Core 0.7.1 0.9.0 delta

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