Update documentation
Bio::AlignIO::stockholm
Fix to allow AlignIO to read multiple stockholm format entries from a file. Contributed by Andreas Kahari
Fix to allow AlignIO to read multiple stockholm format entries from a file. Contributed by Andreas Kahari
Bio::AlternativeLocationHolderI
Added speculative code for multiple alternative feature locations
Bio::AnalysisI
Added interfaces AnalysisI and Factory::AnalysisI; the rest goes to Bio::Tools::Run in bioperl-run
Bio::Annotation::DBLink
Now a GloballyIdentifiableI (was an IdentifiableI)
Bio::Annotation::OntologyTerm
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Bio::Annotation::SimpleValue
Sync'ed RichSeqI with the implementation. RichSeq provides backward compatibility to the old API. Fixed doc bug in SimpleValue.
Migrated 1.9->1.10 (doc bug fix).
Bio::Cluster::ClusterFactory
Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).
Bio::Cluster::UniGene
Made the species map current with NCBI's repository of UniGene sequences.
Migrated fix to UniGene to make species list current.
Documentation change only; reflects being a GloballyIdentifiableI versus an IdentifiableI
Bio::ClusterIO
Fixed Issue #1369
Fixed Issue #1369 on branch.
Bio::ClusterIO::unigene
(on branch) fix Issue #1370, parse Celegans cluster IDs which have 3 letters instead of 2
Fix Issue #1370, parse Celegans cluster IDs which have 3 letters instead of 2
Bio::Coordinate::Collection
Upgrade to handle split locations. They are needed for example to map features from cds to genomic level with all details. Next todo: documentation!
Deep cloning of mapper elements to make them independet of each other, merge split sub locations when they are adjacent to each other.
Cleaning, adding documentation
Moving fully functional coordinate code from head
Make error message informative
Make sure err msg is informative
Bio::Coordinate::ExtrapolatingPair
Fix chr<->gene coordinates when gene is on reverse strand
Upgrade to handle split locations. They are needed for example to map features from cds to genomic level with all details. Next todo: documentation!
Deep cloning of mapper elements to make them independet of each other, merge split sub locations when they are adjacent to each other.
Cleaning, adding documentation
Moving fully functional coordinate code from head
Bio::Coordinate::GeneMapper
Upgrade to handle split locations. They are needed for example to map features from cds to genomic level with all details. Next todo: documentation!
Deep cloning of mapper elements to make them independet of each other, merge split sub locations when they are adjacent to each other.
Cleaning, adding documentation
Cleaning code and documentation
Moving fully functional coordinate code from head
three fixes: 1. Constructor was reading the parameters in wrong order 2. exons() defaulted strand in one mapper to 1 3. map() returned split locations with only only one sublocation and a feature enhancement: 4. if you did not define cds() you got the split locations in reverse strand back in reverse order. Now exons() calls cds() automatically and sets it to span all the exons.
Fixes from HEAD
Doc fix, mispelling
Bio::Coordinate::Graph
Cleaning, adding documentation
Moving fully functional coordinate code from head
Bio::Coordinate::Pair
Upgrade to handle split locations. They are needed for example to map features from cds to genomic level with all details. Next todo: documentation!
Cleaning, adding documentation
Moving fully functional coordinate code from head
Bio::Coordinate::Result
Deep cloning of mapper elements to make them independet of each other, merge split sub locations when they are adjacent to each other.
Cleaning, adding documentation
Moving fully functional coordinate code from head
Bio::Coordinate::Result::Gap
Cleaning, adding documentation
Moving fully functional coordinate code from head
Bio::Coordinate::Result::Match
Cleaning, adding documentation
Moving fully functional coordinate code from head
Bio::Coordinate::ResultI
Initial commit
Moved from head
Bio::Coordinate::Utils
Cleaning, adding documentation
Moving fully functional coordinate code from head
Bio::DB::Ace
Old school - changed from -type to -alphabet
Bio::DB::AggregatingFeatureProviderI
A Bio::DB::FeatureProviderI with additional methods to support the use of Bio::SeqFeature::AggregatorI objects for creating meta-features.
Bio::DB::BioFetch
Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both
Changed config biodbname -> dbname according to new OBDA specs
Added some OBDA documentation plus flat file index load script
Added new heading to biodatabase access doc for Heikki to fill in
Added the dbfetch script
Added a forward-compatibility type() method to Segment
Bio::DB::Failover
Use accession when fetching by accession
Bio::DB::Fasta
Begin addressing concern raised in Issue #1363
Bio::DB::FeatureProviderI
New interfaces; initial docs are in the cvs add.
Minor bugfix
Minor updates
Bio::DB::FileCache
Fix Issue #1376; Make sure we use Bio::Species
Make sure we use Bio::Species
Linewraps
Bio::DB::Flat
Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both
Fixed multiple feature inconsistencies between the bdb and binary search versions of the flat databases
ODBA flat file indexers support swiss,fasta,genbank and embl formats
Added some OBDA documentation plus flat file index load script
Make creating directory information quieter
Bio::DB::Flat::BDB
Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both
Fixed multiple feature inconsistencies between the bdb and binary search versions of the flat databases
Added some OBDA documentation plus flat file index load script
Respect wantarray
Merge improvements from main trunk
Bio::DB::Flat::BDB::embl
Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both
Fixed multiple feature inconsistencies between the bdb and binary search versions of the flat databases
Added some OBDA documentation plus flat file index load script
Bio::DB::Flat::BDB::fasta
Added some OBDA documentation plus flat file index load script
Bio::DB::Flat::BDB::genbank
ODBA flat file indexers support swiss,fasta,genbank and embl formats
Added some OBDA documentation plus flat file index load script
Bio::DB::Flat::BDB::swiss
Check in reasonable howtos for database access and flat databases
Bio::DB::Flat::BDB::swissprot
Added some OBDA documentation plus flat file index load script
Bio::DB::Flat::Binary
Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both
Added some more verbiage to OBDA HOWTO
Bio::DB::Flat::BinarySearch
Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both
Fixed multiple feature inconsistencies between the bdb and binary search versions of the flat databases
Tighten up code, allow cross-platform ability w/ Bio::Root::IO->catfile
ODBA flat file indexers support swiss,fasta,genbank and embl formats
Added some OBDA documentation plus flat file index load script
Code cleanup, documentation added to many more APIs and tests should now pass
Bio::DB::Flat::OBDAIndex
Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both
Bio::DB::GFF
Added some more explanation about how group fields work in GFF2.
Joyous (initial) integration with the collection consolodation
Fixed uc/lc bug in aggregator names; added ability to specify BioGraphics fonts as strings
Bio::DB::GFF::Adaptor::dbi::mysql
Removed binary from the declaration of gname, since most people do not expect object names to be case sensitive
Bio::DB::GFF::Aggregator
Now isa Bio::SeqFeature::AggregatorI
Fixed uc/lc bug in aggregator names; added ability to specify BioGraphics fonts as strings
Bio::DB::GFF::Aggregator::none
Overrides disaggregate_types instead of disaggregate
Bio::DB::GFF::Aggregator::ucsc_acembly
Refining source/method tags for faster querying w/ new gbrowse
Bio::DB::GFF::Aggregator::ucsc_ensgene
Refining source/method tags for faster querying w/ new gbrowse
Bio::DB::GFF::Aggregator::ucsc_genscan
Refining source/method tags for faster querying w/ new gbrowse
Bio::DB::GFF::Aggregator::ucsc_refgene
Refining source/method tags for faster querying w/ new gbrowse
Bio::DB::GFF::Aggregator::ucsc_sanger22
Refining source/method tags for faster querying w/ new gbrowse
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo
Refining source/method tags for faster querying w/ new gbrowse
Bio::DB::GFF::Aggregator::ucsc_softberry
Refining source/method tags for faster querying w/ new gbrowse
Bio::DB::GFF::Aggregator::ucsc_twinscan
Refining source/method tags for faster querying w/ new gbrowse
Bio::DB::GFF::Aggregator::ucsc_unigene
Refining source/method tags for faster querying w/ new gbrowse
Bio::DB::GFF::Featname
Joyous (initial) integration with the collection consolodation
Bio::DB::GFF::Feature
Added attach_seq() dummy method
Initial attempt to merge this into the collection consolodation. Note that RelSegment is now obsolete.
Joyous (initial) integration with the collection consolodation
Bio::DB::GFF::Homol
Joyous (initial) integration with the collection consolodation
Bio::DB::GFF::RelSegment
Now obsolete. TO BE REMOVED.
Bio::DB::GFF::Segment
Added a forward-compatibility type() method to Segment
Initial attempt to merge this into the collection consolodation.
Joyous (initial) integration with the collection consolodation
Added primary_seq() method to Bio::DB::GFF::Segment
Bio::DB::GFF::Typename
Joyous (initial) integration with the collection consolodation
Bio::DB::GFFI
Interface for GFF.pm, was DasI.pm, now isa thin addition to Bio::DB::SegmentProviderI and Bio::DB::AggregatingFeatureProviderI
Bio::DB::NCBIHelper
Hedge bets and use full URL
Hedge bets and use full URL
Bio::DB::Query::GenBank
Get_Ids -> ids
Bio::DB::Registry
Renamed OBDAIndex.pm => BinarySearch.pm and got Bio::DB::Flat to work uniformly with both
* finds seqdatabase.ini from directory in env variable $BIOINFORMATICS * if ini file not found from local directories, copies the default one from net into users home directory
Added some more verbiage to OBDA HOWTO
ODBA flat file indexers support swiss,fasta,genbank and embl formats
Changes to conform to OBDA specs 1.00
Made registry keywords case insensitive by lowercasing them all
Added a forward-compatibility type() method to Segment
Bio::DB::SegmentProviderI
An interface for objects that are both Bio::DB::SequenceProviderIs and Bio::DB::FeatureProviderIs.
An interface for objects that are both Bio::DB::SequenceProviderIs and Bio::DB::FeatureProviderIs.
Minor updates
Bio::DB::SeqI
Minor bugfix: documentation only
Bio::DB::SequenceProviderI
A provider of Bio::PrimarySeqI objects.
Minor updates
Made get_PrimarySeq_stream an alias to whatever get_Seq_stream happens to be, as opposed to a glob ref alias, which isn't very OO-friendly
Bio::DB::SimpleFeatureProvider
A simple implementation of Bio::DB::FeatureProviderI with an in-memory backing store, for testing purposes.
Bio::DB::Taxonomy
Added taxonomy database interface (API subject to change some)
Bio::DB::Taxonomy::entrez
Entrez driver to Taxonomy DB
Bio::DB::WebDBSeqI
Added the dbfetch script
Not very pretty fix to eliminate empty lines returned and keep seqio happy
Removing gimmicks, bug fixed neatly by fasta module commit
Bio::DB::XEMBL
Added some more verbiage to OBDA HOWTO
Added some OBDA documentation plus flat file index load script
Bio::DasI
Interface for Das.pm, was the sole interface for a lot of things; now isa thin addition to Bio::DB::SegmentProviderI and Bio::DB::AggregatingFeatureProviderI
Bio::Factory::AnalysisI
Added interfaces AnalysisI and Factory::AnalysisI; the rest goes to Bio::Tools::Run in bioperl-run
Bio::Factory::EMBOSS
Moving to bioperl-run CVS module
Bio::Factory::ObjectFactory
Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Factory::SeqAnalysisParserFactory
Copied method docs from superclass
Bio::GloballyIdentifiableI
New interfaces; initial docs are in the cvs add.
Bio::Graphics
Cleared up RangeI confusion in synopsis
Bio::Graphics::ConfiguratorI
New interfaces; initial docs are in the cvs add.
Merged speculative changes to bio::graphics into main trunk; regression tests 2&3 will fail; need to be fixed
Bio::Graphics::Feature
Added a redgreen gradient glyph suitable for representing microarray data in genomic context
Bio::Graphics::FeatureFile
Added a redgreen gradient glyph suitable for representing microarray data in genomic context
Made redgreen_box glyph work nicely with feature file
Made Bio::Graphics::FeatureFile compatible with Bio::SeqFeature::Generic
Added web-based feature renderer to script repository; expanded FeatureFile format so that the same feature can appear in multiple tracks
Bio::Graphics::Glyph
Added option for sorting features by name
Fixing obscure bugs in bio::graphics; one change will break regression tests 1-3 temporarily
Merged speculative changes to bio::graphics into main trunk; regression tests 2&3 will fail; need to be fixed
Fixed uc/lc bug in aggregator names; added ability to specify BioGraphics fonts as strings
Added flip parameter to biographics for drawing in minus strand coordinates
Bio::Graphics::Glyph::Factory
Added flip parameter to biographics for drawing in minus strand coordinates
Bio::Graphics::Glyph::arrow
Added flip parameter to biographics for drawing in minus strand coordinates
Bio::Graphics::Glyph::cds
Added sixframe option to cds glyph
Debugging sixframe option
Debugging sixframe option
Bio::Graphics::Glyph::dna
Checked in changes to dna.pm to allow to work with vanilla Bio::SeqFeatureI objects (rather than broken Bio::DB::GFF::Features).
Merged speculative changes to bio::graphics into main trunk; regression tests 2&3 will fail; need to be fixed
Added some more verbiage to OBDA HOWTO
Bio::Graphics::Glyph::extending_arrow
Deprecated extending_arrow; will send message to Shengqiang asking to fix
Merged speculative changes to bio::graphics into main trunk; regression tests 2&3 will fail; need to be fixed
Bio::Graphics::Glyph::generic
Fixed display_name() seqid() discrepancy
Fixed uc/lc bug in aggregator names; added ability to specify BioGraphics fonts as strings
Added flip parameter to biographics for drawing in minus strand coordinates
Bio::Graphics::Glyph::graded_segments
Added a redgreen gradient glyph suitable for representing microarray data in genomic context
Bio::Graphics::Glyph::redgreen_box
Added a redgreen gradient glyph suitable for representing microarray data in genomic context
Made redgreen_box glyph work nicely with feature file
Bio::Graphics::Glyph::transcript
Added flip parameter to biographics for drawing in minus strand coordinates
Bio::Graphics::Glyph::transcript2
Added flip parameter to biographics for drawing in minus strand coordinates
Bio::Graphics::Glyph::xyplot
Added the xyplot glyph
Bio::Graphics::Panel
Fixed Biographics crash when using a v1.2 Bio::Seq as the coordinate system for a panel
Fixed error in calculation of starting coordinate when passing a segment to Panel
Cleared up RangeI confusion in synopsis
Fixing obscure bugs in bio::graphics; one change will break regression tests 1-3 temporarily
Merged speculative changes to bio::graphics into main trunk; regression tests 2&3 will fail; need to be fixed
Bio::graphics fixes for cases in which the subfeatures do not reach the end of the feature, and the end of the feature is >= the border of the panel
Added a redgreen gradient glyph suitable for representing microarray data in genomic context
Added the xyplot glyph
Added flip parameter to biographics for drawing in minus strand coordinates
Added public method for mapping feature coordinates into pixel coordinates
Bio::Graphics::RendererI
New interfaces; initial docs are in the cvs add.
Merged speculative changes to bio::graphics into main trunk; regression tests 2&3 will fail; need to be fixed
Bio::IdCollectionI
Documentation changes only; changed IdentifiableI to LocallyIdentifiableI
Bio::Index::EMBL
Fixing Issue #1413
Fixing Issue #1413
Bio::LocallyIdentifiableI
New interfaces; initial docs are in the cvs add.
Bio::LocatableSeq
- silence spurious warnings in location_from_column() - correct trunc() documentation: arguments are column locatation not residues - fix trunc() for returned start positions - override revcom from Bio::PrimarySeqI to include start, end and strand
Fixes from HEAD
Bio::Location::Atomic
A bugfix in Atomic when a necessary Location class had not been use'd/require'd
Bio::Location::Simple
Modifications for GFF3
Merged my changes with Chris M's; not tested
Unecessary use stmt
Bio::Matrix::PhylipDist
Remove the _parse function -- avaiable through Bio::Tools::Phylo::Phylip::ProtDist
Removed _parse method - this is part of Tool::Phylo::Phylip::PhyloDist now
Bio::Ontology::GOterm
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.
Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::InterProTerm
Initial revision of SimpleOntologyEngine implementation of OntologyEngineI and the InterPro XML parser.
Commiting the latest changes to InterProParser, SimpleOntologyEngine and their respective test files.
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Bio::Ontology::Ontology
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.
Migrating one round of fixes and enhancements to the ontology modules to the branch.
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::OntologyEngineI
Added and updated a good deal of documentation. Fixed a bug in SimpleGOEngine.
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.
Migrating one round of fixes and enhancements to the ontology modules to the branch.
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::OntologyI
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.
Migrating one round of fixes and enhancements to the ontology modules to the branch.
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::OntologyStore
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::Path
Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.
Migrating one round of fixes and enhancements to the ontology modules to the branch.
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::PathI
Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.
Migrating one round of fixes and enhancements to the ontology modules to the branch.
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::Relationship
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.
Migrating one round of fixes and enhancements to the ontology modules to the branch.
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::RelationshipFactory
Forgot to commit the factory for relationships.
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::RelationshipI
Added and updated a good deal of documentation. Fixed a bug in SimpleGOEngine.
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::RelationshipType
Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.
Migrating one round of fixes and enhancements to the ontology modules to the branch.
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::SimpleGOEngine
Added and updated a good deal of documentation. Fixed a bug in SimpleGOEngine.
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.
Few fixes to remove assumptions on precise format of identifier. Added extensive tests for Sequence Ontology, which at the same time tests the SimpleGOEngine. All tests pass.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.
Migrating one round of fixes and enhancements to the ontology modules to the branch.
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::SimpleOntologyEngine
Initial revision of SimpleOntologyEngine implementation of OntologyEngineI and the InterPro XML parser.
Commiting the latest changes to InterProParser, SimpleOntologyEngine and their respective test files.
Removing terms that are repeated in the lists returned by get_ancestor_terms and get_descendant_terms.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.
Migrating one round of fixes and enhancements to the ontology modules to the branch.
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::Term
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.
Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Bio::Ontology::TermFactory
Made fixes to GFF3 added SO validator for GFF3
Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Added factories for relationships and terms (the latter aren't used at this time because none of the engine implementations create term objects).
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::Ontology::TermI
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::OntologyIO
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.
Added the additional formats that are supported.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Bio::OntologyIO::Handlers::InterProHandler
Initial revision of SimpleOntologyEngine implementation of OntologyEngineI and the InterPro XML parser.
Get rid of unitialized variable errors
Commiting the latest changes to InterProParser, SimpleOntologyEngine and their respective test files.
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.
Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::OntologyIO::InterProParser
Initial revision of SimpleOntologyEngine implementation of OntologyEngineI and the InterPro XML parser.
Commiting the latest changes to InterProParser, SimpleOntologyEngine and their respective test files.
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.
Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Bio::OntologyIO::dagflat
Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.
Few fixes to remove assumptions on precise format of identifier. Added extensive tests for Sequence Ontology, which at the same time tests the SimpleGOEngine. All tests pass.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
Migrated one more serious of changes and fixes to the ontology modules to the branch.
Bio::OntologyIO::goflat
Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Bio::OntologyIO::simpleGOparser
Made fixes to GFF3 added SO validator for GFF3
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Next round if Ontology and OntologyIO changes and fixes. All tests pass now, and both the InterPro parser and the GO parser inherited from OntologyIO.pm. Removed the fancy retrieve-by-name scheme implemented for Term::ontology and Relationship::ontology because it invited trouble.
Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Bio::OntologyIO::soflat
Final steps towards stabilizing and cleaning the ontology modules. GOterm is now a thin layer on top of an expanded Term.pm, and goflat.pm and soflat are thin subclasses of dagflat. Standardized many non-standard namings. All tests pass.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Bio::PopGen::Genotype
Initial population objects -- statistical tests to come
Update the docs
Handle missing data and allele frequency counts correctly for this now
Slighlty more compact code for matching blank alleles
Cache allele blank status
Bio::PopGen::GenotypeI
Initial population objects -- statistical tests to come
Bio::PopGen::IO
Parser driver and single csv parser for allele based-data
Bio::PopGen::IO::csv
Parser driver and single csv parser for allele based-data
Assume population is made up everyone in the file (in the absence of any more information in a .csv file)
Bio::PopGen::Individual
Initial population objects -- statistical tests to come
Update docs
Change API to be lowercase for arrays of strings
Handle case when we accidently pass in a Marker not a string
Bio::PopGen::IndividualI
Initial population objects -- statistical tests to come
Change API to be lowercase for arrays of strings
Bio::PopGen::Marker
Initial population objects -- statistical tests to come
Handle missing data and allele frequency counts correctly for this now
Bio::PopGen::MarkerI
Initial population objects -- statistical tests to come
Bio::PopGen::PopStats
First implementation of Fst (to be tested still)
Handle missing data and allele frequency counts correctly for this now
Fix bugs found when re-evaluating equations
Bio::PopGen::Population
Initial population objects -- statistical tests to come
Update the docs
Handle missing data and allele frequency counts correctly for this now
Add the ability to get the unique list of marker names from the population
Fix bug in homozygote count
Bio::PopGen::PopulationI
Initial population objects -- statistical tests to come
Update the docs
Add the ability to get the unique list of marker names from the population
Bio::PrimarySeq
Let's not talk about moltype's at all. And in throw() let's call the values returned by alphabet() 'alphabet'. Also, I think the doc in validate_seq is incorrect, there is no ref() call, all it's doing is looking for non-alphabetic characters.
Changed IdentifiableI to GloballyIdentifiableI
Bio::PrimarySeqI
Fixed logic error regarding initiator codon test. Was throwing when it should have been warning and vice versa.
Made LocallyIdentifiable
Value of verbose() is passed on to new sequence objects created by trunc(), revcom() and translate
Fixes from HEAD
Bio::Range
Added seq_id() and updated some docs
Small bugfix
Bio::RangeI
Added seq_id() and updated some docs
In equals(), no longer throws an exception if the other object is undef or not-a-rangeI. Now it just says no, those are not equal.
Bio::RelRange
Initial checkin for Bio::RelRangeI, a Bio::RangeI with additional methods to support shifting between relative and absolute views.
Added the (EXPORT_OKed) utility function absSeqId() for finding the root seq_id for any Bio::RangeI object, even non-Bio::RelRangeI objects.
Minor updates
Lotsa nice new stuff, plus some bugfixes. New stuff includes orientation_policy and better absolutification.
Bio::RelRangeI
Initial checkin for Bio::RelRangeI, a Bio::RangeI with additional methods to support shifting between relative and absolute views.
Minor updates
Lotsa nice new stuff, plus some bugfixes. New stuff includes orientation_policy and better absolutification.
Bio::Root::HTTPget
Support proxy variables in the object
Bio::Root::IO
Issue #1379, can now read from stdin and filelist
Added documentation.
Mode() under linux was always returning 'r'
Mode() under linux was always returning 'r' moved doc fixes and additions from HEAD
Bio::Root::RootI
Initial global BioPerl versioning scheme
Various ontology module fixes, enhancements. Added find_terms() to engine and ontology interface. Fixed declaration and implementations of get_relationships(). Restructured and expanded tests. Added PathI and class.
Bio::Root::Version
Initial global BioPerl versioning scheme
Bio::Search::HSP::BlastHSP
Copied the hack in strand() to start() and end()
Bio::Search::HSP::FastaHSP
Fix broken seq_str and added the seq() function which will return a Bio::Seq object for query or hitThanks to Brian O for testing this out better
Specifics of get_aln to Fasta are applied from trunk
Bio::Search::HSP::GenericHSP
Changes to parse megablast
Added megablast blast-like report parsing code
Fix broken seq_str and added the seq() function which will return a Bio::Seq object for query or hitThanks to Brian O for testing this out better
Fix Issue #1381 - seq_inds now returns integers and returns all the proper values for the 'conserved' field - support the new 'conserved-not-identical' value
Seq_inds fix merged from main trunk
Fasta start/end starts with 0, hack is to just accept these numbers for now, a +1 needs to happen somewhere
Use regexps to match algorithms now so things are more compact and handle PSITBLASTN
Add sub cigar_string in GenericHSP
Merge changes from the trunk which use regexp for the algorithm matching
Bio::Search::HSP::HSPFactory
Fix broken seq_str and added the seq() function which will return a Bio::Seq object for query or hitThanks to Brian O for testing this out better
Bio::Search::HSP::HSPI
Fix broken seq_str and added the seq() function which will return a Bio::Seq object for query or hitThanks to Brian O for testing this out better
Slightly more intelligent regexps and fix seq creation
Bug fix - seq_str was not acting properly, added documentation
Some code cleanup made during code audit of Ben B's question
Handle list context properly
Expect is an alias for evalue
Bio::Search::Hit::GenericHit
Some code cleanup made during code audit of Ben B's question
Make debug stmts silent without verbose = 1
Missing s/Blast/Search/
Missing s/Blast/Search/
Doc formatting
Bio::Search::Hit::HitI
Alias for some method names of Steve that are in the XXTable writers
Bio::Search::Result::GenericResult
Remove overloaded operator to_string
Bio::Search::SearchUtils
Some code cleanup made during code audit of Ben B's question
Make debug stmts silent without verbose = 1
Handle more algorithms properly
Stupid bug - has mistyped the hash key with a variable name
Stupid bug - has mistyped the hash key with a variable name
Bio::SearchIO::SearchResultEventBuilder
Insure algorithm value is passed down
Added megablast blast-like report parsing code
Bio::SearchIO::Writer::TextResultWriter
Fixing bug reported by Eric Just
Fixing bug reported by Eric Just
Bio::SearchIO::blast
Changes to parse megablast
Added megablast blast-like report parsing code
Slightly more restrictive regexp to insure we're really matching on the right event class
Merged the more restrictive regexp to the branch
Fix Issue #1378 thanks to Simon Andrews -- GCG blast parsing was broken
Fix Issue #1378 thanks to Simon Andrews -- GCG blast parsing was broken
Handle PSITBLASTN parsing
Handle PSITBLASTN correctly by also using regexp later on
Handle PSITBLASTN
Bio::SearchIO::exonerate
Changes based on code from Gene Cutler at Tularik. I also added hit_length and query_length support since I realized these are encoded in cigar string as well
Fix off-by one errors in exonerate parsing - merge from the main trunk, hopefully everything really works, need one more round of testing perhaps
Undo changes, query length and hit length are not actually available from the sugar/cigar output
Undo changes, query length and hit length are not actually available from the sugar/cigar output
Bio::SearchIO::fasta
Fixed parsing for older fasta v3.2
Added megablast blast-like report parsing code
Bio::SearchIO::hmmer
Handle pesky - ----- - lines in hmmer reports
Catch the error and give more information about how this condition could occur
Catch the error and give more information about how this condition could occur
Bug fix merged from trunk to branch
Make it a debug stmt only
Ugh - bug in parsing multiple domains - forgot to finish the HSP
Ugh - bug in parsing multiple domains - forgot to finish the HSP
Bio::SearchIO::megablast
Changes to parse megablast
Bio::Seq
Ouch! And I've been telling people to read this!
Changed IdentifiableI to GloballyIdentifiableI
Bio::Seq::QualI
Minor doc fixes
Bio::Seq::RichSeq
Fixed the locuslink parser. Refactored RichSeq to delegate dates, secondary accessions, and keywords to the annotation bundle.
Fixed instantiation to recognize array ref for -keywords.
Fix Issue #1382; Improve keywords parsing, multiline keywords and seconardy accessions
Sync'ed RichSeqI with the implementation. RichSeq provides backward compatibility to the old API. Fixed doc bug in SimpleValue.
Now a GloballyIdentifiableI
Bio::Seq::RichSeqI
Sync'ed RichSeqI with the implementation. RichSeq provides backward compatibility to the old API. Fixed doc bug in SimpleValue.
Bio::Seq::SeqWithQuality
Minor doc fixes
Bio::Seq::SequenceTrace
Complete SequenceTrace.pm models a sequence trace as found in an scf file (check the staden docs for more information on this). TraceI was my starting point. scf.pm has been completely rewritten to take advantage of the new object and to make it, well, better. All methods are now decoupled and references to hashes are passed around instead of the self references. Methods to synthesize synthetic traces have been moved to SequenceTrace.pm Tests illustrate what I intend to do with these modules. Hope that helps, Chad Matsalla
Minor doc fixes
Bio::Seq::TraceI
Complete SequenceTrace.pm models a sequence trace as found in an scf file (check the staden docs for more information on this). TraceI was my starting point. scf.pm has been completely rewritten to take advantage of the new object and to make it, well, better. All methods are now decoupled and references to hashes are passed around instead of the self references. Methods to synthesize synthetic traces have been moved to SequenceTrace.pm Tests illustrate what I intend to do with these modules. Hope that helps, Chad Matsalla
Bio::SeqFeature::AggregatorI
Factory for grouping features into components of a containing feature.
More collection consolodation updates.
Bio::SeqFeature::Collection
Get rid of warnings on OSF1
Plane changes: Implemented Lincoln's idea of serializing feature objects in the collection via Storable, this allows collection reuse from different programs. 2 api changes, init params -file and -keep replace the previous -usefile (which was a tempfile)
Bio::SeqFeature::CollectionI
Removed -category option from features()
Further enrichments
Minor updates
Bio::SeqFeature::CollectionProviderI
New interfaces; initial docs are in the cvs add.
Removed -category option from get_collection()
Further enhancements to get_collection(), plus added types() to retrieve the possible types provided, plus added parent_collection_provider() to return the 'factory', and a factory() method aliased to it.
Minor updates
Merged my changes with Chris M's; not tested
Bio::SeqFeature::Computation
Updates because Generic is now a Bio::SeqFeature::SimpleSegment
Bio::SeqFeature::FeaturePair
Updates because Generic is now a Bio::SeqFeature::SimpleSegment
Merged my changes with Chris M's; not tested
Bio::SeqFeature::Gene::Transcript
Fixed bugs in adding exons
Bio::SeqFeature::Generic
Added speculative code for multiple alternative feature locations
Support for soon-to-be-proposed GFF3 format
Added option for sorting features by name
Modifications for GFF3
Made fixes to GFF3 added SO validator for GFF3
Made SeqFeatureI a Bio::SeqFeature::CollectionI and a Bio::LocallyIdentifiableI. Also added the type() method for keeping a Bio::SeqFeature::TypeI (and then type_string and primary_tag are defined in relation to type()).
Now a Bio::SeqFeature::SimpleSegment
More collection consolodation updates.
Bio::SeqFeature::IteratorI
New interface; initial docs are in the cvs add.
Documentation changes
Bio::SeqFeature::PositionProxy
Updated for the changes to SeqFeatureI, plus changed it to use AUTOLOAD for proxy delegation.
Bio::SeqFeature::SegmentI
New interfaces; initial docs are in the cvs add.
Minor updates
Bio::SeqFeature::SimpleCollection
Initial checkin. Note that the present features() implementation is severely crippled.
Minor updates
More collection consolodation updates.
Bio::SeqFeature::SimpleCollectionProvider
Initial checkin. Note that get_collection() has yet to be implemented.
Note that the present get_collection() implementation is severely crippled.
Implementation of enhancements to get_collection()
Minor updates
More collection consolodation updates.
Bio::SeqFeature::SimpleIterator
A simple implementation of the Bio::SeqFeature::IteratorI interface. An iterator over Bio::SeqFeatureI objects.
Minor updates
Bio::SeqFeature::SimpleSegment
A simple implementation of a Bio::SeqFeature::CollectionI that is also a Bio::RelRangeI. Implemented as a Bio::SeqFeature::SimpleCollection that is also a Bio::RelRange.
More collection consolodation updates.
Bio::SeqFeature::SimpleType
A simple implementation of the Bio::SeqFeature::TypeI interface. A feature type.
Bio::SeqFeature::TypeI
New interface; initial docs are in the cvs add.
Fixes & updates; minor
Bio::SeqFeatureI
Fix to spliced_seq on branch; will also commit on head
Added speculative code for multiple alternative feature locations
Made fixes to GFF3 added SO validator for GFF3
Made SeqFeatureI a Bio::SeqFeature::CollectionI and a Bio::LocallyIdentifiableI. Also added the type() method for keeping a Bio::SeqFeature::TypeI (and then type_string and primary_tag are defined in relation to type()).
Now a Bio::SeqFeature::SegmentI
Copied a little code from the non-freaky branch to fix a bug (in spliced_seq())
Bio::SeqIO
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Bio::SeqIO::bsml
Fixed Issue #1367, SeqFactory migrated to method create() from create_sequence()
(branch) fixed Issue #1367, SeqFactory migrated to method create() from create_sequence()
Bio::SeqIO::embl
Fix Issue #1393; multiple keywords handled okay, swiss and embl more robust now I hope
Bio::SeqIO::fasta
Changes to handle Issue #1403
Allow fasta-formatted sequence files to have leading whitespace before first entry
Migrated Jason's (see log/diff for 1.42) and Aaron's fix (allow empty lines before the first entry (see 1.43).
Get rid of warnings on some empty sequence cases
Make empty sequences not complain
Make warnings go away for empty sequences
Bio::SeqIO::genbank
Fixes Issue #1326
Fixes Issue #1326 on branch-1-2
Applied Peter Chines' patch to genbank.pm to handle entries without sequence.
Fix Issue #1382; Improve keywords parsing, multiline keywords and seconardy accessions
Migrated fix to deal with entries without sequence.
Issue #1382; Also fixed multi-line Accessions and definitions and keywords parsing
Fix small bug introduced in fixing
Fix Issue #1393; multiple keywords handled okay, swiss and embl more robust now I hope
Add trailing period
Fix periods - Issue #1395) on the branch
Fix periods - Issue #1395) - even if user has added the last keyword with a trailing '.'
Bio::SeqIO::locuslink
Fixed a bug in the LL parser.
Propagated fix to the branch.
Fixed the locuslink parser. Refactored RichSeq to delegate dates, secondary accessions, and keywords to the annotation bundle.
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Migrated the ontology overhaul changes from the main trunk to the branch. All tests pass.
Bio::SeqIO::raw
Issue #1377
Issue #1377
Bio::SeqIO::scf
Bio/SeqIO/scf.pm: fix for incorrect extraction of trace data from 8-bit-encoded SCF files. Added a perl emulation of a signed/unsigned cast that is implicit in the c-implementation of the code. Works correctly now.
Bio/SeqIO/scf.pm: added slightly faster version of the trace double delta code
Complete SequenceTrace.pm models a sequence trace as found in an scf file (check the staden docs for more information on this). TraceI was my starting point. scf.pm has been completely rewritten to take advantage of the new object and to make it, well, better. All methods are now decoupled and references to hashes are passed around instead of the self references. Methods to synthesize synthetic traces have been moved to SequenceTrace.pm Tests illustrate what I intend to do with these modules. Hope that helps, Chad Matsalla
Bio::SeqIO::swiss
Issue #1387
Issue #1387
Use get_keywords api and send in pre-parsed keywords when initializing a richseq object so to eventually phase out the expected keyword separator for all formats
Fix Issue #1393; multiple keywords handled okay, swiss and embl more robust now I hope
Bio::SeqIO::swissprot
Added Bio::SeqIO::swissprot for the purposes of OBDA naming compatibility; this is just a subclass of Bio::SeqIO::swiss and doesnt add new functionality
Check in reasonable howtos for database access and flat databases
Bio::SimpleAlign
Added remove gaps methods
Bio::Species
Code cleanup
Use underscores in data field names
Reworked the ontology to add ontology objects and interfaces. Also, changed ontology IO system to better follow the same model used by other IO subsystems.
Removed left-over print statement.
Bio::Tools::BPbl2seq
Fix problems with BPbl2seq when parsing blastn reports because we can't detect which blast program was used -- force user to provide this information
Bio::Tools::BPlite
Fix applied for Issue #1216 supplied by Sami Ashour
Fix applied for Issue #1216 supplied by Sami Ashour
Bug fixes provided Paracel developers to parse BTK formats
Changes for Paracel BTK Genewise output -- contributed by Sami Ashour
Paracel BTK parsing supported as provided by Sami Ashour
Bio::Tools::BPlite::HSP
Bug fixes provided Paracel developers to parse BTK formats
Paracel BTK parsing supported as provided by Sami Ashour
Bio::Tools::BPlite::Sbjct
Bug fixes provided Paracel developers to parse BTK formats
Changes for Paracel BTK Genewise output -- contributed by Sami Ashour
Paracel BTK parsing supported as provided by Sami Ashour
Bio::Tools::Blat
Parser for Blat
Bio::Tools::GFF
Added speculative code for multiple alternative feature locations
Support for soon-to-be-proposed GFF3 format
Modifications for GFF3
Made fixes to GFF3 added SO validator for GFF3
Merged my changes with Chris M's; not tested
This had been checked in with a bunch of cvs conflict garbage. Removed that and synced it as best I could with the apparent intention. Added feat->ensure_orientation() because the start and end positions might be reversed.
Bio::Tools::Genewise
Added setting exon coding flag true
Bio::Tools::HMMER::Results
Issue #1177
Merging fix for Issue #1177 to branch
Bio::Tools::Hmmpfam
Change to seq_id from seqname
Bio::Tools::IUPAC
Type -> alphabet in new() documentation
Bio::Tools::Lagan
Added Lagan.pm in
Moving into bioperl-run. Note: name change: Bio::Tools::Lagan -> Bio::Tools::Run::Lagan
Bio::Tools::OddCodes
Warn if used on nucleotide sequence
Bio::Tools::Phylo::PAML
Return at least something for get_seqs when parsing yn00
Oops remove unecessary parameter passing
Deal with slightly different format and the NOTE: information
Bio::Tools::Phylo::Phylip::ProtDist
Fix to support parsing multi-line protdist files
Handle case where distance is -1.000 for the wraparound line
Removed _parse method - this is part of Tool::Phylo::Phylip::PhyloDist now
Bio::Tools::Prediction::Gene
Support primary_tag argument as well as primary
Bio::Tools::Promoterwise
Jet lag commits
Bio::Tools::Pseudowise
Eliminate WrapperBase non-needed include
Bio::Tools::Run::StandAloneBlast
Fixing Issue #1168
Fixing Issue #1168
Need to implement program method (or alias the method) in the class, also implementing program_dir and program_name -- a little more complicated since there is not a 1-1 correspondance of module to program here
Fixed small bug in StandAloneBlast when using with BPbl2seq
Migrate changes from trunk to branch -- includes fix for Issue #1406
Fixed unclosed filehandle bug
Reinstated tempfile in constructor
Explicitly close a filehandle rather than assigning it to undef which will keep it open
Tempfile creation should be correct and not cause out tempfile handle problems
Bio::Tools::Run::WrapperBase
Adding to the branch - migrating from bioperl-run
Moving executable mathod to WrapperBase
Remove alias, which was giving StandAloneBlast problems
Migrate changes from trunk to branch -- includes fix for Issue #1406
Doc fix to cleanup()
Removing "use warnings" which < 5.6 perls do not know
Default wrapperbase behavior should be to clean up after oneself
Bio::Tools::SeqStats
SeqStat was not able to handle RNA RichSeqs from databases. get_mol_wt() and count_monomers() now converts T->U internally.
RNA RichSeq objects from databases whichactually have sequence in DNA alphabet are now accommodated
Bio::Tools::SeqWords
Issue #1403 - removed assumption of DNA alphabet from the word counter
Issue #1403 fixed on the 1.2 branch
Bio::Tools::Sim4::Results
Fix docs - Bio::Tools::Sim4::Results is what should be initialized
Fix docs - Bio::Tools::Sim4::Results is what should be initialized.
Bio::Tools::pICalculator
Added pICalcutor.pm. Standalone module by Mark Southern, I changed new() and the documentation to fit into Bioperl
Removing "use warnings" which < 5.6 perls do not know
Bio::Tree::Node
More appropriate way to set data in get/set methods (so that undefs can be passed in to reset data)
Use object method rather than internal hashkey
Properly remove descendents by eliminating intermediete nodes when they are not needed (recursively as well)
Debugging stmts missing newlines
Mistakenly was using same hashkey on description and descendents -- merging fix from trunk to branch
Bio::Tree::NodeI
Get_all_Descendents is a more explicit name - aliasing get_Descendents as well
Debugging stmts missing newlines
Missing newline
Bio::Tree::TreeFunctionsI
Support rerooting the tree
Remove a node from the tree as a top level method
Bio::TreeIO::TreeEventBuilder
Support passing in verbosity settings to the instatiated objects - useful for debugging
Bio::TreeIO::newick
Fixed bug that messed up nodes with 0 branch lengths
Merge Aaron's bugfix to the branch from the main trunk -- was problem with empty branchlength value
Bio::TreeIO::nhx
Fixed bug that messed up nodes with 0 branch lengths
Merge Aaron's bugfix to the branch from the main trunk -- was problem with empty branchlength value
Bio::Variation::IO::xml
Fix bug with newer IO::String which causes seg fault when closing an IO::String FH
Fix bug with closing filehandle on IO::String with later versions of IO::String
FAQ
Update the blast info
Updated
Makefile.PL
Initial global BioPerl versioning scheme
Removed references to bio*PL files, added doc/makedoc.PL
On the Web or locally
Added description of Data::Stag
Value strings in %packages have specific format, delimited by /
Wants both key and value for PL_FILES
Can't check this but should work
biodatabases.PL
Capitialization of GenBank
Added note on setting env's
Added VERSION, read from bioperl.conf
Missing =cut statements - I think this fixes Issue #1396 but I'm not sure, I can't reproduce this bug
Found and escaped a few more embedded variable names
(hopefully) fixing some interpolation issues with heredocs.
Removing \'s to see if hilmar's make problem is fixed by non-interpolated heredocs
Removed the backslashes and corrected the output stream in bioperl.PL. Enabled use strict.
biodatabases.pod
System works, let's replace version number with ==VERSION==
Add back @@VERSION@@. The programmers all seemed to like '@@', they never told me why. Odd, those...
Added mention of Biosql
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
biodesign.PL
Minor changes, some necessary for corresponding HTML versions
Added VERSION, read from bioperl.conf
Missing =cut statements - I think this fixes Issue #1396 but I'm not sure, I can't reproduce this bug
Found and escaped a few more embedded variable names
(hopefully) fixing some interpolation issues with heredocs.
Removed the backslashes and corrected the output stream in bioperl.PL. Enabled use strict.
biodesign.pod
Minor changes, some necessary for corresponding HTML versions
Applied Peter Chines' patch to genbank.pm to handle entries without sequence.
System works, let's replace version number with ==VERSION==
Add back @@VERSION@@. The programmers all seemed to like '@@', they never told me why. Odd, those...
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
bioperl.PL
Minor changes, some necessary for corresponding HTML versions
(hopefully) fixing some interpolation issues with heredocs.
Removed the backslashes and corrected the output stream in bioperl.PL. Enabled use strict.
bioperl.lisp
Simple stuff
Added macro for array get/add/remove.
bioperl.pod
Minor changes, some necessary for corresponding HTML versions
Applied Peter Chines' patch to genbank.pm to handle entries without sequence.
System works, let's replace version number with ==VERSION==
Add back @@VERSION@@. The programmers all seemed to like '@@', they never told me why. Odd, those...
Changed parent/child/reltype terminology for relationships to subject/ predicate/object, and fixed the ensuing problems.
bioscripts.PL
Missing script
Added VERSION, read from bioperl.conf
Added new *PLS scripts - thank you Lincoln, Heikki, Ewan, and Jason
(hopefully) fixing some interpolation issues with heredocs.
Removed the backslashes and corrected the output stream in bioperl.PL. Enabled use strict.
bioscripts.pod
System works, let's replace version number with ==VERSION==
Update
Add back @@VERSION@@. The programmers all seemed to like '@@', they never told me why. Odd, those...
Two worth mentioning
bptutorial.pl
Replace \' with '
Add in software link to clustalw at EBI ftp server as well
README should be INSTALL, minor stuff...
Added additional sequence formats
Link DB section to SeqIO section
Describe all SeqIO formats
Both Bio::Index::Fasta and Bio::DB::Fasta can retrieve substrings of the header as ids - here's how
Fixed bugs in bptutorial option 100 subroutine
Added more on Bio::Index::Fasta, multiple keys per sequence
Insure that tutorial ends with a 1 so that require will play nicely
Documentation updates
Allow the tutorial to be testable and silent when running with -1 as initial argument
Complete this type -> alphabet exercise, hopefully
Added mention of chado
Corrected paths to scripts
Matt's fixes
doc/makedoc.PL
Remove File::Find, use @ARGV
examples/biblio/biblio_soap.pl
Reintroducing biblio scrips into head
examples/bioperl.pl
Moving from scripts/ to examples/
examples/generate_random_seq.pl
Moving from scripts/ to examples/
examples/liveseq/change_gene.pl
Put an old script back as an example
examples/longorf.pl
Moving from scripts/ to examples/
examples/make_mrna_protein.pl
Moving from scripts/ to examples/
examples/rev_and_trans.pl
Moving from scripts/ to examples/
examples/revcom_dir.pl
Moving from scripts/ to examples/
Removing "use warnings" which < 5.6 perls do not know
examples/root/README
README for scripts located in examples/root.
examples/root/exceptions1.pl
Sample scripts demonstrating exception handling.
examples/root/exceptions2.pl
Sample scripts demonstrating exception handling.
examples/root/exceptions3.pl
Sample scripts demonstrating exception handling.
examples/root/exceptions4.pl
Sample scripts demonstrating exception handling.
examples/root/lib/Bio/PrimarySeq.pm
Versions of Bio:: modules that demonstrate how to throw Error.pm-compliant exceptions.
examples/root/lib/Bio/PrimarySeqI.pm
Versions of Bio:: modules that demonstrate how to throw Error.pm-compliant exceptions.
examples/root/lib/Bio/Seq.pm
Versions of Bio:: modules that demonstrate how to throw Error.pm-compliant exceptions.
examples/root/lib/Bio/SeqI.pm
Versions of Bio:: modules that demonstrate how to throw Error.pm-compliant exceptions.
examples/root/lib/Error.pm
Graham Barr's module for fancy exception handling. Including it so the example/root/exceptions* scripts work out of the box.
examples/root/lib/TestInterface.pm
Modules for use with the examples/root exceptions scripts.
examples/root/lib/TestObject.pm
Modules for use with the examples/root exceptions scripts.
examples/searchio/blast_example.pl
Simple SearchIO example for blast
Minor additions...
Cross-reference to SearchIO HOWTO
examples/searchio/custom_writer.pl
Moving scripts from scripts/ to examples/
examples/searchio/hitwriter.pl
Moving scripts from scripts/ to examples/
examples/searchio/hspwriter.pl
Moving scripts from scripts/ to examples/
examples/searchio/htmlwriter.pl
Moving scripts from scripts/ to examples/
examples/searchio/psiblast_features.pl
Moving scripts from scripts/ to examples/
examples/searchio/rawwriter.pl
Moving scripts from scripts/ to examples/
examples/searchio/resultwriter.pl
Moving scripts from scripts/ to examples/
examples/subsequence.cgi
Moving from scripts/ to examples/
models/coordinatemapper.dia
Initial commit
scripts/Bio-DB-GFF/README
Changed to reflect new locations
Correct
scripts/Bio-DB-GFF/bulk_load_gff.PLS
Added GFF loaders in correctly documented .PLS form
scripts/Bio-DB-GFF/bulk_load_gff.pl
A few minor changes to make bulk_load_gff.pl run on Windows: - STDIN used instead of TTY - Backslashes in paths are escaped when needed - Approprate line terminators are used when needed
Stripped annoying DOS line terminators
Added back code inadvertently removed from revision 1.9.
Removed potentially disastrous windows workaround
Added a note to the usage text for Windows users.
Added code to die if using on Windows with out --create.
Changed $^O regex so that Darwin will not be considered a MS OS.
Moving scripts from scripts/ to examples/
scripts/Bio-DB-GFF/fast_load_gff.PLS
Added GFF loaders in correctly documented .PLS form
scripts/Bio-DB-GFF/fast_load_gff.pl
Moving scripts from scripts/ to examples/
scripts/Bio-DB-GFF/generate_histogram.PLS
Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS
scripts/Bio-DB-GFF/generate_histogram.pl
Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...
scripts/Bio-DB-GFF/load_gff.PLS
Added GFF loaders in correctly documented .PLS form
scripts/Bio-DB-GFF/load_gff.pl
Moving scripts from scripts/ to examples/
scripts/Bio-DB-GFF/process_gadfly.PLS
Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS
scripts/Bio-DB-GFF/process_gadfly.pl
Updated the process_*.pl scripts for gff tweaking
Stupid mistake in gadfly url
Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...
scripts/Bio-DB-GFF/process_ncbi_human.PLS
Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS
scripts/Bio-DB-GFF/process_ncbi_human.pl
Updated the process_*.pl scripts for gff tweaking
Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...
scripts/Bio-DB-GFF/process_sgd.PLS
Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS
scripts/Bio-DB-GFF/process_sgd.pl
Updated the process_*.pl scripts for gff tweaking
Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...
scripts/Bio-DB-GFF/process_wormbase.PLS
Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS
scripts/Bio-DB-GFF/process_wormbase.pl
Updated the process_*.pl scripts for gff tweaking
Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...
scripts/Bio-DB-GFF/ucsc2gff.pl
Moving scripts from scripts/ to examples/
scripts/DB/biofetch_genbank_proxy.PLS
Added the dbfetch script
Fixed bug that caused script to crap out on "default" format
scripts/DB/bioflat_index.pl
Added some OBDA documentation plus flat file index load script
Moving scripts from scripts/ to examples/
scripts/DB/biogetseq
Initial commit of ODBA Registry compliant sequence retrieval script
Added namespace processing
Failing to find sequence handled better
Moved biogetseq to biogetseq.PLS
scripts/DB/biogetseq.PLS
Moved biogetseq to biogetseq.PLS
scripts/DB/blast_fetch.pl
Moving scripts from scripts/ to examples/
scripts/DB/blast_fetch_local.pl
Moving scripts from scripts/ to examples/
scripts/DB/dbfetch.pl
Moving scripts from scripts/ to examples/
scripts/DB/est_tissue_query.pl
Moving scripts from scripts/ to examples/
scripts/DB/flanks.PLS
Putting back the 1.0 bioperl release flanks.pl with a name and new interface and better documentation
Putting back the 1.0 bioperl elease flanks.pl with a name and new interface and better documentation
Doc fixes
scripts/DB/gb2features.pl
Moving scripts from scripts/ to examples/
scripts/DB/getGenBank.pl
Moving scripts from scripts/ to examples/
scripts/DB/get_seqs.pl
Moving scripts from scripts/ to examples/
scripts/DB/rfetch.pl
Moving scripts from scripts/ to examples/
scripts/DB/use_registry.pl
Moving scripts from scripts/ to examples/
scripts/biblio/biblio.PLS
Reintroducing biblio scrips into head
scripts/biblio/biblio.pl
Moving from scripts/ to examples/
scripts/biblio/biblio_examples.pl
Some simple queries using Bio::Biblio
Moving from scripts/ to examples/
scripts/biblio/biblio_soap.pl
Moving scripts from scripts/ to examples/
scripts/biographics/README
Redundant directory with scripts/graphics
scripts/biographics/frend
Redundant directory with scripts/graphics
scripts/biographics/render_sequence.pl
Redundant directory with scripts/graphics
scripts/bioperl.pl
Moving from scripts/ to examples/
scripts/generate_random_seq.pl
Moving from scripts/ to examples/
scripts/graphics/README
Moved from biographics
Changed to reflect new locations
Correct
scripts/graphics/feature_draw.PLS
Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS
scripts/graphics/feature_draw.pl
Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...
scripts/graphics/frend
Moved from biographics
Moving scripts
scripts/graphics/frend.PLS
Added web-based feature renderer to script repository; expanded FeatureFile format so that the same feature can appear in multiple tracks
scripts/graphics/render_sequence.pl
Moved from biographics
Changed display_name to display_id to accomodate some changes in Bio::SeqFeatureI
Fixed RangeI problem
Moving scripts
scripts/index/bpfetch.PLS
Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS
Moved branch fixes over .PLS in index directory
scripts/index/bpfetch.pl
Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...
Fixed bpindex for genbank
scripts/index/bpindex.PLS
Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS
Moved branch fixes over .PLS in index directory
scripts/index/bpindex.pl
Added ability to index Genbank and SwissPfam
Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...
Fixed bpindex for genbank
scripts/longorf.pl
Moving from scripts/ to examples/
scripts/make_mrna_protein.pl
Moving from scripts/ to examples/
scripts/make_primers.pl
Moving scripts from scripts/ to examples/
scripts/rev_and_trans.pl
Moving from scripts/ to examples/
scripts/revcom_dir.pl
Moving from scripts/ to examples/
Replacing 'use warnings' with -w
scripts/searchio/custom_writer.pl
Moving scripts from scripts/ to examples/
scripts/searchio/hitwriter.pl
Moving scripts from scripts/ to examples/
scripts/searchio/hspwriter.pl
Moving scripts from scripts/ to examples/
scripts/searchio/htmlwriter.pl
Moving scripts from scripts/ to examples/
scripts/searchio/psiblast_features.pl
Moving scripts from scripts/ to examples/
scripts/searchio/rawwriter.pl
Moving scripts from scripts/ to examples/
scripts/searchio/resultwriter.pl
Moving scripts from scripts/ to examples/
scripts/searchio/waba2gff.pl
Moving scripts from scripts/ to examples/
scripts/seq/extract_cds.pl
Moving scripts from scripts/ to examples/
scripts/seq/extract_feature_seq.PLS
More general implementation to extract features and properly name the sequence that is extracted
scripts/seq/id.list
Moving scripts from scripts/ to examples/
scripts/seq/seq.fasta.gz
Moving scripts from scripts/ to examples/
scripts/seq/seq1.fasta
Moving scripts from scripts/ to examples/
scripts/seq/seq2.fasta
Moving scripts from scripts/ to examples/
scripts/seq/seqs1.pl
Moving scripts from scripts/ to examples/
scripts/seq/seqs2.pl
Moving scripts from scripts/ to examples/
scripts/seq/seqs3.pl
Moving scripts from scripts/ to examples/
scripts/seq/seqtools.pl
Moving scripts from scripts/ to examples/
scripts/seq_length.pl
Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...
scripts/seqstats/aacomp.pl
Moving scripts from scripts/ to examples/
scripts/seqstats/chaos_plot.PLS
Reworking old scripts into new standard
Doc update
scripts/seqstats/chaos_plot.pl
Moving scripts from scripts/ to examples/
scripts/seqstats/gccalc.pl
Moving scripts from scripts/ to examples/
scripts/seqstats/oligo_count.pl
Moving scripts from scripts/ to examples/
scripts/subsequence.cgi
Moving from scripts/ to examples/
scripts/tree/blast2tree.PLS
Certain scripts are being renamed, from *pl to *PLS, so I've removed them, now I'll add them back as *PLS
scripts/tree/blast2tree.pl
Certain scripts are being renamed, from *pl to *PLS, so let's remove them first...
scripts/tree/paup2phylip.pl
Moving scripts from scripts/ to examples/
scripts/utilities/bp_mrtrans.PLS
Removing "use warnings" which < 5.6 perls do not know
scripts/utilities/bp_nrdb.PLS
Nrdb makes a sequence unique database -- still needs some thorough debugging
Added some perldoc and fleshed out cmd line arguments -- still need a bit more testing
scripts/utilities/dbsplit.PLS
Simple script to split database into chunks
Make sure scount gets reset to 0
Use prefix to get current count
scripts/utilities/pairwise_kaks.PLS
Utility script to run PAML on cDNA sequences
Missing bug URL
Add some percent identity information
Simple script to split database into chunks
Should be perl 5.8.0 compliant
scripts/utilities/remote_blast.PLS
No sense in having both a tools/ and a utilities/ directory
scripts/utilities/search2tribe.PLS
A script to turn SearchIO-parseable reports into a Tribe matrix
Use tabs, it is simplier
scripts/utilities/seq_length.PLS
No sense in having both a tools/ and a utilities/ directory
scripts/validate_gff_via_ontology.pl
Made fixes to GFF3 added SO validator for GFF3
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