Core 0.7.1 0.9.0 delta

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These are detailed notes on changes made between release-0-7-1 and release-0-9-0.

Bio::DB::Fasta
Fixed an error in Bio::DB::Fasta that prevented index for being rebuilt automatically when source file is updated
Bio::DB::GFF
Added functional but undocumented GFF database routines - for lightweight DAS server
Started adding documentation for the Bio::DB::GFF hierarchy.
Put Makefile.PL back into MANIFEST - why was it gone?\nAdded more documentation to Bio::DB::GFF\n
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
Added a bit more document to the Bio::DB::GFF module and fixed some bugs. Also implemented iterators (stream fetches) and ability to find all features of a particular type on the genome.
More documentation. Relative offsets from features should now work correctly. Data loading abstraction has been improved. Group class parsing is better but possibly still buggy.
- More documentation added. - Fixed a relative coordinate addressing bug when calling refseq() with a Bio::DB::GFF::RelSegment object as the reference.
More documentation...
Added more documentation to Bio::DB::GFF and reorganized api for aggregators. May not be entirely functional.
Started documenting Bio::DB::GFF::Adaptor subclasses.
Documentation nearly done
Added a contained_features() method
Fixed documentation bug (dbi::mysql with two colons). Fixed types() query, which left the right end of the range open.
Modified order of arguments in (internal) procedure get_dna().
Bio::DB::GFF::Adaptor::dbi
Added functional but undocumented GFF database routines - for lightweight DAS server
Started adding documentation for the Bio::DB::GFF hierarchy.
Put Makefile.PL back into MANIFEST - why was it gone?\nAdded more documentation to Bio::DB::GFF\n
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
Added a bit more document to the Bio::DB::GFF module and fixed some bugs. Also implemented iterators (stream fetches) and ability to find all features of a particular type on the genome.
More documentation. Relative offsets from features should now work correctly. Data loading abstraction has been improved. Group class parsing is better but possibly still buggy.
- More documentation added. - Fixed a relative coordinate addressing bug when calling refseq() with a Bio::DB::GFF::RelSegment object as the reference.
Documented Aggregator and Typename classes
Started documenting Bio::DB::GFF::Adaptor subclasses.
Documentation nearly done
Added a contained_features() method
Fixed bug that occurs when fetching an iterator across all features.
Modified order of arguments in (internal) procedure get_dna().
Bio::DB::GFF::Adaptor::dbi::mysql
Added functional but undocumented GFF database routines - for lightweight DAS server
Started adding documentation for the Bio::DB::GFF hierarchy.
Put Makefile.PL back into MANIFEST - why was it gone?\nAdded more documentation to Bio::DB::GFF\n
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
Added a bit more document to the Bio::DB::GFF module and fixed some bugs. Also implemented iterators (stream fetches) and ability to find all features of a particular type on the genome.
More documentation. Relative offsets from features should now work correctly. Data loading abstraction has been improved. Group class parsing is better but possibly still buggy.
More documentation...
Documented Aggregator and Typename classes
Documentation nearly done
Added a contained_features() method
Bio::DB::GFF::Adaptor::dbi::mysqlopt
Added functional but undocumented GFF database routines - for lightweight DAS server
Started adding documentation for the Bio::DB::GFF hierarchy.
Put Makefile.PL back into MANIFEST - why was it gone?\nAdded more documentation to Bio::DB::GFF\n
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
Added a bit more document to the Bio::DB::GFF module and fixed some bugs. Also implemented iterators (stream fetches) and ability to find all features of a particular type on the genome.
More documentation. Relative offsets from features should now work correctly. Data loading abstraction has been improved. Group class parsing is better but possibly still buggy.
Added a contained_features() method
Modified order of arguments in (internal) procedure get_dna().
Fixed an error in Bio::DB::Fasta that prevented index for being rebuilt automatically when source file is updated
Bio::DB::GFF::Aggregator
Added functional but undocumented GFF database routines - for lightweight DAS server
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
More documentation...
Added more documentation to Bio::DB::GFF and reorganized api for aggregators. May not be entirely functional.
Documented Aggregator and Typename classes
Bio::DB::GFF::Aggregator::alignment
Added functional but undocumented GFF database routines - for lightweight DAS server
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
Added more documentation to Bio::DB::GFF and reorganized api for aggregators. May not be entirely functional.
Started documenting Bio::DB::GFF::Adaptor subclasses.
Bio::DB::GFF::Aggregator::clone
Added functional but undocumented GFF database routines - for lightweight DAS server
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
Added more documentation to Bio::DB::GFF and reorganized api for aggregators. May not be entirely functional.
Started documenting Bio::DB::GFF::Adaptor subclasses.
Bio::DB::GFF::Aggregator::none
Added functional but undocumented GFF database routines - for lightweight DAS server
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
Started documenting Bio::DB::GFF::Adaptor subclasses.
Bio::DB::GFF::Aggregator::transcript
Added functional but undocumented GFF database routines - for lightweight DAS server
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
More documentation...
Started documenting Bio::DB::GFF::Adaptor subclasses.
Bio::DB::GFF::Featname
Added functional but undocumented GFF database routines - for lightweight DAS server
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
More documentation. Relative offsets from features should now work correctly. Data loading abstraction has been improved. Group class parsing is better but possibly still buggy.
More documentation...
Bio::DB::GFF::Feature
Added functional but undocumented GFF database routines - for lightweight DAS server
Started adding documentation for the Bio::DB::GFF hierarchy.
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
Added a bit more document to the Bio::DB::GFF module and fixed some bugs. Also implemented iterators (stream fetches) and ability to find all features of a particular type on the genome.
More documentation. Relative offsets from features should now work correctly. Data loading abstraction has been improved. Group class parsing is better but possibly still buggy.
- More documentation added. - Fixed a relative coordinate addressing bug when calling refseq() with a Bio::DB::GFF::RelSegment object as the reference.
More documentation...
Bio::DB::GFF::Homol
Added functional but undocumented GFF database routines - for lightweight DAS server
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
More documentation...
Bio::DB::GFF::RelSegment
Added functional but undocumented GFF database routines - for lightweight DAS server
Started adding documentation for the Bio::DB::GFF hierarchy.
Put Makefile.PL back into MANIFEST - why was it gone?\nAdded more documentation to Bio::DB::GFF\n
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
Added a bit more document to the Bio::DB::GFF module and fixed some bugs. Also implemented iterators (stream fetches) and ability to find all features of a particular type on the genome.
More documentation. Relative offsets from features should now work correctly. Data loading abstraction has been improved. Group class parsing is better but possibly still buggy.
- More documentation added. - Fixed a relative coordinate addressing bug when calling refseq() with a Bio::DB::GFF::RelSegment object as the reference.
More documentation...
Added a contained_features() method
Modified order of arguments in (internal) procedure get_dna().
Small consistency checking addition in RelSegment.pm
Bio::DB::GFF::Segment
Added functional but undocumented GFF database routines - for lightweight DAS server
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
More documentation. Relative offsets from features should now work correctly. Data loading abstraction has been improved. Group class parsing is better but possibly still buggy.
- More documentation added. - Fixed a relative coordinate addressing bug when calling refseq() with a Bio::DB::GFF::RelSegment object as the reference.
More documentation...
Modified order of arguments in (internal) procedure get_dna().
Bio::DB::GFF::Type
Added functional but undocumented GFF database routines - for lightweight DAS server
Documented Aggregator and Typename classes
Bio::DB::GFF::Typename
Added functional but undocumented GFF database routines - for lightweight DAS server
Downgraded Bio::DB::GFF for perl versions earlier than 5.6
Documented Aggregator and Typename classes
Bio::DB::GFF::Util::Binning
Added functional but undocumented GFF database routines - for lightweight DAS server
Started adding documentation for the Bio::DB::GFF hierarchy.
Bio::DB::GFF::Util::Rearrange
Added functional but undocumented GFF database routines - for lightweight DAS server
Bio::DB::GenBank
Synopsis code is cut and paste runnable
Bio::DB::MANIFEST
More documentation. Relative offsets from features should now work correctly. Data loading abstraction has been improved. Group class parsing is better but possibly still buggy.
Bio::DB::Makefile.PL
More documentation. Relative offsets from features should now work correctly. Data loading abstraction has been improved. Group class parsing is better but possibly still buggy.
Bio::DB::SeqI
Documentation correction, still need to tighten up definition of SeqI w or w/o a SeqStream
Bio::Factory::ApplicationFactoryI
A better location to these modules
Bio::Factory::EMBOSS
A better location to these modules
Bio::Factory::SeqAnalysisParserFactory
Added epcr to factory
Bio::LiveSeq::Mutator
Exon number was off by one
Exon number was off by one
Bio::LocatableSeq
Added Bio::LocatableSeq::location_from_column (complement of Bio::SimpleAlign::column_from_residue_number), docs and tests
Bio::PrimarySeq
Adding much needed documentation to PrimarySeq
Documentation about 'new' to be added to 0.7.2
Update synopsis documentation
Bio::PrimarySeqI
Documentation update
Bio::Seq
Prepare for 0.7.2 release
Bio::Seq::RichSeq
Initialize parameters in constructor
Bio::SeqFeature::Exon
Adding much needed documentation to PrimarySeq
Bio::SeqFeature::Generic
Adding much needed documentation to PrimarySeq
Bio::SeqIO
Consolidated suffix match
Adding much needed documentation to PrimarySeq
Bio::SeqIO::embl
Adding much needed documentation to PrimarySeq
Bio::SeqIO::fasta
Remove '>' in the regex if present
Documentation update
Bio::SeqIO::gcg
Make GCG a little more format strict -- still some minor issues to resolve
Bio::SeqIO::pir
Pir read/write w/o quality info
Bio::SimpleAlign
Added Bio::LocatableSeq::location_from_column (complement of Bio::SimpleAlign::column_from_residue_number), docs and tests
Bio::Tools::ApplicationFactoryI
Classes for wrapping EMBOSS suite
Added Bio::LocatableSeq::location_from_column (complement of Bio::SimpleAlign::column_from_residue_number), docs and tests
Bio::Tools::BPlite
Handle commas in the qlength
Bio::Tools::BPlite::HSP
Gaps method from Kris Vlahovicek hsplength method to handle consensus length of HSP percent identity is now relative to hsplength not just sjbct
Bio::Tools::BPlite::Sbjct
Gaps method from Kris Vlahovicek hsplength method to handle consensus length of HSP percent identity is now relative to hsplength not just sjbct
Calculate hsplength properly - derived from Identities directly
Bio::Tools::CodonTable
Further prompting from Amir got me to reorganize translation code for easier reading and maintainability. As a side effect, overall performace increased again a bit (25-50%). The speedup is most notable in short sequncences, so the total speedup from 0.7 translation is now 6-10x.
Translate() throws without a sequence argument
Bio::Tools::EMBOSSFactory
Classes for wrapping EMBOSS suite
Added Bio::LocatableSeq::location_from_column (complement of Bio::SimpleAlign::column_from_residue_number), docs and tests
Bio::Tools::EPCR
EPCR parsing
Bio::Tools::IUPAC
Documentation update
Bio::Tools::Run::EMBOSSApplication
Classes for wrapping EMBOSS suite
Claning. Needs code to compare input and ACD options
Bio::Tools::Run::RemoteBlast
Documentation for retrieve_blast method
Bio::Variation::AAChange
New method similarity_score() gives a value for amino acid change using BLOSUM62
Makefile.PL
Prepare for 0.7.2 release
Made version number CPAN compatible
Preparing for 0.9.0 tagging and release
$VERSION: "0.9.0" > "0.90"
0.9 branch will require 5.005 minimally
bioperl.lisp
Methods are more what we need
models/maps_and_markers.dia
Conceptual model for maps and marker objects begun by Heikki and Jason
scripts/blast_fetch_local.pl
Retrieve sequences for a blast report from a local index of the db
scripts/est_tissue_query.pl
Query for tissues from an est BLAST
scripts/generate_random_seq.pl
Generate a random sequence (normal distribution) in fasta format
scripts/get_seqs.pl
Added script to download seqs from remote dbs
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