Core 1.2.1 1.2.2 delta

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

Bio::Align::Utilities
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::AlignIO
SYNOPSIS is now runnable
Bio::AlignIO::bl2seq
Push -report_type flag through to object which needs it
Bio::AlignIO::fasta
Force sequences with ending gaps to be filled in all the way to be same length as the rest of the alignment
Bio::AlignIO::metafasta
Inital commit of sequence class with meta data
Bio::AlignIO::msf
For now, we will lose "~", but better than falling on ones face
Bio::AlignIO::nexus
Make next_aln() read in multiple MSAs from BioPerl written files and die of error
Make next_aln read in multiple MSAs from bioperl written filesbioperl
Bio::AlternativeLocationHolderI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::AnalysisI
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Adding these modules to synchronize between bioperl-run and bioperl core for 1.2.2 release
Bio::AnalysisParserI
Removed the result_factory methods. Only defined next_result(). Factories are managed by event handlers.
Bio::AnnotatableI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::Annotation::DBLink
Lots of fixes to the Ontology parser and term classes. Solves a whole series of issues that came up when trying to load GO into biosql.
Bio::Annotation::OntologyTerm
Fix several omitted methods from Annotation::OntologyTerm's implementation of Ontology::TermI.
Fix several omitted methods from Annotation::OntologyTerm's implementation of Ontology::TermI.
Fixed problem w/ accessing annotation hash from ont. term
Bio::AnnotationCollectionI
Adding docs for standard bio::annotation::ontologyterm tag name
Bio::Assembly::Contig
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Assembly::Scaffold
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Biblio
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
[Freaky-dev] From Nat Goodman: Added logic to handle ncbi_eutils parameter combinations
Bio::Biblio::AlzforumCitation
[freaky-dev] Nat Goodman initial checkin of Biblio extenstions for Alzforum datbase and NCBI's linkout information
Bio::Biblio::AlzforumCitation.pod
[freaky-dev] Nat Goodman initial checkin of Biblio extenstions for Alzforum datbase and NCBI's linkout information
Bio::Biblio::Article
SYNOPSIS is now runnable
Bio::Biblio::Book
SYNOPSIS is now runnable
Bio::Biblio::BookArticle
SYNOPSIS is now runnable
Bio::Biblio::IO
SYNOPSIS is now runnable
Bio::Biblio::IO::alzforum
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::Biblio::IO::alzforum.pod
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::Biblio::IO::medline2ref
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Biblio::IO::medlinexml
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Biblio::IO::ncbi_elink
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::Biblio::IO::ncbi_elink.pod
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::Biblio::IO::ncbi_eutils
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::Biblio::IO::ncbi_eutils.pod
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::Biblio::IO::pubmed2ref
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Biblio::IO::pubmedxml
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Biblio::Journal
SYNOPSIS is now runnable
Bio::Biblio::JournalArticle
SYNOPSIS is now runnable
Bio::Biblio::MedlineArticle
SYNOPSIS is now runnable
Bio::Biblio::MedlineBook
SYNOPSIS is now runnable
Bio::Biblio::MedlineBookArticle
SYNOPSIS is now runnable
Bio::Biblio::MedlineJournal
SYNOPSIS is now runnable
Bio::Biblio::MedlineJournalArticle
SYNOPSIS is now runnable
Bio::Biblio::Organisation
SYNOPSIS is now runnable
Bio::Biblio::Patent
SYNOPSIS is now runnable
Bio::Biblio::Person
SYNOPSIS is now runnable
Bio::Biblio::Proceeding
SYNOPSIS is now runnable
Bio::Biblio::Provider
SYNOPSIS is now runnable
Bio::Biblio::PubmedArticle
SYNOPSIS is now runnable
[freaky-dev] Nat Goodman initial checkin of Biblio extenstions for Alzforum datbase and NCBI's linkout information
Bio::Biblio::PubmedBookArticle
SYNOPSIS is now runnable
Bio::Biblio::PubmedJournalArticle
SYNOPSIS is now runnable
Bio::Biblio::PubmedLinkout
[freaky-dev] Nat Goodman initial checkin of Biblio extenstions for Alzforum datbase and NCBI's linkout information
Bio::Biblio::PubmedLinkout.pod
[freaky-dev] Nat Goodman initial checkin of Biblio extenstions for Alzforum datbase and NCBI's linkout information
Bio::Biblio::Ref
SYNOPSIS is now runnable
Bio::Biblio::Service
SYNOPSIS is now runnable
Bio::Biblio::Thesis
SYNOPSIS is now runnable
Bio::Biblio::WebResource
SYNOPSIS is now runnable
Bio::Cluster::SequenceFamily
SYNOPSIS is now runnable
Bio::Cluster::UniGene
Added Cre and Ddi to the species map.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Cluster::UniGeneI
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::ClusterIO::unigene
Added parsing for SEQTYPE and TRACE which are now part of the file format.
Bio::Coordinate::Collection
SYNOPSIS is now runnable
Bio::Coordinate::Pair
Fixed Location::Atomic to not make up a value for strand if there wasn't one set. Fixed a whole series of knock-on effects - strand now had to become unsettable, which had another series of knock-on effects. All tests pass now.
Bio::Coordinate::Result::Gap
Fixed Location::Atomic to not make up a value for strand if there wasn't one set. Fixed a whole series of knock-on effects - strand now had to become unsettable, which had another series of knock-on effects. All tests pass now.
Bio::Coordinate::Result::Match
Fixed Location::Atomic to not make up a value for strand if there wasn't one set. Fixed a whole series of knock-on effects - strand now had to become unsettable, which had another series of knock-on effects. All tests pass now.
Bio::Coordinate::Utils
Tests pass again after using SimpleAlign->gap_line rather than consensus_string()
Bio::DB::Biblio::AlzforumQuery
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::AlzforumQuery.pod
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::alzforum
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::alzforum.pod
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::alzforum_file
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::alzforum_file.pod
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::biofetch
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::DB::Biblio::ncbi_eutils
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::ncbi_eutils.pod
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::ncbi_eutils_file
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::ncbi_eutils_file.pod
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::pubmed_dbi
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::pubmed_dbi.pod
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::pubmed_gdbm
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::pubmed_gdbm.pod
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::DB::Biblio::soap
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::DB::BiblioI
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::DB::BioFetch
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Fix OBDA Registry and while searching the bug upgraded other modules from HEAD
Bio::DB::CompoundSegmentProvider
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Freaky-dev branch development is temporarily geared towards in-house stability; these changes are to that end.
[Freaky dev] minor fixes
[Freaky-dev] More checkins for our freaky, freaky dev.
[Freaky-dev] more small bugfixes.
[Freaky-dev] teensy tiny bugfix
Bio::DB::EMBL
SYNOPSIS is now runnable
Fix OBDA Registry and while searching the bug upgraded other modules from HEAD
Bio::DB::Failover
Fix OBDA Registry and while searching the bug upgraded other modules from HEAD
Bio::DB::Fasta
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::DB::FeatureProviderI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::DB::Flat
One must specify an indexing scheme
Bio::DB::Flat::BDB
SYNOPSIS is now runnable
Bio::DB::Flat::BinarySearch
Make index cmts print only when debugging
SYNOPSIS is now runnable
More OS/Perl independent-- tested on 5.8.0 to make it work
Bio::DB::Flat::OBDAIndex
Go ahead and update - although this is superceeded by Bio::DB::Flat::BinarySearch which is not on 1.2 branch
Bio::DB::GFF
Removed dependencies on hard-wired "Sequence" reference class
Added ability to restrict get_feature_by_name() to named features within a range
When loading a GFF file from a directory path, will look for extensions .fa, .fasta and .dna
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Added display_name() to Bio::DB::GFF::RelSegment
Started adding SO-compatible GFF aggregators and glyphs
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Added Sequence Ontology-compatible match aggregator
Fixed tied i/o issues which caused Bio::DB::Fasta to hang when run under modperl; made biofetch better at fetching refseq entries
Added GFF3 parsing to Bio::DB::GFF
[Freaky-dev] More changes for in-house joy here at the ISB.
[Freaky-dev] More checkins for our freaky, freaky dev.
[Freaky-dev] keep 'em coming..
[Freaky-dev] They're coming to take me away hoho hehe haha
[Freaky-dev] freaky freaky
In-memory adaptor more robust in Bio::DB::GFF
[Freaky-dev] Added accessor to the 'link' tag via the 'link' method and its alias, 'make_link'; this is convenient for gbrowse, which previously assumed its features came from Bio::DB::GFF, where the Feature object had these methods.
[Freaky-dev] minor bugfix.
[Freaky-dev] minor bugfix.
[Freaky-dev] teensy tiny bugfix
Bio::DB::GFF::Adaptor::biofetch
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Changed biofetch to allow loading from a local embl formatted file
Fixed mishandling of hypothetical proteins
Fixed tied i/o issues which caused Bio::DB::Fasta to hang when run under modperl; made biofetch better at fetching refseq entries
Added GFF3 parsing to Bio::DB::GFF
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Adaptor::dbi
Added attribute method
Added ability to restrict get_feature_by_name() to named features within a range
Three orders of magnitude improvement in get_feature_by_name() performance on MySQL achieved by giving query optimizer a hint
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Adaptor::dbi::caching_handle
Removed the horrible faux_sth hack and replaced with the official DBI way of detecting active statement handles
Added attribute method
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Adaptor::dbi::iterator
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::DB::GFF::Adaptor::dbi::mysql
Removed the horrible faux_sth hack and replaced with the official DBI way of detecting active statement handles
Three orders of magnitude improvement in get_feature_by_name() performance on MySQL achieved by giving query optimizer a hint
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Adaptor::dbi::oracle
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Adaptor::dbi::pg
Postgress-GFF adaptor initial commit
Fixed dsn bug
Documentation updates
Significant performace boost in the "central dogma" query (ie, overlaps query).
Woot! passes all tests.
Added back some documentation inadvertantly removed a few commits ago.
Modified SQL in _feature_by_name for big boost in speed
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Several changes: for pg.pm, removed UNIQUE constraint on fdata; a straight btree index takes its place. The unique constraint can cause bulk loads to fail. For pg_bulk_load_gff.PLS, several things: * failure to load the fmeta table fixed. * actual loading method improved, giving both increased performance and the possibility of running on Windows (not yet tested). * separated table creation from index creation.
Syncing docs to code
Bio::DB::GFF::Adaptor::jdrf_lod
[Freaky-dev] Our in-house lod track stuff. Will be shared when it's done.
[Freaky-dev] Added accessor to the 'link' tag via the 'link' method and its alias, 'make_link'; this is convenient for gbrowse, which previously assumed its features came from Bio::DB::GFF, where the Feature object had these methods.
[Freaky-dev] minor bugfix.
[Freaky-dev] minor bugfix.
[Freaky-dev] more small bugfixes.
[Freaky-dev] fixed description of lod features to use the correct score.
[Freaky-dev] Minor bugfix to the lod track fuzziness.
Bio::DB::GFF::Adaptor::memory
Added documentation to Bio::DB::GFF in-memory adaptor
In-memory Bio::DB::GFF adaptor now works well enough to support gbrowse from flat files; works OK with a yeast chromosome
Added ability to restrict get_feature_by_name() to named features within a range
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Fixed tied i/o issues which caused Bio::DB::Fasta to hang when run under modperl; made biofetch better at fetching refseq entries
In-memory adaptor more robust in Bio::DB::GFF
In-memory adaptor has a problem with test 25 - will fix
Fixed bug in regression test that was making memory adaptor *appear* to fail
Bio::DB::GFF::Adaptor::memory_iterator
In-memory Bio::DB::GFF adaptor now works well enough to support gbrowse from flat files; works OK with a yeast chromosome
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator
Fixed a bug in aggregator that appeared when aggregating features in both + and - strands
There are problems with aggregation when the subparts are in different strands; it is not certain whether this is now fixed
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Refined behavior of the cds glyph to make it more intelligent about deciding when to display reading frame for unspliced coding features
Freaky-dev branch development is temporarily geared towards in-house stability; these changes are to that end.
[Freaky dev] minor fixes
[Freaky-dev] more freaky development. Don't be alarmed, it's not on your branch.
[Freaky-dev] small stuff, wee and minor
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::alignment
Started adding SO-compatible GFF aggregators and glyphs
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Added Sequence Ontology-compatible match aggregator
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::clone
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::coding
Added a sequence ontology-compatible CDS aggregator
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::match
Added Sequence Ontology-compatible match aggregator
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::none
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::processed_transcript
Started adding SO-compatible GFF aggregators and glyphs
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Added a sequence ontology-compatible CDS aggregator
Made very subtle change to Bio::Graphics::Glyph::transcript2 API to be consist with other glyphs, and had to change regression test to unfix the fix!
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::transcript
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::ucsc_acembly
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::ucsc_ensgene
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::ucsc_genscan
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::ucsc_refgene
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::ucsc_sanger22
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::ucsc_softberry
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::ucsc_twinscan
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Aggregator::ucsc_unigene
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Feature
Fixed bug in merged_segments
Fixed merging again!
Fixed a bug in aggregator that appeared when aggregating features in both + and - strands
There are problems with aggregation when the subparts are in different strands; it is not certain whether this is now fixed
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Added display_name() to Bio::DB::GFF::RelSegment
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
The method name has changed from each_tag_value to get_tag_values, support old method through aliasing, but update docs too
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
[Freaky-dev] More checkins for our freaky, freaky dev.
[Freaky-dev] More checkins for our freaky, freaky dev.
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::RelSegment
Removed dependencies on hard-wired "Sequence" reference class
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Segment
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Added display_name() to Bio::DB::GFF::RelSegment
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
[Freaky-dev] More changes for in-house joy here at the ISB.
[Freaky-dev] More checkins for our freaky, freaky dev.
[Freaky-dev] keep 'em coming..
[Freaky-dev] They're coming to take me away hoho hehe haha
In-memory adaptor more robust in Bio::DB::GFF
[Freaky-dev] more small bugfixes.
Bio::DB::GFF::Typename
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
In-memory adaptor more robust in Bio::DB::GFF
Bio::DB::GFF::Util::Binning
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::DB::GFF::Util::Rearrange
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::DB::GenBank
Updated Bio::DB::GenBank synopsis example to show the approved way of fetching lots of ESTs
Ahem, someone had set the default db to protein instead of nucleotide here, very BAD
Copied (URL) fixes from head
Fixed the bug reported by James Wasmuth where NCBI eutils now need 'gb|' prepended to a accession number. get_Seq_by_acc() fixed, I made sure get_Stream_by_acc is not affected.
Fixed the bug reported by James Wasmuth where NCBI eutils now need 'gb|' prepended to a accession number. get_Seq_by_acc() fixed, I made sure get_Stream_by_acc is not affected.
Bio::DB::LocusLinkHugoNormalizer
First steps towards standardizing a feature-name-standardizer interface
[Freaky-dev] More changes for in-house joy here at the ISB.
[Freaky-dev] More checkins for our freaky, freaky dev.
[Freaky-dev] They're coming to take me away hoho hehe haha
Bio::DB::NCBIHelper
Code fmting
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
The eutils base URL has changed to http://eutils.ncbi.nlm.nih.gov/entrez/eutils
Copied (URL) fixes from head
Bio::DB::Query::GenBank
Updated Bio::DB::GenBank synopsis example to show the approved way of fetching lots of ESTs
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::DB::Query::WebQuery
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::DB::QueryI
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::DB::Registry
Error message says '/etc/.bioinformatics' but code searches '/etc/bioinformatics'
More information
The delimiter for OBDA_SEARCH_PATH is ;
Fix OBDA Registry and while searching the bug upgraded other modules from HEAD
Adding $VERSION so that scripts using registry can test it. Value is now 1.2 which means that the same tests should work on future releases.
Bio::DB::SegmentProviderI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::DB::SequenceProviderI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::DB::SimpleFeatureProvider
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::DB::SimpleSegmentProvider
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::DB::SimpleSequenceProvider
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::DB::Taxonomy
Changed to appease the pedantics
Bio::DB::Taxonomy::entrez
Fix API so it respects the documented type (and supports the old style, also improve error message
Changed to appease the pedantics
Bio::DB::Taxonomy::flatfile
Implementation of local taxonomy DB species -> taxonid only implemented now - rest of methods will come soon
Support creation of taxonomy node from flatfile Bio::DB::Taxonomy dbh
Bio::DB::WebDBSeqI
Request_format returns an array - only want first item
Copied (URL) fixes from head
Bio::DB::XEMBL
SYNOPSIS is now runnable
Bio::DB::XEMBLService
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Das::SegmentI
Added display_name() to Bio::DB::GFF::RelSegment
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Event::EventGeneratorI
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Expression::FeatureGroup
FeatureSet modules updated naming to FeatureGroup. FeatureSet modules kept.
Bio::Expression::FeatureGroup::FeatureGroupMas50
FeatureSet modules updated naming to FeatureGroup. FeatureSet modules kept.
Bio::Expression::FeatureI
Pure interface file should inherit from Bio::Root::RootI
Bio::Expression::FeatureSet::FeatureSetMas50
Added for mas5 parser
Bio::Factory::AnalysisI
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Adding these modules to synchronize between bioperl-run and bioperl core for 1.2.2 release
Bio::Factory::BlastHitFactory
Updated for module name change: BlastHit -> PsiBlastHit.
SYNOPSIS is now runnable
Bio::Factory::BlastResultFactory
Updated for module name change: BlastResult -> PsiBlastResult. This is used by psiblast.pm.
SYNOPSIS is now runnable
Bio::Factory::FTLocationFactory
Fixes Issue #1371 where nonstandard bond FT key killed the parser
Bio::Factory::GenericObjectFactory
A generic impl of ObjectFactoryI for creating any type of object.
Removed Factory::GenericObjectFactory, as Factory::ObjectFactory provides the same functionality (and more), and was there earlier. Seems I preempted you Steve by a few weeks :-))
Bio::Factory::HitFactoryI
Insure error message is sufficiently verbose - Issue #1439
Bio::Factory::SeqAnalysisParserFactory
SYNOPSIS is now runnable
Bio::GloballyIdentifiableI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::Graphics
Updated the biographics FAQ to accomodate changes in meaning of -seq_id vs -display_name in Bio::SeqFeature::Generic
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Script installer now adds bp_ prefix to all scripts if they don't have them already; biographics now can create gene diagrams in the UCSC Genome Browser Style in addition to the default EnsEMBL/WormBase style; new processed_transcript glyph is Sequence Ontology (tm) compatible
Brought bioperl-live bug fixes over branch-1-2
Bio::Graphics::AutoAggregatorFactoryI
An interface for autogenerators of aggregators, based on sections in the Configurator.
Bio::Graphics::ConfiguratorI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::Graphics::DasAutoAggregatorFactory
An implementation of AutoAggregatorFactoryI that uses the special keys DAS_id and DAS_category from the Configurator to generate appropriate aggregators.
Bio::Graphics::Feature
Fixed bug in merged_segments
Added a notes() method to Bio::Graphics::Feature to avoid warning in gbrowse
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought bioperl-live bug fixes over branch-1-2
Bio::Graphics::FeatureFile
Fixed truncation bugs in the primer glyph; added an init_code section to featureFile
SYNOPSIS is now runnable
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Can use "stop" as an alternative link rule to "end"
Fixed problem involving unescaped links in annotated imagemaps
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Fixed bugs in FeatureFile when running on windows
Added $description as a valid link rule
Brought bioperl-live bug fixes over branch-1-2
Bio::Graphics::Glyph
Added an always_sort option to glyphs
When loading a GFF file from a directory path, will look for extensions .fa, .fasta and .dna
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Script installer now adds bp_ prefix to all scripts if they don't have them already; biographics now can create gene diagrams in the UCSC Genome Browser Style in addition to the default EnsEMBL/WormBase style; new processed_transcript glyph is Sequence Ontology (tm) compatible
Freaky-dev branch development is temporarily geared towards in-house stability; these changes are to that end.
[Freaky-dev] more freaky development. Don't be alarmed, it's not on your branch.
[Freaky-dev] Removed some debugging code
Brought bioperl-live bug fixes over branch-1-2
[Freaky-dev] Added accessor to the 'link' tag via the 'link' method and its alias, 'make_link'; this is convenient for gbrowse, which previously assumed its features came from Bio::DB::GFF, where the Feature object had these methods.
Removed lines using Bio::Root::Version which is not in the branch
Bio::Graphics::Glyph::Factory
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Freaky-dev branch development is temporarily geared towards in-house stability; these changes are to that end.
[Freaky-dev] more freaky development. Don't be alarmed, it's not on your branch.
Strip whitespace, newline from glyphclass var
Brought Bio::Graphics bug fixes over branch-1-2
[Freaky-dev] Added accessor to the 'link' tag via the 'link' method and its alias, 'make_link'; this is convenient for gbrowse, which previously assumed its features came from Bio::DB::GFF, where the Feature object had these methods.
[Freaky-dev] minor bugfix.
Removed lines using Bio::Root::Version which is not in the branch
Bio::Graphics::Glyph::anchored_arrow
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Fixed inconsistencies between documentation and behavior in anchored_arrow; span glyph is now a specialization of anchored_arrow rather than an alias for generic glyph
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::arrow
Fixed arrows so that the arrowhead is not drawn if off screen
Fixed arrow glyph to respect panel flip state
Added a 'relative_coords_offset' to go along with the 'relative_coords' option. This is useful when you want to start your numbering at an arbitrary number. For instance, if you set relative_coords_offset at -10000, the 10000th base pair in will be labeled as 0.
Clarified what true and false mean to perl
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Fixed inconsistencies between documentation and behavior in anchored_arrow; span glyph is now a specialization of anchored_arrow rather than an alias for generic glyph
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::box
Aesthetic improvements to xyplot
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::cds
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Big cleanup of the alignment methods in cds and segments glyphs
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Added a sequence ontology-compatible CDS aggregator
Refined behavior of the cds glyph to make it more intelligent about deciding when to display reading frame for unspliced coding features
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::crossbox
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::diamond
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::dna
When loading a GFF file from a directory path, will look for extensions .fa, .fasta and .dna
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::extending_arrow
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::generic
Added a splice acceptor/donor glyph and allow glyph padding to be adjusted dynamically
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Added ability to decorate a glyph with a wee red asterix on top, to highlite interesting features
Erp. Small bugfix.
[Freaky-dev] more freaky development. Don't be alarmed, it's not on your branch.
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::graded_segments
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::line
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::lod
[Freaky-dev] This is our track. We like it.
[Freaky-dev] Added accessor to the 'link' tag via the 'link' method and its alias, 'make_link'; this is convenient for gbrowse, which previously assumed its features came from Bio::DB::GFF, where the Feature object had these methods.
[Freaky-dev] minor bugfix.
[Freaky-dev] minor bugfix.
[Freaky-dev] Minor bugfix to the lod track fuzziness.
Bio::Graphics::Glyph::pinsertion
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::primers
Fixed truncation bugs in the primer glyph; added an init_code section to featureFile
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::processed_transcript
Started adding SO-compatible GFF aggregators and glyphs
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Script installer now adds bp_ prefix to all scripts if they don't have them already; biographics now can create gene diagrams in the UCSC Genome Browser Style in addition to the default EnsEMBL/WormBase style; new processed_transcript glyph is Sequence Ontology (tm) compatible
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::redgreen_box
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::redgreen_segment
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::segmented_keyglyph
Freaky-dev branch development is temporarily geared towards in-house stability; these changes are to that end.
Bio::Graphics::Glyph::segments
When loading a GFF file from a directory path, will look for extensions .fa, .fasta and .dna
Added display_name() to Bio::DB::GFF::RelSegment
Big cleanup of the alignment methods in cds and segments glyphs
Fixed problem involving unescaped links in annotated imagemaps
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Segments was crashing if draw_target was on and show_mismatch was off
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::snps
New gbrowse files
Bio::Graphics::Glyph::span
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Fixed inconsistencies between documentation and behavior in anchored_arrow; span glyph is now a specialization of anchored_arrow rather than an alias for generic glyph
Arrowhead vs base confusion
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::splice_site
Added a splice acceptor/donor glyph and allow glyph padding to be adjusted dynamically
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
"my" variable $top was declared twice
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::toomany
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::track
[Freaky-dev] more freaky development. Don't be alarmed, it's not on your branch.
Bio::Graphics::Glyph::transcript
When loading a GFF file from a directory path, will look for extensions .fa, .fasta and .dna
Script installer now adds bp_ prefix to all scripts if they don't have them already; biographics now can create gene diagrams in the UCSC Genome Browser Style in addition to the default EnsEMBL/WormBase style; new processed_transcript glyph is Sequence Ontology (tm) compatible
[Freaky-dev] more freaky development. Don't be alarmed, it's not on your branch.
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::transcript2
When loading a GFF file from a directory path, will look for extensions .fa, .fasta and .dna
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Script installer now adds bp_ prefix to all scripts if they don't have them already; biographics now can create gene diagrams in the UCSC Genome Browser Style in addition to the default EnsEMBL/WormBase style; new processed_transcript glyph is Sequence Ontology (tm) compatible
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::translation
Added decent default colors to the six-frame translation glyph
Fixed tied i/o issues which caused Bio::DB::Fasta to hang when run under modperl; made biofetch better at fetching refseq entries
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::triangle
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Glyph::xyplot
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Added missing documentation for scale option in xyplot
Aesthetic improvements to xyplot
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Panel
Fix docs to show code which does not assume that Seq is a range
Fix docs to show code which does not assume that Seq is a range
Added fix from Eric Just to show at least one major tick
When loading a GFF file from a directory path, will look for extensions .fa, .fasta and .dna
SYNOPSIS is now runnable
Quenched uninit string eq warnings in Panel
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Script installer now adds bp_ prefix to all scripts if they don't have them already; biographics now can create gene diagrams in the UCSC Genome Browser Style in addition to the default EnsEMBL/WormBase style; new processed_transcript glyph is Sequence Ontology (tm) compatible
Added processed_transcript and anchored_arrow documentation to list of glyphs in Bio::Graphics::Panel
Freaky-dev branch development is temporarily geared towards in-house stability; these changes are to that end.
[Freaky-dev] more freaky development. Don't be alarmed, it's not on your branch.
Brought Bio::Graphics bug fixes over branch-1-2
Bio::Graphics::Pictogram
Module for drawing svg consensus motifs
SYNOPSIS is now runnable
Bio::Graphics::RendererI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::Graphics::SimpleConfigurator
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
[Freaky-dev] more freaky development. Don't be alarmed, it's not on your branch.
Bio::Graphics::SimpleRenderer
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::Graphics::Util
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Brought Bio::Graphics bug fixes over branch-1-2
Removed lines using Bio::Root::Version which is not in the branch
Bio::Index::Blast
SYNOPSIS is now runnable
Support the notion of not closing the filehandle to support a shared filehandle for the Index object. Index::Blast now used SearchIO by default
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Respect noclose
Bio::Index::EMBL
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Index::Fasta
More references to example code, note on id_parser()
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Index::Fastq
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Index::GenBank
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Index::SwissPfam
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Index::Swissprot
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::AARange
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::Chain
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::ChainI
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::DNA
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::Exon
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::Gene
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::IO::BioPerl
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Deal with unloadable DB::EMBL (due to HTTP::Request or LWP) so that make test doesn't fall over
Bio::LiveSeq::IO::Loader
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::IO::SRS
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::Intron
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::Mutation
Got rid of type conversion warnings when seq() or seqori() were not set
Bio::LiveSeq::Mutator
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::Prim_Transcript
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::Range
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::Repeat_Region
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::Repeat_Unit
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::SeqI
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::LiveSeq::Transcript
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::LiveSeq::Translation
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Got rid of a spurious warning
Bio::LocallyIdentifiableI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::LocatableSeq
Improve error message
Bio::Location::Atomic
Fixed Location::Atomic to not make up a value for strand if there wasn't one set. Fixed a whole series of knock-on effects - strand now had to become unsettable, which had another series of knock-on effects. All tests pass now.
Bio::Location::Fuzzy
SYNOPSIS is now runnable
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Bio::Map::CytoPosition
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Map::Marker
SYNOPSIS is now runnable
Bio::Matrix::PhylipDist
Removed depreciated usage of an array/hash as a reference %a->{$b} -> $a{$b}
Add some space in case the name is too long
Don't use deprecated syntax
Bio::Ontology::GOterm
Migrated all the ontology parser and Term fixes to the branch.
Lots of fixes to the Ontology parser and term classes. Solves a whole series of issues that came up when trying to load GO into biosql.
Fixed code that assumed predicate terms would always come with an (mostly artificial) identifier. Reverted a change in the locuslink parser that set the ontology name for term annotations to an artificial name.
Migrated fix to code that expected artifical identifiers for predicate terms.
Bio::Ontology::Ontology
Changes that allow custom relationship types to be defined. this allows parsing of dag-edit files that have relationships which are not part of GO or SO
Bio::Ontology::OntologyEngineI
Fix several omitted methods from Annotation::OntologyTerm's implementation of Ontology::TermI.
Fixed test failures in Genpred.t (the previous test count was wrong, which concealed a bug that Heikki fixed), and Pictogram.t (not graceful if SVG.pm is not installed). Fixed lots of knock-on bugs made effective by someone changing the implementation of SeqFeatureI methods in Generic. There is still one failure in SeqFeature.t.
Adding interface methods add_relationship_type() and get_relationship_type()... these manage construction/retrieval of arbitrary predicate terms
Bio::Ontology::RelationshipType
Migrated all the ontology parser and Term fixes to the branch.
Lots of fixes to the Ontology parser and term classes. Solves a whole series of issues that came up when trying to load GO into biosql.
Changes that allow custom relationship types to be defined. this allows parsing of dag-edit files that have relationships which are not part of GO or SO
Bio::Ontology::SimpleGOEngine
Verbosity on request
SYNOPSIS is now runnable
Migrated all the ontology parser and Term fixes to the branch.
Lots of fixes to the Ontology parser and term classes. Solves a whole series of issues that came up when trying to load GO into biosql.
Verbosity on demand
Changes that allow custom relationship types to be defined. this allows parsing of dag-edit files that have relationships which are not part of GO or SO
Removed debug warnings
Committing additions to change log. Relaxing the ID format requirements for ontology terms to require less digits.
Moved over additions to the change log. Migrated term ID relaxation to the branch.
Bio::Ontology::SimpleOntologyEngine
Migrated all the ontology parser and Term fixes to the branch.
Lots of fixes to the Ontology parser and term classes. Solves a whole series of issues that came up when trying to load GO into biosql.
Fixed code that assumed predicate terms would always come with an (mostly artificial) identifier. Reverted a change in the locuslink parser that set the ontology name for term annotations to an artificial name.
Migrated fix to code that expected artifical identifiers for predicate terms.
Bio::Ontology::Term
Migrated all the ontology parser and Term fixes to the branch.
Lots of fixes to the Ontology parser and term classes. Solves a whole series of issues that came up when trying to load GO into biosql.
Bio::Ontology::TermI
Migrated all the ontology parser and Term fixes to the branch.
Lots of fixes to the Ontology parser and term classes. Solves a whole series of issues that came up when trying to load GO into biosql.
Bio::OntologyIO
SYNOPSIS is now runnable
Bio::OntologyIO::dagflat
Made the dagflat parser auto-discover the name of the ontology. Changed the test to test for this.
Made the dagflat parser auto-discover the ontology name. Changed test suite to test for this.
Small doc fix and otherwise small changes that will make the code break less likely upon future changes.
Migrated all the ontology parser and Term fixes to the branch.
Lots of fixes to the Ontology parser and term classes. Solves a whole series of issues that came up when trying to load GO into biosql.
Don't require IDs to be zero-filled
Fix for OBO_REL
Adding capability to add new relationship types on-the-fly... this allows compatibility with dag-edit files that have custom relationship types (see cell ontology)
Less stringency on zero-filled identifiers. stripping @reltype@ syntax from termnames
Stripped out debug warnings. still some problems parsing out secondary relationships in line, i don't quite understand the syntax. someone more familiar with dag-edit should be able to fix this in a jiffy.
Committing additions to change log. Relaxing the ID format requirements for ontology terms to require less digits.
Moved over additions to the change log. Migrated term ID relaxation to the branch.
Bio::OntologyIO::goflat
Made the dagflat parser auto-discover the name of the ontology. Changed the test to test for this.
Made the dagflat parser auto-discover the ontology name. Changed test suite to test for this.
Migrated all the ontology parser and Term fixes to the branch.
Bio::OntologyIO::simplehierarchy
Adding a generic parser for non-dagedit hierarchical flatfiles. still rough.
Bugfix, ha
Bugfix to prevent infinite recursion when a parent has a subterm of the same name
Changed default edge type to "is_a". fixed a bug that the "is_a" RelationshipType wasn't properly initialized.
Bio::OntologyIO::soflat
Made the dagflat parser auto-discover the name of the ontology. Changed the test to test for this.
Made the dagflat parser auto-discover the ontology name. Changed test suite to test for this.
Migrated all the ontology parser and Term fixes to the branch.
Bio::Perl
Insure error message is sufficiently verbose - Issue #1439
Deal with not-present HTTP::Request::Common gracefully
Bio::Phenotype::PhenotypeI
Pure interface file need not 'use' or inherit from other than Bio::Root::RootI
Bio::PopGen::Individual
Fix marker obj -> string conversion so that it is protected
1st step in merging pedigree and popgen objects
Properly bail when a scalar is provided
Bio::PopGen::IndividualI
1st step in merging pedigree and popgen objects
Bio::PopGen::Marker
1st step in merging pedigree and popgen objects
Sort alleles
Bio::PopGen::MarkerI
1st step in merging pedigree and popgen objects
Bio::PopGen::Population
Allow setting of Allele Frequency directly rather than inferred from genotypes of all individuals
Fix marker obj -> string conversion so that it is protected
Protect marker -> name de-objectifying
1st step in merging pedigree and popgen objects
Support removal of an individual
Argument order was wrong
Bio::PopGen::PopulationI
1st step in merging pedigree and popgen objects
Bio::PrimarySeq
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Support is_circular properly
Relocated is_circular to the object away from the interface as this is not getting set with a value upon initialization from SeqIO
Bio::PrimarySeqI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Support is_circular properly
Relocated is_circular to the object away from the interface as this is not getting set with a value upon initialization from SeqIO
Bio::Range
SYNOPSIS is now runnable
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::RangeI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::RelRange
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
[Freaky-dev] Changed start() and end() to allow real numbers (it just takes the int truncation).
Bio::RelRangeI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::Root::AutoClass
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::Root::AutoClass.pod
[Freaky-dev] From Nat Goodman: Initial checkins of new AutoClass stuff, and new Biblio online access to PubMed @ NCBI and local storage of pubs.
Bio::Root::Err
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Root::Exception
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Root::Global
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Root::HTTPget
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Root::IO
Don't try and close a filehandle when it is an IO::String filehandle, this causes seg fault on RHL 7.3 and perl 5.6.1 at least
Remove extra debugging comment - probably not necessary
Support the notion of not closing the filehandle to support a shared filehandle for the Index object
Don't close if it is STDERR,STDOUT, or STDIN
Don't need to check this twice
Fix OBDA Registry and while searching the bug upgraded other modules from HEAD
Respect noclose
Bio::Root::IOManager
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Root::Object
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Root::Root
Prevent undef warnings on empty verbose field
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Root::RootI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Fixed Location::Atomic to not make up a value for strand if there wasn't one set. Fixed a whole series of knock-on effects - strand now had to become unsettable, which had another series of knock-on effects. All tests pass now.
Bio::Root::Utilities
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Root::Vector
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Root::Version
SYNOPSIS is now runnable
Brought over from the trunk.
Bio::Root::Xref
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Search::BlastUtils
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Search::HSP::BlastHSP
SYNOPSIS is now runnable
Removed hack to detect when feature pair is being initialized. Shouldn't be necessary anymore.
Bio::Search::HSP::GenericHSP
Various modifications as part of merging functionality from the old BlastHSP used by psiblast.pm.
Added AXT to NT-NT match
Full parsing of paracel BTK/Blast-like output for genewsise sw tsw etc
Support for SIM4
SYNOPSIS is now runnable
Regexp should be faster
Bio::Search::HSP::HSPFactory
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Bio::Search::HSP::HSPI
Handle list context for strand correctly (was acting as sbjct)
SYNOPSIS is now runnable
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Fixed Location::Atomic to not make up a value for strand if there wasn't one set. Fixed a whole series of knock-on effects - strand now had to become unsettable, which had another series of knock-on effects. All tests pass now.
Bio::Search::HSP::PsiBlastHSP
Re-naming the BlastHit.pm that is used by SearchIO::psiblast.pm to make it clear that this module goes along with the other PsiBlast Search objects.
SYNOPSIS is now runnable
Removed hack to detect when feature pair is being initialized. Shouldn't be necessary anymore.
Bio::Search::Hit::BlastHit
Now relies on GenericHit for most of its implementation. Contains only iteration-related functionality. Used by the new PSI-blast compatible SearchIO::blast.
Bio::Search::Hit::Fasta
SYNOPSIS is now runnable
Bio::Search::Hit::PsiBlastHit
Re-naming the BlastHit.pm that is used by SearchIO::psiblast.pm to make way for the new version of BlastHit.pm that is tied to SearchIO::blast
SYNOPSIS is now runnable
Bio::Search::Iteration::GenericIteration
Modules for working with Search results that contain hits segregated into one or more iterations (e.g., PSI-BLAST).
* Added converged() implementation. * Updated new() to call converged() as necessary.
Bio::Search::Iteration::IterationI
Modules for working with Search results that contain hits segregated into one or more iterations (e.g., PSI-BLAST).
* Added converged() method. * Improved the SYNOPSIS code (this code is currently identical to examples/searchio/psiblast_iterations.pl)
Bio::Search::Processor
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Search::Result::BlastResult
Now derives from GenericResult and contains only blast-specific things, mostly stuff dealing with iterations (PSI-BLAST). Used by the new version of SearchIO::blast that can handle PSI-Blast results. The previous version of BlastResult.pm is now in PsiBlastResult.pm
Bio::Search::Result::PsiBlastResult
Re-naming the BlastResult.pm that is used by SearchIO::psiblast.pm to make way for the new version of BlastResult.pm that is tied to SearchIO::blast
SYNOPSIS is now runnable
Bio::Search::SearchUtils
SYNOPSIS is now runnable
Runnable synopsis (forgottot save the file)
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::SearchIO
Removed factory-related methods and the use-factory stuff. This is now only specific to psiblast.pm.
Only print the end_result once
Fix Issue #1432
Do an initialization step too
SYNOPSIS is now runnable
Insure error message is sufficiently verbose - Issue #1439
* Moved the declaration of InternalParserError exception from blast.pm to SearchIO.pm so that other modules can use it if desired.
The || was calling array in scalar context which was true even when we were passing in a '0' as the array content
Bio::SearchIO::FastHitEventBuilder
Need to derive an interface for these listeners - for now add the method
Bio::SearchIO::IteratedSearchResultEventBuilder
Event handler that builds Search objects for results that may contain multiple iterations (PSI-BLAST).
Bl2seq parsing enabled
Removed Factory::GenericObjectFactory, as Factory::ObjectFactory provides the same functionality (and more), and was there earlier. Seems I preempted you Steve by a few weeks :-))
Added -interface parameter to the ObjectFactory calls.
Bio::SearchIO::SearchResultEventBuilder
End_hit() now calls _add_hit() to store the hit locally. This allows for filtering and classification that happens in the ISREB module. factory() throws a typed exception.
Import significance value from HSP when the hit wasn't part of the report's Hit summary
Bl2seq parsing enabled
Double check hsp creation before assuming we can call method there
Using Bio::Factory::ObjectFactory instead of the various Bio::Search factories. Also calling create_object instead of create since ObjectFactoryI recommends create_object.
Handle only CIGAR lines for parsing exonerate reports
Need to derive an interface for these listeners - for now add the method
Bio::SearchIO::SearchWriterI
Make the header a method to so people can override
Bio::SearchIO::Writer::BSMLResultWriter
Not finished - but framework is started - I don't know what all the fields are supposed to mean for BSML
Better implementation as inferred by Incogen's NCBI Blast XML to BSML XSLT stylesheet
Bio::SearchIO::Writer::HTMLResultWriter
Make the header a method to so people can override
Fix Issue #1432
Added missing '$' in $Revision.
Added $Revision to footer.
Issue #1458
Issue #1458 fixed on branch
Issue #1459 fixed by dealing with translated BLAST differently from each other
Handle TBLASTX properly
Oops - missing brackets in regexep for TBLASTX match
Bio::SearchIO::Writer::TextResultWriter
Issue #1458
Issue #1458 fixed on branch
Issue #1459 fixed by dealing with translated BLAST differently from each other
Handle TBLASTX properly
Oops - missing brackets in regexep for TBLASTX match
Bio::SearchIO::axt
Axt parser
Add some coordinate fixes
Bio::SearchIO::blast
Adding in support for PSI-BLAST result parsing and other functionality provided by psiblast.pm (not all of which is fully implemented here yet). Other stuff: caching will_handle() calls to reduce method call overhead. Adding '1' to e-values starting with 'e-' so perl will consider them numeric. Refactored some calls into _start_blastoutput(). Checking for ^Lambda to detect parameters section in ecoli_domains.rpsblast.
Fix so that iteration is only called when needed (when we're within an iteration) this avoids the double call to iteration which was duplicating Hits in Result
Check before calling end_iteration in all cases
Fixing Neil's reported megablast parsing problem - iterations weren't getting closed with Steve's new changes
One more round to make sure we've already closed Hit and Hsp events
Merging changes from main trunk which fixing Neil's reported megablast parsing problem - iterations weren't getting closed with Steve's new changes and need to make sure we close all events
Bl2seq parsing enabled
Added docs and support for BTK output
Full parsing of paracel BTK/Blast-like output for genewsise sw tsw etc
Changes to support BLAT Blast-like parsing (where there are no parameters at the bottom)
Issue #1445
Fix Issue #1443 - make sure event calls close Hits properly
Insure that multi-(RPS|MEGA) reports are properly parsed and separated
* Fixed bug in the processing of NCBI BLAST descriptions (while loop starting at line 491. For some reports, this was slurping up the whole report and reporting no hits found.) * Checking for 'CONVERGED' line (PSI-BLAST reports only) and recording this for the Iteration object. * Converted `print STDERR` lines to debug() calls and commented most of them out so they won't impact performance. * Moved the declaration of InternalParserError exception into SearchIO.pm so that other modules can use it if desired. * Added a 'Developer Notes' section explaining the basic strategy used by this module to unmarshall data. This type of info should help improve the maintainability of the code.
Fix bug spotted by Matt Vaughn
Fix Issue #1443 again, lines need to be flipped around
Check for loop exit at the beginning not the end
Bio::SearchIO::blastxml
Attempt to fix problems with embedded encoded characters and deal with those sections which prefix with <?xml ...> and those that don't
Bio::SearchIO::exonerate
Handle only CIGAR lines for parsing exonerate reports
Bio::SearchIO::fasta
Using Bio::Factory::ObjectFactory instead of Bio::Search::HSP::HSPFactory.
Bio::SearchIO::hmmer
Removing the DEFAULT_*_FACTORY_CLASS variables. Not used. _initialize() now uses GenericObjectFactory to create result/hit/hsp objects. De-tabified.
Fix HMMPFAM parse bug where individual domain but not summary information reported
Removed Factory::GenericObjectFactory, as Factory::ObjectFactory provides the same functionality (and more), and was there earlier. Seems I preempted you Steve by a few weeks :-))
Added -interface parameter to the ObjectFactory calls.
Bio::SearchIO::psiblast
Added factory-related methods since this no longer supported by SearchIO.pm. Using PsiBlastResult.pm instead of BlastResult.pm.
Bio::SearchIO::sim4
Sim4 SearchIO parser and tests
Bio::SearchIO::waba
Handle opp strand negative coordinates
Goahead and change back to pos coordinates
Added use <module> for the factories. I got bad throw-ups without.
Bio::SearchIO::wise
SearchIO parsing of genewise/genomewise using Bio::Tools::Genewise as helper
Bio::Seq
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Fix Issue #1448 about is_circular() not getting set
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Support is_circular properly
Update Bio::Seq documentation to explicitly say this is a Get/Setter to avoid confusing new users
Update Bio::Seq documentation to explicitly say this is a Get/Setter to avoid confusing new users
Bio::Seq::EncodedSeq
Issue #1436
Issue #1436
Bio::Seq::IteratorI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::Seq::Meta
Inital commit of sequence class with meta data
Test arguments in trunc()
SYNOPSIS is now runnable
Bio::Seq::Meta::Array
Array implementation of Bio::Seq::MetaI
SYNOPSIS is now runnable
Bio::Seq::MetaI
Inital commit of sequence class with meta data
Bio::Seq::PrimedSeq
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::Seq::QualI
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Seq::RichSeq
SYNOPSIS is now runnable
Bio::Seq::SeqWithQuality
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::Seq::SequenceTrace
Removed depreciated use of array as a reference
Bio::Seq::SimpleIterator
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::Seq::TraceI
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::SeqFeature::AggregatorI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::SeqFeature::Collection
Use feature_count method and thaw features when retrieving the list
Get BTREE right - were only returning first object for multi feature bin - use formal 'seq' call to get this right (I hope)
Bio::SeqFeature::CollectionI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::SeqFeature::CollectionProviderI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bio::SeqFeature::CompoundIterator
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Freaky-dev branch development is temporarily geared towards in-house stability; these changes are to that end.
Bio::SeqFeature::CompoundSegment
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Freaky-dev branch development is temporarily geared towards in-house stability; these changes are to that end.
[Freaky-dev] More checkins for our freaky, freaky dev.
Bio::SeqFeature::FeaturePair
Fixed test failures in Genpred.t (the previous test count was wrong, which concealed a bug that Heikki fixed), and Pictogram.t (not graceful if SVG.pm is not installed). Fixed lots of knock-on bugs made effective by someone changing the implementation of SeqFeatureI methods in Generic. There is still one failure in SeqFeature.t.
Solved the dreaded feature1/feature2 not set chicken-and-egg problem by making the assumption that we can safely call set_attributes() after setting up ourselves. Not super-super-clean, but lets us get rid of ugly, error-prone, and slow code in SimilarityPair.
Fixed a few dormant bugs in the Gene features. SeqFeature.t passes all tests again, but Sim4 still doesn't. Adapted delegation calls to the best practice implementation.
Bio::SeqFeature::Gene::Exon
Fixed a few dormant bugs in the Gene features. SeqFeature.t passes all tests again, but Sim4 still doesn't. Adapted delegation calls to the best practice implementation.
Bio::SeqFeature::Gene::ExonI
Some experimental fixes to try and get rid of mem cycles with GeneStructure-Transcript objects - see Issue #1431
Bio::SeqFeature::Gene::GeneStructure
Some experimental fixes to try and get rid of mem cycles with GeneStructure-Transcript objects - see Issue #1431
SYNOPSIS is now runnable
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Bio::SeqFeature::Gene::Intron
Added methods for introns to pull out consensus splice sites, logic from ensembl's old intron module
Fixed a few dormant bugs in the Gene features. SeqFeature.t passes all tests again, but Sim4 still doesn't. Adapted delegation calls to the best practice implementation.
Bio::SeqFeature::Gene::NC_Feature
No change yet supposedly.
Fixed a few dormant bugs in the Gene features. SeqFeature.t passes all tests again, but Sim4 still doesn't. Adapted delegation calls to the best practice implementation.
Bio::SeqFeature::Gene::Transcript
Some experimental fixes to try and get rid of mem cycles with GeneStructure-Transcript objects - see Issue #1431
Added methods for introns to pull out consensus splice sites, logic from ensembl's old intron module
Attach seq only if provided
SYNOPSIS is now runnable
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::SeqFeature::Gene::TranscriptI
Allow resetting the parent to undef
Bio::SeqFeature::Gene::UTR
Fixed a few dormant bugs in the Gene features. SeqFeature.t passes all tests again, but Sim4 still doesn't. Adapted delegation calls to the best practice implementation.
Bio::SeqFeature::Generic
In score() checking that score is non-zero in conjunction with the number-checking regexp before throwing exception. Throwing a typed exception.
Insure sorted order of tags (so that they can at least be predictable- also allow resetting of values to undef via the newer more approved get/set code
Updated the biographics FAQ to accomodate changes in meaning of -seq_id vs -display_name in Bio::SeqFeature::Generic
Magically fixed the hmmer tests. Primarily I streamlined a lot of delegation calls to pass an array of arguments, rather than capturing a value and then passing it on. The latter is how we used to do it, but is incompatible with the new template for getter/setters.
Solved the dreaded feature1/feature2 not set chicken-and-egg problem by making the assumption that we can safely call set_attributes() after setting up ourselves. Not super-super-clean, but lets us get rid of ugly, error-prone, and slow code in SimilarityPair.
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
[Freaky dev] minor fixes
[Freaky-dev] more freaky development. Don't be alarmed, it's not on your branch.
[Freaky-dev] small stuff, wee and minor
[Freaky-dev] More changes for in-house joy here at the ISB.
[Freaky-dev] Added accessor to the 'link' tag via the 'link' method and its alias, 'make_link'; this is convenient for gbrowse, which previously assumed its features came from Bio::DB::GFF, where the Feature object had these methods.
[Freaky-dev] minor bugfix.
[Freaky-dev] I keep waffling on what to do about calling get_tag_values in scalar context. I put it back now so it returns the first entry in the list
Bio::SeqFeature::IteratorI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Freaky-dev branch development is temporarily geared towards in-house stability; these changes are to that end.
Bio::SeqFeature::NameNormalizerI
First steps towards standardizing a feature-name-standardizer interface
Bio::SeqFeature::PositionProxy
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::SeqFeature::Primer
SYNOPSIS is now runnable
Bio::SeqFeature::SegmentI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::SeqFeature::SegmentPositionProxy
The PositionProxy isa SeqFeatureI, so we've made this SegmentPositionProxy just the same, only it's a SegmentI not a SeqFeatureI
Erp! Wrong branch. Sorry!
The PositionProxy isa SeqFeatureI, so we've made this SegmentPositionProxy just the same, only it's a SegmentI not a SeqFeatureI
Bio::SeqFeature::SiRNA::Oligo
Added modules for small interfering RNA (siRNA) reagent design. Bio::Tools::SiRNA.pm designs reagents Bio::Tools::Mdust.pm uses the mdust algorithm to mask low-complexity regions. Bio::SeqFeature::SiRNA::Oligo.pm is the container for a single siRNA oligo Bio::SeqFeature::SiRNA::Pair.pm is the container for a dsRNA duplex t/sirna.t is the test program t/data/NM_002254.gb is the input for sirna.t (the available .gb files weren't suitable). Donald Jackson (donald.jackson@bms.com)
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::SeqFeature::SiRNA::Pair
Added modules for small interfering RNA (siRNA) reagent design. Bio::Tools::SiRNA.pm designs reagents Bio::Tools::Mdust.pm uses the mdust algorithm to mask low-complexity regions. Bio::SeqFeature::SiRNA::Oligo.pm is the container for a single siRNA oligo Bio::SeqFeature::SiRNA::Pair.pm is the container for a dsRNA duplex t/sirna.t is the test program t/data/NM_002254.gb is the input for sirna.t (the available .gb files weren't suitable). Donald Jackson (donald.jackson@bms.com)
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::SeqFeature::Similarity
Magically fixed the hmmer tests. Primarily I streamlined a lot of delegation calls to pass an array of arguments, rather than capturing a value and then passing it on. The latter is how we used to do it, but is incompatible with the new template for getter/setters.
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::SeqFeature::SimilarityPair
Added comment to score().
Magically fixed the hmmer tests. Primarily I streamlined a lot of delegation calls to pass an array of arguments, rather than capturing a value and then passing it on. The latter is how we used to do it, but is incompatible with the new template for getter/setters.
Solved the dreaded feature1/feature2 not set chicken-and-egg problem by making the assumption that we can safely call set_attributes() after setting up ourselves. Not super-super-clean, but lets us get rid of ugly, error-prone, and slow code in SimilarityPair.
Fixed Location::Atomic to not make up a value for strand if there wasn't one set. Fixed a whole series of knock-on effects - strand now had to become unsettable, which had another series of knock-on effects. All tests pass now.
Removed hack to detect when feature pair is being initialized. Shouldn't be necessary anymore.
Bio::SeqFeature::SimpleCollection
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
[Freaky-dev] small stuff, wee and minor
Bio::SeqFeature::SimpleCollectionProvider
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Bio::SeqFeature::SimpleIterator
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Freaky-dev branch development is temporarily geared towards in-house stability; these changes are to that end.
Bio::SeqFeature::SimpleSegment
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
The PositionProxy isa SeqFeatureI, so we've made this SegmentPositionProxy just the same, only it's a SegmentI not a SeqFeatureI
Freaky-dev branch development is temporarily geared towards in-house stability; these changes are to that end.
[Freaky-dev] More changes for in-house joy here at the ISB.
[Freaky-dev] More checkins for our freaky, freaky dev.
Bio::SeqFeature::Tools::Unflattener
Object for unflattening GenBank-style records into nested seqfeatures; al the tests for this are in Unflattener.t for more info, see the thread on bioperl-l Re: [Bioperl-l] module for unflattening GenBank/EMBL/DDBJ records June 2003 mail list archive
Bio::SeqFeature::TypeI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
[Freaky dev] minor fixes
Bio::SeqFeatureI
Temporary mass checkin of snapshot of Collection Consolodation, with hopes of more frequent checkins in the future. No need to freak out about these changes; they are on the freaky dev branch and affect only Paul Edlefsen and Lincoln Stein. Generic Genome Browser 2 alpha (for lack of a better designation) is checked in at gmod, and depends on these changes.
Bugfix in primary_tag() implementation: it wasn't handling arguments at all.
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Freaky-dev branch development is temporarily geared towards in-house stability; these changes are to that end.
Word wrapping verbatinm docs
Bio::SeqIO
SYNOPSIS is now runnable
Added locuslink info. alphabetized format list
Swissprot exports *fas files
Bio::SeqIO::chado
Use accession_number consistently
Bio::SeqIO::embl
Removed <15 letter check on tag names in feature table dumps for embl and genbank
Handle multiple dates
Handle multiple dates
Brought up to date with the HEAD
Bio::SeqIO::game
Use IO is deprecated in perl 5.8.0
Remove IO include since it is not necessary and perl5.8.0 complains about it
Bio::SeqIO::genbank
Fix e-mail contact
Removed <15 letter check on tag names in feature table dumps for embl and genbank
Fix Issue #1449 by adding redo in parsing loop for references since exact order is not required
Fix #1456 "sometimes generates extra sequence line". The new equence output code is from embl.pm
Removing redeclartion of a variable
Fix #1456 "sometimes generates extra sequence line".
Fixing again Issue #1456
Fixed Issue #1456 again
Issue #1455 write moltype for genpept records correctly
Issue #1455 write moltype for genpept records correctly
Bio::SeqIO::locuslink
Now, OntologyTerm annotations on the RichSeq go under AnnotationCollection tag 'ontology_term'. Let's make this standard!
Fixed code that assumed predicate terms would always come with an (mostly artificial) identifier. Reverted a change in the locuslink parser that set the ontology name for term annotations to an artificial name.
Bio::SeqIO::metafasta
Inital commit of sequence class with meta data
Bio::SeqIO::pir
modified so that roundtrip is possible: writer adds '>P1;' before the id and parser ignores it and the '>F1;' variant
Bio::SeqIO::swiss
Fix e-mail contact
Bugfixes on the freaky dev branch. Some of the tests were failing. A few still do. This is a work in progres..
Removed some temporary documentation that was no longer apropos
Brought up to date with the HEAD
Bio::SeqIO::tab
Initial commit
Bio::SeqUtils
Added mutate()
Mutate() now accepts an array of mutations as the second argument
More docs about mutate()
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::SimpleAlign
Displayname() was testing internally if a name inside a hash was true. Sometimes it returned false, although I do not understand how. Fixed it by testing the existance of the name.
Use gap character in addition to '.'
SYNOPSIS is now runnable
Fix inconsistency in determining sequence type as caught by Rob Finn
Bio::SimpleAnalysisI
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Structure::IO
SYNOPSIS is now runnable
Bio::Structure::SecStr::DSSP::Res
SYNOPSIS is now runnable
Bio::Taxonomy::Node
Support taxonomy node which is explicitly db awre - soon to replace Bio::Species
Some more documentation
Bio::Tools::Alignment::Consed
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Tools::Alignment::Trim
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Tools::Analysis::Protein::NetPhos
First commit of Bio::SimpleAnalysisI implementation NetPhos which isa WebAgent subclass
Bio::Tools::AnalysisResult
SYNOPSIS is now runnable
Bio::Tools::BPbl2seq
Small change (not really an API change I think) to allow BLAST report setting when initializing an object since bl2seq rpt doesn't contain this
Handle empty reports
Handle empty reports
Bio::Tools::BPlite::HSP
SYNOPSIS is now runnable
Bio::Tools::BPlite::Iteration
SYNOPSIS is now runnable
Bio::Tools::BPlite::Sbjct
SYNOPSIS is now runnable
Bio::Tools::Blast
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Tools::CodonTable
SYNOPSIS is now runnable
Bio::Tools::Eponine
SYNOPSIS is now runnable
Bio::Tools::Est2Genome
Provide option to return GeneStructure objects
Better return undef else infinite loop!
Bio::Tools::FootPrinter
Issue #1398 enhancement changes to grab parsimony score - object creation may need to change depending on how subfeatures behave in the future. Enhancements written by Mark Wagner
Bio::Tools::Geneid
Added geneid parser, tests and test data
Bio::Tools::Genemark
Last gene was not added into predictions I removed space characters at the end of the line which are now annoyingly highlighted by the emacs cperl mode.
Last gene was not added into predictions
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Bio::Tools::Genewise
Handle more than one gene prediction
Capture pseudogene tag
Some code formatting, add_tag_value proper
Bio::Tools::Genscan
Make array global since it is invariant AFAIK
Overhaul to the RelRange system: vast simplification and a new assumption, that folks will be giving coords on the plus strand unless they explictly say they're in minus-stranded coordinates (ie. indexed with 1 at the start of the minus strand, going up along the minus strand), using the nice new position_policy feature
Runnable synopsis
Bio::Tools::Glimmer
GlimmerM 3.0 parser
Bio::Tools::HMMER::Domain
Magically fixed the hmmer tests. Primarily I streamlined a lot of delegation calls to pass an array of arguments, rather than capturing a value and then passing it on. The latter is how we used to do it, but is incompatible with the new template for getter/setters.
Bio::Tools::Lucy
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Tools::Mdust
Added modules for small interfering RNA (siRNA) reagent design. Bio::Tools::SiRNA.pm designs reagents Bio::Tools::Mdust.pm uses the mdust algorithm to mask low-complexity regions. Bio::SeqFeature::SiRNA::Oligo.pm is the container for a single siRNA oligo Bio::SeqFeature::SiRNA::Pair.pm is the container for a dsRNA duplex t/sirna.t is the test program t/data/NM_002254.gb is the input for sirna.t (the available .gb files weren't suitable). Donald Jackson (donald.jackson@bms.com)
Moved Mdust.pm from Bio::Tools to Bio::Tools::Run (bioperl-run repository). Modified SiRNA.pm so it no longer runs Mdust automatically - must be done by user. Documentation has been updated to reflect this.
Bio::Tools::OddCodes
Fixed syntax in synopsis
Copied changes from HEAD: - warns on non-protein sequences - syntax correction in synopsis
SYNOPSIS is now runnable
Bio::Tools::Phylo::Molphy
Improve documentation, parse both types of probablity matricies, and provide runnable synopsis
SYNOPSIS is now runnable
Bio::Tools::Phylo::Molphy::Result
Improve documentation, parse both types of probablity matricies, and provide runnable synopsis
SYNOPSIS is now runnable
Bio::Tools::Phylo::PAML
SYNOPSIS is now runnable
Added support for:Pairwise AAML parsingAdded 2 methods to PAML::Result - AAMLDistMatrix for ML dist matrix from aaml - AADistMatrix regular pairwiwse dist matrix for aamlThese are both use Bio::Matrix::PhylipDist (for now) to store the pairwise distances, and can be output and provided to neighbor or other apps which use distmatriciesAlso added support for parsing Trees from codeml and aaml empirical models\n The loglikelihood for a tree is available via the 'score' field for the tree.Finally I added methods to get and set 'stats' which are basically misc. additionally information about the result. Things like the # of constant sites, etc. The methods get_stat_names, add_stat, get_stat are for this.Oh yeah, and I added a set_AAFreqs and get_AAFreqs for PAML::Result to store/retrieve the AA frequency data provided by aaml results as well. Data is hashed by sequence name and each sequence will have a hash with keys for all the AAs. The Average for the entire data set is also available with seqname 'Average' (so don't name any input sequence 'Average')
Bio::Tools::Phylo::PAML::Result
Added support for:Pairwise AAML parsingAdded 2 methods to PAML::Result - AAMLDistMatrix for ML dist matrix from aaml - AADistMatrix regular pairwiwse dist matrix for aamlThese are both use Bio::Matrix::PhylipDist (for now) to store the pairwise distances, and can be output and provided to neighbor or other apps which use distmatriciesAlso added support for parsing Trees from codeml and aaml empirical models\n The loglikelihood for a tree is available via the 'score' field for the tree.Finally I added methods to get and set 'stats' which are basically misc. additionally information about the result. Things like the # of constant sites, etc. The methods get_stat_names, add_stat, get_stat are for this.Oh yeah, and I added a set_AAFreqs and get_AAFreqs for PAML::Result to store/retrieve the AA frequency data provided by aaml results as well. Data is hashed by sequence name and each sequence will have a hash with keys for all the AAs. The Average for the entire data set is also available with seqname 'Average' (so don't name any input sequence 'Average')
Bio::Tools::Prediction::Exon
Fixed a few dormant bugs in the Gene features. SeqFeature.t passes all tests again, but Sim4 still doesn't. Adapted delegation calls to the best practice implementation.
SYNOPSIS is now runnable
Bio::Tools::Prediction::Gene
Fixed a few dormant bugs in the Gene features. SeqFeature.t passes all tests again, but Sim4 still doesn't. Adapted delegation calls to the best practice implementation.
SYNOPSIS is now runnable
Bio::Tools::Promoterwise
SYNOPSIS is now runnable
Adding these modules to synchronize between bioperl-run and bioperl core for 1.2.2 release
Bio::Tools::RestrictionEnzyme
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Issue #1454
Issue #1454 on 1.2 branch
Bio::Tools::Run::StandAloneBlast
SYNOPSIS is now runnable
Bio::Tools::SeqAnal
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Tools::SeqPattern
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Tools::SeqWords
SYNOPSIS is now runnable
Bio::Tools::SiRNA
Added modules for small interfering RNA (siRNA) reagent design. Bio::Tools::SiRNA.pm designs reagents Bio::Tools::Mdust.pm uses the mdust algorithm to mask low-complexity regions. Bio::SeqFeature::SiRNA::Oligo.pm is the container for a single siRNA oligo Bio::SeqFeature::SiRNA::Pair.pm is the container for a dsRNA duplex t/sirna.t is the test program t/data/NM_002254.gb is the input for sirna.t (the available .gb files weren't suitable). Donald Jackson (donald.jackson@bms.com)
Removed apparently superfluous import of GD::Text::Align.
Moved Mdust.pm from Bio::Tools to Bio::Tools::Run (bioperl-run repository). Modified SiRNA.pm so it no longer runs Mdust automatically - must be done by user. Documentation has been updated to reflect this.
Removed superfluous import of GD::Text::Align from my last commit (per Hilmar)
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Tools::Sigcleave
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Tools::Signalp
SYNOPSIS is now runnable
Bio::Tools::Sim4::Exon
Fixed a few dormant bugs in the Gene features. SeqFeature.t passes all tests again, but Sim4 still doesn't. Adapted delegation calls to the best practice implementation.
Bio::Tools::WWW
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Tools::dpAlign
Added Yee Man Chan's dpAlign alternative to pSW for pairwise alignments; requires latest CVS bioperl-ext
Bio::Tools::pICalculator
Mention that module allows multiple pK sets
Bio::Tree::AlleleNode
Some more docs for allele node
Bio::Tree::Node
Added code and warning: "Illegal characters ();: and space in the id [$value], converting to _ " based on: <http://evolution.genetics.washington.edu/phylip/newicktree.html> A name can be any string of printable characters except blanks, colons, semcolons, parentheses, and square brackets. Because you may want to include a blank in a name, it is assumed that an underscore character ("_") stands for a blank; any of these in a name will be converted to a blank when it is read in.
Fix docs a little
Generic tag/value adding allowed now
Some documentation addition
Bio::Tree::NodeI
Generic tag/value adding allowed now
Some documentation addition
Bio::Tree::NodeNHX
Generic tag/value adding allowed now
Bio::Tree::RandomFactory
SYNOPSIS is now runnable
Allow precision setting in add_Mutations
Some more docs
Bio::Tree::Statistics
Adding more popstats, need more work and might be moved to PopGen
Bio::Tree::TreeFunctionsI
Fix inconsistent SYNOPSIS
Bio::Tree::TreeI
Fixed method name in interface - should have been total_branch_length
Bio::TreeIO
Insure error message is sufficiently verbose - Issue #1439
Bio::TreeIO::TreeEventBuilder
Fix for labeled internal nodes as raised by Mike Eisen
Revert to a working version - will fall over when parsing with labeled nodes (but not leaves)
Auto load the modules
2nd attempt to parse internal node labels properly - tests pass - added the '-leaf' internal event for treebuilder
Bio::TreeIO::newick
Fix for labeled internal nodes as raised by Mike Eisen
Revert to a working version - will fall over when parsing with labeled nodes (but not leaves)
Include the id even on internal nodes - so we can store bootstrap values here and see them
For internal node printing in newick: use bootstrap as a label when it is present, otherwise use id, or nothing when both are empty
2nd attempt to parse internal node labels properly - tests pass - added the '-leaf' internal event for treebuilder
Probably a better check in case $chars is 0
Merged labeled node parsing from trunk to branch
Bio::TreeIO::nhx
Fix for labeled internal nodes as raised by Mike Eisen
Revert to a working version - will fall over when parsing with labeled nodes (but not leaves)
NHX writing won't write an empty node as the root of the tree, insure that the last node is also built
2nd attempt to parse internal node labels properly - tests pass - added the '-leaf' internal event for treebuilder
Bio::Variation::AAChange
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Variation::AAReverseMutate
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Variation::Allele
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Variation::DNAMutation
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Variation::IO
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Variation::IO::flat
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Variation::IO::xml
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Variation::RNAChange
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Variation::SNP
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Variation::SeqDiff
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::Variation::VariantI
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Bio::WebAgent
First commit of Bio::SimpleAnalysisI implementation NetPhos which isa WebAgent subclass
SYNOPSIS is now runnable
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
FAQ
Added Q1.12 & some format cleaning
SeqIO both from and to a string
Certainly an FAQ...
Minor changes
Whoops!
Fixed formatting error
Retrieve nucleotide CDS given a protein gi number
Added Q/A on spliced_seq, clarified 5.3
Changed version
Updated BLAST section
Makefile.PL
Added option to change Bio::DB::GFF driver between mysql, oracle and postgres
Minor fixes to BioDBGFF questioning for Postgres
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
Significantly improved the way that script installation works; should now be compatible with ppm-style packaging
Cleaned up command-line switches for GFF database loading scripts. Also changed Makefile.PL so that bp scripts are installed by default.
Set the version to 1.2.2 for what it is worth
Insure conf VERSION is up to date
bioscripts.pod
Added script
Added seqconvert.PLS
New scripts
Add pg_bulk_load_gff.PLS
Added local_taxonomydb_query.PLS
Install_bioperl_scripts will install the scripts/ scripts
More detail on examples/searchio scripts
Added mention of bp_ prefix
Added mention of bp_genbank2gff.PLS
Added mention of examples/biographics scripts. At one point I had GD working in Cygwin, but no longer, so I'm unable to see the *png files or correctly describe them.
Gccalc is in scripts/, not examples/
Gsequence is now gsequence.pl
Oligo_count is now in scripts/
No need for both examples/graphics and examples/biographics, I don't think
I believe vector.pl is no longer relevant, but I could be mistaken
bptutorial.pl
Mention of SeqIO HOWTO
Prettify
Need to explicitly set 'noclose' to 1 since default action on object cleanup is to close FH and in this case one is closing STDOUT fh
Fail nicely when necessary modules are not installed
Added Bio::DB::Fasta example
Version
examples/align/align_on_codons.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/align/aligntutorial.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/align/clustalw.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/align/simplealign.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/biblio/biblio_examples.pl
Adding this back - how did it vanish?
examples/biographics/render_sequence.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/cluster/dbsnp.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/contributed/nmrpdb_parse.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/contributed/prosite2perl.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/contributed/rebase2list.pl
And let's not forget these as well...
examples/db/est_tissue_query.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/db/gb2features.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/db/getGenBank.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/db/get_seqs.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/db/rfetch.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/db/use_registry.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/make_primers.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/root/lib/Bio/Seq.pm
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
examples/root/lib/Error.pm
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
examples/searchio/blast_example.pl
Prints usage message if there's no argument.
examples/searchio/custom_writer.pl
Using -format => blast instead of psiblast. Updated Updated comments a bit.
examples/searchio/hitwriter.pl
Using -format => blast instead of psiblast. Updated Updated comments a bit.
examples/searchio/hspwriter.pl
Using -format => blast instead of psiblast. Updated Updated comments a bit.
examples/searchio/htmlwriter.pl
Changed -format to 'blast' from 'psiblast'
Using -format => blast instead of psiblast. Updated Updated comments a bit.
Changed usage to accept a report filename on command-line. Generates usage msg and exits if not supplied. Seems more appropriate for HTML generation.
examples/searchio/psiblast_iterations.pl
* Demonstrates how to process a PSI-BLAST report one iteration at a time. This code is currently identical to that in the SYNOPSIS section of Bio::Search::Iteration::IterationI.
examples/searchio/resultwriter.pl
Using -format => blast instead of psiblast. Updated Updated comments a bit.
examples/tk/gsequence.pl
And let's not forget these as well...
examples/tk/hitdisplay.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/tools/gb_to_gff.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/tools/gff2ps.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/tools/parse_codeml.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/tools/psw.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/tools/restriction.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/tools/run_genscan.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/tools/seq_pattern.pl
Big mistake on my part - I lost track of some examples/ scripts
examples/tree/paup2phylip.pl
Big mistake on my part - I lost track of some examples/ scripts
maintenance/README
Initial commit
maintenance/modules.pl
Initial commit
Slightly improved version: Now it parses the modules to extract information about them. --untested option excludes classes if they are superclasses or used by tested classes.
Added first test for inheritance patterns, option --inherit
Added --synopsis and --dir options. The defaultdirectory is now relative and should work for anyone using bioperl_all cvs module
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Small touchup so that modules.pl works on a less-than-stable checkout
Fixed --version
maintenance/pod.pl
Initial commit
scripts/Bio-DB-GFF/TAG
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
scripts/Bio-DB-GFF/bp_genbank2gff.PLS
Added a genbank/embl loader for Bio::DB::GFF
scripts/Bio-DB-GFF/bulk_load_gff.PLS
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
Fixed problem with DNA not loading correctly on windows platforms
Cleaned up command-line switches for GFF database loading scripts. Also changed Makefile.PL so that bp scripts are installed by default.
scripts/Bio-DB-GFF/fast_load_gff.PLS
Cleaned up command-line switches for GFF database loading scripts. Also changed Makefile.PL so that bp scripts are installed by default.
scripts/Bio-DB-GFF/load_gff.PLS
Cleaned up command-line switches for GFF database loading scripts. Also changed Makefile.PL so that bp scripts are installed by default.
scripts/Bio-DB-GFF/load_ucsc.pl
Adding per mummi's req
scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS
Added Scott Cain's PostgreSQL Bio::DB::GFF bulk loader
Fixed choking on malformed gff line
Several changes: for pg.pm, removed UNIQUE constraint on fdata; a straight btree index takes its place. The unique constraint can cause bulk loads to fail. For pg_bulk_load_gff.PLS, several things: * failure to load the fmeta table fixed. * actual loading method improved, giving both increased performance and the possibility of running on Windows (not yet tested). * separated table creation from index creation.
Added a message about creating indexes
Do_initialize needs to return true
Changed UI to be consistent with the MySQL bulk loader
scripts/Bio-DB-GFF/process_gadfly.PLS
Updated the wormbase GFF munging script to use public access AceDB server
scripts/Bio-DB-GFF/process_wormbase.PLS
Updated the wormbase GFF munging script to use public access AceDB server
scripts/DB/TAG
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
scripts/biblio/TAG
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
scripts/das/TAG
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
scripts/graphics/TAG
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
scripts/index/TAG
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
scripts/index/bpfetch.PLS
Less strict on loading remote modules for non LWP sites
scripts/install_bioperl_scripts.pl
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
Script installer now adds bp_ prefix to all scripts if they don't have them already; biographics now can create gene diagrams in the UCSC Genome Browser Style in addition to the default EnsEMBL/WormBase style; new processed_transcript glyph is Sequence Ontology (tm) compatible
Changed default from y to n
scripts/seq/TAG
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
scripts/seq/seqconvert.PLS
Initial commit
More formats
scripts/seq/split_seq.PLS
Added in some new sequence manipulation scripts
scripts/seq/translate_seq.PLS
Added in some new sequence manipulation scripts
scripts/seqstats/TAG
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
scripts/taxa/TAG
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
scripts/taxa/local_taxonomydb_query.PLS
Implementation of local taxonomy DB species -> taxonid only implemented now - rest of methods will come soon
scripts/tree/TAG
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
scripts/tree/blast2tree.PLS
Feature API has changed some
scripts/utilities/TAG
Added system for interactive or batch installation of the contents of the Bioperl scripts directory.
scripts/utilities/bp_sreformat.PLS
Doc fixes
Support the -idlength initializer value so you can override the default 10 char limit for sequence ids for PHYLIP files
scripts/utilities/pairwise_kaks.PLS
Add info to the error
scripts/utilities/search2BSML.PLS
Dump BSML from a SearchIO parsed report
scripts/utilities/search2gff.PLS
Turn Search reports into GFF
NAME
Allow a cutoff value to be specified
More general way to get the features and not have to go about dropping fields
Add a number to the end of hits which occur more than once in a sequence which will otherwise screw up in gbrowse
scripts/utilities/search2tribe.PLS
Case insensitive
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