Core 1.2.3 1.4.0 delta

These are detailed notes on changes made between bioperl-release-1-2-3 and bioperl-release-1-4-0.

Bio::Align::DNAStatistics

Made it possible to silence the warnings

Code alignment formatting

Runnable synopsis

Bio::AlignIO

Adding a parser and tests for UCSC maf (multiple alignment format) format. added a method SimpleAlign::splice_by_seq_pos to allow splicing of all sequences based on the gap locations of one sequence within the alignment. this could in principle be called repeatedly to remove all gaps from the MSA.

Guessing sequence and align formats by looking into file

Make format guessing to follow same logic as in Bio::SeqIO. Tests pass.

Fail better with no arguments to new()

Changed GuessSeqFormat to return undef

Bio::AlignIO::bl2seq

Johnathan Segal's fixes for Issue #1541 - problem with reverse complement alignments in bl2seq

Use SearchIO instead BPbl2seq

Bio::AlignIO::maf

Adding a parser and tests for UCSC maf (multiple alignment format) format. added a method SimpleAlign::splice_by_seq_pos to allow splicing of all sequences based on the gap locations of one sequence within the alignment. this could in principle be called repeatedly to remove all gaps from the MSA.

Cleaned up unit test spurious warnings. bugfix in maf parser for detecting last record in file. added functionality to trim gaps from a MSA for a given sequence to SimpleAlign. trimming allowed implementation of exporting Seq and SeqFeatures from SimpleAlign. the api here is still rough, comments appreciated.

Offset location of new seq with features by location of original seq requested to build from. added rudimentary key/value parsing for maf 'a' lines

Silencing a warning when running tests

Bio::Annotation::Comment

Overload double quot as as_text. but comment them, since it does not work with other modules

Bio::Annotation::DBLink

Overload double quot as as_text. but comment them, since it does not work with other modules

Bio::Annotation::OntologyTerm

Replaced call to phased out each_synonym by get_synonyms.

Replaced call to phased out each_synonym by get_synonyms.

Bio::Annotation::Reference

Overload double quot as as_text. but comment them, since it does not work with other modules

Bio::Coordinate::Collection

Add a method mapper_count - to get the number of stored mappers

Bio::Coordinate::GeneMapper

Cleanup code a little. use debug instead of print STDERR

Bio::Coordinate::Pair

Need to treat 0 as +1 for protein based strands

Bio::Coordinate::Result

Cleanup code a little

Bio::Coordinate::Utils

Each_mapper returns an array, not arrayref

Bio::DB::Fasta

Fixed issue of _split_group() being called as class method

Modified Bio::DB::Fasta so as to correctly reindex files created using the NDBM .pag and .dir files

Bio::DB::Fasta now handles CRLF files generated on windows platforms

Bio::DB::Flat

Some -index value has to be passed, it's required and there's no default value. Fixes Daniel Lang's bug.

The following regression tests now pass: GFF, SeqFeature, Registry

Bio::DB::Flat::BinarySearch

More detail on secondary namespaces

Bio::DB::GFF

Added minor workarounds for Bio::DB::GFF roundtripping to artemis

Caveat emptor and all other disclaimers. I just need to get Sheldon's changes into the CVS so that I can merge it with my own changes. Again, if this causes anyone heartache I have made backups of the original and I can roll back. The changes here are primarily to deal with the GFF2.5 format GFF that handles alignment features

Generalized Mark and Sheldon's GFF 2.5 unflattening scheme

Improved API for preferred_groups() method

Fixed issue of _split_group() being called as class method

Made a small change in group assignments so that the order in which preferred groups are listed determines precedence

Retracting edits on the _split_gff2_method until after the 1.4 release. Manipulating GFF group assignments requires further testing

Bio::DB::GFF::Adaptor::biofetch

Changes making genbank2gff.pl use SOFA terms for type names in generated GFF3

Minor, probably temporary, fixes to biofetch adaptor for genbank2gff

This biofetch adaptor and genbank2gff are better than before, but not yet perfect. Fixed: - Gets right the parentage of CDSs (belong to mRNAs) and exons (belong to chromosomes or other regions). - variation features are now clasified as SNPs (if the length is 1), else chromosome_variation. - no longer creates CDS lines that span introns. Remaining problems: - with multiple transcript genes, it can get confused as to which CDSs go with which mRNA (solution: reimplement with Unflattener) - SNP features can all get assigned the same ID, which is illegal in GFF3, though I don't think it will cause problems with gbrowse (though it probably will with chado).

Bio::DB::GFF::Adaptor::dbi

Fixed Issue #1384; histograms not working

Bio::DB::GFF::Adaptor::dbi::iterator

Added postgres adaptor

Bio::DB::GFF::Adaptor::dbi::oracle

Added postgres adaptor

I need to commit some of Sheldon's changes in order to merge them with my own changes at home. Hopefully this doesn't break anyone elses code - it should not affect anyone who is not using alignmnet features in Gbrowse GFF format, or GFF3 format. If this hurts anyone let me know and I will rollback the changes. I'm in purgatory anyway, so...

Bio::DB::GFF::Adaptor::dbi::pg

Added postgres adaptor

Bio::DB::GFF::Adaptor::memory

Added postgres adaptor

Removed global $VERSION

Generalized Mark and Sheldon's GFF 2.5 unflattening scheme

Fixed a bug that caused wildcard search to return unexpected results.

Bio::DB::GFF::Adaptor::memory_iterator

Added postgres adaptor

Bio::DB::GFF::Aggregator

Fixed errors in the high-mag sequence alignments shown by the segments glyph

Bio::DB::GFF::Feature

Added recursive gff3 dumping to Bio::DB::GFF

Added minor workarounds for Bio::DB::GFF roundtripping to artemis

Fixed overly-promiscuous regexp for detecting FASTA files

I need to commit some of Sheldon's changes in order to merge them with my own changes at home. Hopefully this doesn't break anyone elses code - it should not affect anyone who is not using alignmnet features in Gbrowse GFF format, or GFF3 format. If this hurts anyone let me know and I will rollback the changes. I'm in purgatory anyway, so...

Removing debugging messages

Silence the uninitialized value error

Reworked the following methods to more closely resemble the corresponding Bio::SeqFeatureI methods: all_tags (alias get_all_tags) gff_string get_tag_values aliased sub_SeqFeature to get_SeqFeatures

Generalized Mark and Sheldon's GFF 2.5 unflattening scheme

Quoting freetext in group name value of GFF2 output

Bio::DB::GFF::RelSegment

Added minor workarounds for Bio::DB::GFF roundtripping to artemis

Bio::DB::Query::WebQuery

Quell undef warnings - not sure why version is not properly set

Honour proxy environment variables like suggested in #1482

Bio::DB::Registry

ActiveState has no getpwuid() so AS users can use /home/bosborne

The HOWTO says that one should be able to use 1 or more seqdatabase.ini files. This is right, since the administrator could put one in /etc/bioinformatics and I might want my own in /home/bosborne/.bioinformatics. The old code was reading 1 *ini file and skipping the rest in OBDA_SEARCH_PATH, now it reads all the files specified in OBDA_SEARCH_PATH, as well as the standard locations.

Bio::DB::WebDBSeqI

Reset MODVERSION to use Packagewide Version system - change agent string to be 'bioperl-Bio_DB_GenBank/1.3' for example

Honour proxy environment variables like suggested in #1482

Bio::Expression::FeatureGroup

Allowing an underscore in ontology IDs. this is necessary to be able to parse cjm's OBO_REL relationship ontology, which otherwise observes DAG-Edit format

Bio::Factory::BlastHitFactory

Removing PSIBLAST modules

Bio::Factory::BlastResultFactory

Removing PSIBLAST modules

Bio::Factory::SequenceFactoryI

Some teeny bit of background/justification in the docs

Bio::Graphics::Feature

Substantial changes to Bio::Graphics::Feature to remain in synch with Bio::Tools::GFF

Fixed GFF2 dumping functions which broke when I added GFF3 dumping

Methods added so that a Feature really complies with the SeqI interface... Needed primary_seq especially, but added get_SeqFeatures and the rest to bring it up to spec for 1.3.x

Bio::Graphics::FeatureFile

Fixed errors in score handling in FeatureFile

Fixed various problems in the graphics layer when dealing with scored features

Substantial changes to Bio::Graphics::Feature to remain in synch with Bio::Tools::GFF

All functionality moved to Bio::DB::GFF->split_group, however still see major perf problems, not sure if this is localized to FeatureFile or not

Bio::Graphics::FeatureFile: remove uninit variable warning when calling features() without arguments; fixed frend web-based feature renderer to accomodate recent changes in FeatureFile API

Adding a symbol to access a feature's primary ID (eg, database PK)

Added a finished() method to Bio::Graphics::Panel in order to break cycles that lead to memory leaks when multiple panels are created and used

Bio::Graphics::Glyph

Added -codontable options to the glyphs that produce protein translations; courtesy Linda Sperling

Fixed implementation of user-defined glyph sort routines

Fixed implementation of user-defined glyph sort routines

Partial fix for incorrectly-rendered half-open intervals

Preliminary support for SVG output using GD::SVG

Fixed errors in the high-mag sequence alignments shown by the segments glyph

Polygon-based approach in filled_arrow to support SVG

Made the filled_oval and oval methods compatible with SVG (were just drawing closed arcs)

Fixed crashes that occured when calling boxes() before gd()

Made image_class, image_package, and polygon_package methods public (and fixed glyphs accordingly)

Added the track to the information retrieved by the boxes() method

Fixed issue of _split_group() being called as class method

Added a finished() method to Bio::Graphics::Panel in order to break cycles that lead to memory leaks when multiple panels are created and used

Added docs describing how subclassers should handle generic image packages

Bio::Graphics::Glyph::Factory

Fixed implementation of user-defined glyph sort routines

Fixed implementation of user-defined glyph sort routines

Preliminary support for SVG output using GD::SVG

Bio::Graphics::Glyph::arrow

Partial fix for incorrectly-rendered half-open intervals

Bio::Graphics::Glyph::box

Fixed behavior of the "box" glyph; there are still anomalies in drawing due to SVG addition

Bio::Graphics::Glyph::cds

Added -codontable options to the glyphs that produce protein translations; courtesy Linda Sperling

Bio::Graphics::Glyph::diamond

Converted line-based outline to polygon calls

Simplified the call to the polygon package

Removed the hardcoded image class conditional for filled triangles

Made image_class, image_package, and polygon_package methods public (and fixed glyphs accordingly)

Bio::Graphics::Glyph::dot

SVG compliancy marches on: changed the closed-arc method to ellipse and filledEllipse

Bio::Graphics::Glyph::ellipse

Inherits from generic instead of Glyph so that it can now draw labels!

Bio::Graphics::Glyph::generic

Added -codontable options to the glyphs that produce protein translations; courtesy Linda Sperling

Generalized some code to support SVG output

Line-based arrows now render properly when drawn in SVG

Made image_class, image_package, and polygon_package methods public (and fixed glyphs accordingly)

Minor code formatting changes.

Fixed behavior of the "box" glyph; there are still anomalies in drawing due to SVG addition

Fixed the arrow glyph to be consistent with pre-SVG appearance

Bio::Graphics::Glyph::graded_segments

General fixups of the xyplot and graded_segment glyphs

Fixed various problems in the graphics layer when dealing with scored features

Fixed Bio::SeqFeature::Generic so that it will accept a score of 0; modified Bio::Graphics::Glyph::graded_segment so that it draws a fg box around each segment by default (can restore default behavior with -vary_fg=>1)

Bio::Graphics::Glyph::minmax

General fixups of the xyplot and graded_segment glyphs

Fixed various problems in the graphics layer when dealing with scored features

Bio::Graphics::Glyph::pinsertion

Generalized the image_class call fo SVG support; enabled bordered fills

Made image_class, image_package, and polygon_package methods public (and fixed glyphs accordingly)

Bio::Graphics::Glyph::rndrect

Generalized image_class; now supports SVG

Made image_class, image_package, and polygon_package methods public (and fixed glyphs accordingly)

Bio::Graphics::Glyph::segments

Added a new "canonical_strand" option to the segments glyph

Fixed errors in the high-mag sequence alignments shown by the segments glyph

Added additional documentation for displaying multiple alignments with the segments glyph

Bio::Graphics::Glyph::translation

Added -codontable options to the glyphs that produce protein translations; courtesy Linda Sperling

Bio::Graphics::Glyph::triangle

Try to fix GD buffer overrun in triangle glyph

More range checking on triangle glyph before fillToBorder call

Preliminary support for polygon-based approach - needs full testing

Converted to plygon method for SVG-compliancy

Made image_class, image_package, and polygon_package methods public (and fixed glyphs accordingly)

Bio::Graphics::Glyph::xyplot

General fixups of the xyplot and graded_segment glyphs

Fixed errors in score handling in FeatureFile

Fixed various problems in the graphics layer when dealing with scored features

Removed function-oriented GD calls for compatability with SVG output

Removed a superfluous comment. hohum.

Bio::Graphics::Panel

Fixed implementation of user-defined glyph sort routines

Fixed implementation of user-defined glyph sort routines

Preliminary support for SVG output using GD::SVG

Fixed crashes that occured when calling boxes() before gd()

Shmooshed the hard-coded key-label font color - still hard-coded - needs to be worked into config

Removed redundant variable declaration in same scope

Made image_class, image_package, and polygon_package methods public (and fixed glyphs accordingly)

Minor code formatting changes.

Fixed the call to panel->height() to avoid a font exception when not running in SVG mode

Added the track to the information retrieved by the boxes() method

Added missing documentation for the Bio::Graphics::Panel->insert_track() method

Added a finished() method to Bio::Graphics::Panel in order to break cycles that lead to memory leaks when multiple panels are created and used

Brackets wrong way round. Thanks, Aaron!

Still trying to get this right

Added and svg() for lazy coders (well, more to mimic the png())

Bio::Graphics::Pictogram

This was spewing out huge numbers of warnings: 'Use of uninitialized value in division'

Support lowercase

Now supporting Bio::Matrix::PSM::SiteMatrix objects

Bio::Index::Abstract

Don't warn if we set verbose to -1

Bio::LocatableSeq

Johnathan Segal's fixes for Issue #1541 - problem with reverse complement alignments in bl2seq

Adding a parser and tests for UCSC maf (multiple alignment format) format. added a method SimpleAlign::splice_by_seq_pos to allow splicing of all sequences based on the gap locations of one sequence within the alignment. this could in principle be called repeatedly to remove all gaps from the MSA.

Fixed trunc() when strand is -1. Also made end() calculate its value based on the length of the sequence and start. no need to set end() expicitely any more

Silence a spurious warning arising from unset strand

Start() and end() now return undef if there is no sequence string

The following regression tests now pass: GFF, SeqFeature, Registry

Restoring previous functionality, clearer code from Lincoln

Bio::Location::Atomic

Corrected destructive getter in strand function

Comments per Issue #1572 - experimental method trunc() is undocumented

Bio::Location::Fuzzy

Don't emit warnings if/when strand is undef

Bio::Location::Simple

Fixes Issue #1535: "complement" was lost in single residue features in to_FTstring()

Comments per Issue #1572 - experimental method trunc() is undocumented

Bio::Matrix::PSM::IO

Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers

Start up cleanup - tests run but not all pass just yet

Bio::Root::Root missing from @ISA, added

Bio::Matrix::PSM::IO::mast

Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers

Start up cleanup - tests run but not all pass just yet

Capitalization fixed when rearranging in new

Two bug fixes: sequence is unknown, but width is, so we supply it as 'NNN..' Accession number should be supplied as -accession_number

Doc formatting fixes

Fixed a bug- warns instead of throwing an exception when the MAST report is empty

Ooops.. misssed some()

Cannot read HTML, would hang, fixed

Bio::Matrix::PSM::IO::meme

Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers

Change in meme parser: definition of primary id vs. accession number

Start up cleanup - tests run but not all pass just yet

Capitalization fixed when rearranging in new

Rare bug, actually not exactly bug: If MEME fails during the analysis it will create the proper file that terminates prematurely. The parser now will warn user of that instead of the dying. User will still be able to get the data for the successfully predicted ones. If no motifs were predicted the parser still dies with message that wrong format was passed (which is reasonable I think).

Rare bug, actually not exactly bug: If MEME fails during the analysis it will create the proper file that terminates prematurely. The parser now will warn user of that instead of the dying. User will still be able to get the data for the successfully predicted ones. If no motifs were predicted the parser still dies with message that wrong format was passed (which is reasonable I think). oops, works now

Bio::Matrix::PSM::IO::transfac

Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers

Start up cleanup - tests run but not all pass just yet

Capitalization fixed when rearranging in new

Throw exception if a position is not defined

Bio::Matrix::PSM::InstanceSite

Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers

Bug fix: accession vs accession_number, removed redundant identifiers

Start up cleanup - tests run but not all pass just yet

Bug fix: start method was overriding LocatableSeq method, and it shouldn't, fixed.

Synopsis and doc fixes

Bio::Matrix::PSM::InstanceSiteI

Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers

Start up cleanup - tests run but not all pass just yet

Bio::Matrix::PSM::Psm

Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers

Start up cleanup - tests run but not all pass just yet

Capitalization fixed when rearranging in new

Bio::Matrix::PSM::PsmHeader

Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers

Start up cleanup - tests run but not all pass just yet

Synopsis and doc fixes

Bio::Matrix::PSM::PsmHeaderI

Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers

Start up cleanup - tests run but not all pass just yet

Bio::Matrix::PSM::PsmI

Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers

Start up cleanup - tests run but not all pass just yet

Bio::Matrix::PSM::SiteMatrix

Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers

Start up cleanup - tests run but not all pass just yet

Remove spurious warnings

Commented out some spurious(?) lines from the new()

Fixed bug Heikki pointed with the constructor when no input data for the vectors (A,G,C,T) is supplied This is still a temp solution

Get/set method added to access accession_number

Bio::Matrix::PSM::SiteMatrixI

Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers

Get/set method added to access accession_number

Bio::Ontology::InterProTerm

Make to_string work

Fix a tricky bug that the identifier will be set as undef if you call interpro_id without arguments

Bio::Ontology::SimpleGOEngine

Allowing an underscore in ontology IDs. this is necessary to be able to parse cjm's OBO_REL relationship ontology, which otherwise observes DAG-Edit format

MPATH ontology doesn't have at least 3 digits in all identifiers

Fixes to ontology regex to parse a greater subset of DAG-Edit files. i have tracked down the files where DAG-Edit IDs are validated: GOFlatFileAdapter.java the regex still only matches a subset of the allowed characters in an identifier. identifiers can be any non-whitespace, non ;$,:!\? characters > length 1 on either side of a : separator. i've opted to match \w+:\w+, hopefully we don't need to go beyond this.

Bio::Ontology::Term

Tests fail better without network access

Add references as an attribute of term

Make the interpro parser handle publication etc.

Bio::OntologyIO

Adding escape of SGML and newlines/tabs. is there a generic SGML escape module we want to add as a dependency?

Bio::OntologyIO::Handlers::BaseSAXHandler

Add BaseSAXHandler and modify InterPro_BioSQL_Handler to inherit it

Base Handler has the new method as _current_hash;

Bio::OntologyIO::Handlers::InterProHandler

Have new root terms for Active_site and Binding_site. It can run throughout the complete Interpro xml file.

A SAX handler to parse interpro.xml and store in biosql. The example to use this module is load_interpro.pl in bioperl-db/scripts/biosql/

Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler

A SAX handler to parse interpro.xml and store in biosql. The example to use this module is load_interpro.pl in bioperl-db/scripts/biosql/

Add BaseSAXHandler and modify InterPro_BioSQL_Handler to inherit it

Should be able to load dbxref

Make the interpro parser handle publication etc.

Runnable synopsis

Bio::OntologyIO::dagflat

Allowing an underscore in ontology IDs. this is necessary to be able to parse cjm's OBO_REL relationship ontology, which otherwise observes DAG-Edit format

MPATH ontology doesn't have at least 3 digits in all identifiers

Reverted previous change as it breaks the parser.

Fixes to ontology regex to parse a greater subset of DAG-Edit files. i have tracked down the files where DAG-Edit IDs are validated: GOFlatFileAdapter.java the regex still only matches a subset of the allowed characters in an identifier. identifiers can be any non-whitespace, non ;$,:!\? characters > length 1 on either side of a : separator. i've opted to match \w+:\w+, hopefully we don't need to go beyond this.

Adding escape of SGML and newlines/tabs. is there a generic SGML escape module we want to add as a dependency?

Bio::Phenotype::OMIM::OMIMentry

Finer parse the symptoms

Make the methods accept undef as argument. The methods are edited, created, contributors, and additional_references.

Bio::Phenotype::OMIM::OMIMparser

Finer parse the symptoms

In the original code, the clinical symptoms record returns \'clinical symptoms\' if there is not such record in the parsed file. I change it to return \'\' if nothing is in the file there.

The fields in entry object will return undef, if the info is not available in the parsed file.

Bio::Phenotype::Phenotype

Make the methods, comment and description, able to accept undef as argument.

Bio::PopGen::Simulation::Coalescent

Remove unnecessary event-handler stuff

Lost a use Bio::Tree::Tree somehow

Bio::PopGen::Statistics

Update LD so that it will a) return an pair of values, LD and chiSQ. Also fix it so that composite_LD will calculate correctly with missing data

Properly reset the internal variable counts

Better calculations because need to reset some variables- per Matt's corrections that HW was not being calculated correctly on subsequent iterations

Bio::PrimarySeqI

Translate() can take in a custom codon table

Bio::RangeI

Unflattener now works for multicopy genes RangeI changes - see email to bioperl list > > both intersection() and union() are documented as returning a (start, end, > strand) triple. in actual fact, intersection returns a RangeI compliant > object, and union() returns either a RangeI object or a triple depending > on wantarray() > > I have fixed things so that both intersection() and union() return either > RangeI or triple depending on wantarray() - following the principle of > least surprise - and documented this. The test suite passes. > > This will break code like this: > > $h = { 'range' => $sf->intersection($sf2) } > > since wantarray will be true here; however, this code violates the > previously documented interface anyway. > > I have also added a new method disconnected_ranges() to RangeI > > I could easily migrate this method somewhere else, but it seems to belong > with other geometrical methods such as intersection and union

Fixing spurious warnings caused by strand() now capable of returning undef

Make it so 'disconnected_ranges' sub don't cause warnings

Bio::Restriction::Analysis

Apply fix for big #1548

Added correct support for circular sequences in Bio::Restriction::Analysis (Issue #1540) Added multiple digests with any enzyme combinations

Updated Analysis.pm to incorporate changes from Peter Blaiklock and to move away from using the ^ notation in cut sites. Also tried to implement speed/memory saving devices, mainly now the only data that is stored is the cut positions of each enzyme (rather than fragments). Everything else is calculated when demanded.

Bio::Restriction::Enzyme

Fixes Issue #1518: Enzymes with a cut position of 0 have wrong cut() and site()

Added correct support for circular sequences in Bio::Restriction::Analysis (Issue #1540) Added multiple digests with any enzyme combinations

Updated Analysis.pm to incorporate changes from Peter Blaiklock and to move away from using the ^ notation in cut sites. Also tried to implement speed/memory saving devices, mainly now the only data that is stored is the cut positions of each enzyme (rather than fragments). Everything else is calculated when demanded.

Bio::Restriction::Enzyme::MultiSite

Added correct support for circular sequences in Bio::Restriction::Analysis (Issue #1540) Added multiple digests with any enzyme combinations

Bio::Restriction::EnzymeCollection

Added correct support for circular sequences in Bio::Restriction::Analysis (Issue #1540) Added multiple digests with any enzyme combinations

Updated Analysis.pm to incorporate changes from Peter Blaiklock and to move away from using the ^ notation in cut sites. Also tried to implement speed/memory saving devices, mainly now the only data that is stored is the cut positions of each enzyme (rather than fragments). Everything else is calculated when demanded.

Bio::Restriction::IO

Added correct support for circular sequences in Bio::Restriction::Analysis (Issue #1540) Added multiple digests with any enzyme combinations

Updated Analysis.pm to incorporate changes from Peter Blaiklock and to move away from using the ^ notation in cut sites. Also tried to implement speed/memory saving devices, mainly now the only data that is stored is the cut positions of each enzyme (rather than fragments). Everything else is calculated when demanded.

Bio::Restriction::IO::bairoch

Updated Analysis.pm to incorporate changes from Peter Blaiklock and to move away from using the ^ notation in cut sites. Also tried to implement speed/memory saving devices, mainly now the only data that is stored is the cut positions of each enzyme (rather than fragments). Everything else is calculated when demanded.

Bio::Restriction::IO::base

Fix suggested in Issue #1538

Added correct support for circular sequences in Bio::Restriction::Analysis (Issue #1540) Added multiple digests with any enzyme combinations

Updated Analysis.pm to incorporate changes from Peter Blaiklock and to move away from using the ^ notation in cut sites. Also tried to implement speed/memory saving devices, mainly now the only data that is stored is the cut positions of each enzyme (rather than fragments). Everything else is calculated when demanded.

Bio::Root::IO

In order for rmtree() to work in cygwin

Cleanup of debugging a little for uniformity

The following regression tests now pass: GFF, SeqFeature, Registry

Bio::Root::Version

Set version to 1.302

Version 1.4

Bio::Search::HSP::BlastHSP

Parse/store Links from WU-BLAST run with -links param

BlastHSP really doesn't work, migrate links to GenericHSP. Links is for WU-BLAST links parsing

Bio::Search::HSP::FastaHSP

Trim leading spaces for what it is worth

Bio::Search::HSP::GenericHSP

BlastHSP really doesn't work, migrate links to GenericHSP. Links is for WU-BLAST links parsing

Fix so that we don't have undef warnings

Bio::Search::Hit::GenericHit

Some more protection for when there are no HSPs for a Hit

Issue #1558

Bio::Search::Result::PsiBlastResult

Old directory name

Removing PSIBLAST modules

Bio::Search::SearchUtils

Some more protection for when there are no HSPs for a Hit

Bio::SearchIO

Avoid warnings for empty reports

Bio::SearchIO::IteratedSearchResultEventBuilder

Insure we explicitly set the HSP type in the Factory

Bio::SearchIO::Writer::GbrowseGFF

Gbrowse now allows tstart and tend tags for alignment features to make it more like normal GFF.

Bio::SearchIO::Writer::HTMLResultWriter

Only output HSP's Hit header when there are actual HSPs (when there are more hits than B, and B and V are not equal)

Allow toggling of WU-BLAST link display

Bio::SearchIO::Writer::TextResultWriter

Only output HSP's Hit header when there are actual HSPs (when there are more hits than B, and B and V are not equal)

Allow toggling of WU-BLAST link display

Bio::SearchIO::blast

Can parse B=0 BLAST output and at least produce minimal Hit objects

Parse more BLAST statistics, WU-BLAST frame specific lambda,entropy,kappa stored. Gapped lambda stored separately as well

Parse/store Links from WU-BLAST run with -links param

Grab statistics, posted date from WU-BLAST reports

Why bother with a complicated regexp - just grab the whole thing

Bio::SearchIO::blastxml

Blastxml expected <!DOCTYPE> and <BlastOutput> on the same line. my version of blastall puts them on different lines, which caused the parse to fail (from internal refactoring of <?xml> and <!DOCTYPE> tags). this change fixes the bug. tests added to SearchIO.t and a test blastxml file added.

Bio::SearchIO::chado

These are now redundant

Bio::SearchIO::chadosxpr

These are now redundant

Bio::SearchIO::exonerate

Started vulgar line parsing in exonerate.pm; need some hints about how to handle gaps (inside HSPs or outside?)

Bio::SearchIO::fasta

Better FASTA family program matching - was not parsing SSEARCH properly, cleaner regexp

I think we need to jump to the query line if we are presented with non-numbered opening line

More work to parse dreaded fasta context in alignments - this should work for the 2 examples Robin Emig has provided

Avoid inifinite loops when coordinate line ends with a number and no extra ws

Bio::SearchIO::hmmer

Store db name for hmmsearch results in r->database_name

Store both database_name and seqfile_name even though redundant - keep consistency with rest of SearchIO

Bio::SearchIO::psiblast

Removing PSIBLAST modules

Bio::SearchIO::psl

Fix to detect file header for psLayout3 (psl version 3)

Remove some warnings when running tests with warnings on

Bio::SearchIO::sim4

Make it so empty fields don't cause warnings

Bio::SearchIO::wise

Was swapping query/target improperly

Bio::Seq

Hope this change will keep the Examples section at the top of the module's HTML page

Bio::Seq::EncodedSeq

Fixed strandedness issues

Bio::Seq::Meta

Doc fixes from #1553

Bio::Seq::MetaI

Doc fixes from #1553

Bio::Seq::PrimedSeq

Removed global $version

Bio::SeqFeature::Generic

Fixed Bio::SeqFeature::Generic so that it will accept a score of 0; modified Bio::Graphics::Glyph::graded_segment so that it draws a fg box around each segment by default (can restore default behavior with -vary_fg=>1)

Bio::SeqFeature::Primer

Removed global $version

Bio::SeqFeature::Tools::TypeMapper

Updated type sequence_variant to reflect SO

Bio::SeqFeature::Tools::Unflattener

Unflattener now works for multicopy genes RangeI changes - see email to bioperl list > > both intersection() and union() are documented as returning a (start, end, > strand) triple. in actual fact, intersection returns a RangeI compliant > object, and union() returns either a RangeI object or a triple depending > on wantarray() > > I have fixed things so that both intersection() and union() return either > RangeI or triple depending on wantarray() - following the principle of > least surprise - and documented this. The test suite passes. > > This will break code like this: > > $h = { 'range' => $sf->intersection($sf2) } > > since wantarray will be true here; however, this code violates the > previously documented interface anyway. > > I have also added a new method disconnected_ranges() to RangeI > > I could easily migrate this method somewhere else, but it seems to belong > with other geometrical methods such as intersection and union

Reuses exons (eg containment graph not a tree) improved algorithm for matching mRNAs with CDSs

Added convenience method get_tagset_values() to SeqFeatureI fixed Unflattener to deal with strange NT_078847 record

Made the Unflattener more informative in certain problemmatic situations; added a new test

Bio::SeqFeatureI

Added convenience method get_tagset_values() to SeqFeatureI fixed Unflattener to deal with strange NT_078847 record

Bio::SeqIO

Alternate ABI extension for newer versions of software (requested by Jan Aerts)

Guessing sequence and align formats by looking into file

Don't need to guess if is supplied

Fail better with no arguments to new()

Changed GuessSeqFormat to return undef

Bio::SeqIO::asciitree

Runnable synopsis

Bio::SeqIO::chado

These are now redundant

Bio::SeqIO::chadoitext

These are now redundant

Bio::SeqIO::chadosxpr

These are now redundant

Bio::SeqIO::chadoxml

Version 1.0 of the GenBank to chadoxml converter .

Add more comments, and implement "match" operation for pubs.

Add exception handling in response to Issue #1532. please note that this chadoxml module is written to work with DNA sequence and annotation data from whole genome projects that are deposited in GenBank.

Fixed Issue #1532 with regard to filehandle; modified code to eliminate warrnings when run with 'perl -w'.

Comment out debugging output and use of environment variable $CodeBase .

Fix bug of null srcfeature_id for featureloc when srcfeature is not given on write_seq() invocation; fix bug of not calling unflattener when -seq_so_type is explicitly supplied.

Fix so that it will use the Root::IO filehandle rather than rely on filenames to be specified. Clean up documentation formatting some. Issue throws rather than dies. Code formatting changes

Bio::SeqIO::embl

Better parsis of virus names

Resolves Issue #1516. Feature qualifier value quotation is now exactly according to spesifications

Accession numbers in AC line are separated by '; ' not by ';'

SV line was mangled (like 'SV M20132; J03180.1') if there were secondary accession numbers

Fixed embl dumping to allow breaks at hyphens

Warn if whitespace in display_id()

Bio::SeqIO::fasta

Warn if whitespace in display_id()

Bio::SeqIO::game

Getting ready to add new SeqIO::game modules

Added new Bio::SeqIO::game modules, added tests to t/SeqIO.t

1) updated game XML parser/writer to deal more effectively with mRNA/CDS pairs and retain UTR splice info and play nicely with Bio::SeqFeature::Tools::Unflattener 2) moved game XML tests from SeqIO.t to game.t; added new tests 3) updated Bio::Tools::GuessSeqFormat for new game format

Bio::SeqIO::game::featHandler

Added new Bio::SeqIO::game modules, added tests to t/SeqIO.t

Avoid warning for when set->{Attributes}->{produces_seq} is undef

Added some changes to the ways mRNAs and UTRs are handled. Silenced some squawks (sorry!)

Bio::SeqIO::game::featureHandler

Getting ready to add new SeqIO::game modules

Bio::SeqIO::game::gameHandler

Added new Bio::SeqIO::game modules, added tests to t/SeqIO.t

Bio::SeqIO::game::gameSubs

Added new Bio::SeqIO::game modules, added tests to t/SeqIO.t

1) updated game XML parser/writer to deal more effectively with mRNA/CDS pairs and retain UTR splice info and play nicely with Bio::SeqFeature::Tools::Unflattener 2) moved game XML tests from SeqIO.t to game.t; added new tests 3) updated Bio::Tools::GuessSeqFormat for new game format

Bio::SeqIO::game::gameWriter

Added new Bio::SeqIO::game modules, added tests to t/SeqIO.t

1) updated game XML parser/writer to deal more effectively with mRNA/CDS pairs and retain UTR splice info and play nicely with Bio::SeqFeature::Tools::Unflattener 2) moved game XML tests from SeqIO.t to game.t; added new tests 3) updated Bio::Tools::GuessSeqFormat for new game format

Bio::SeqIO::game::idHandler

Getting ready to add new SeqIO::game modules

Bio::SeqIO::game::seqHandler

Getting ready to add new SeqIO::game modules

Added new Bio::SeqIO::game modules, added tests to t/SeqIO.t

1) updated game XML parser/writer to deal more effectively with mRNA/CDS pairs and retain UTR splice info and play nicely with Bio::SeqFeature::Tools::Unflattener 2) moved game XML tests from SeqIO.t to game.t; added new tests 3) updated Bio::Tools::GuessSeqFormat for new game format

Bio::SeqIO::gcg

Simple fix to Issue #1549 - would still benefit from changes suggested by Derek

Warn if whitespace in display_id()

Bio::SeqIO::genbank

Better parsis of virus names

Resolves Issue #1516. Feature qualifier value quotation is now exactly according to spesifications

Never print empty residue range on REFERENCE line. Fixes this 'REFERENCE 1 (bases 0 to 0)'

Fix Issue #1543. Do some parsing cleanup

Warn if whitespace in display_id()

Bio::SeqIO::kegg

Adding a parser for KEGG sequence records. currently does not support parsing of the CODON_USAGE and POSITION tags. -allen

Need to set the species tag to an object, not a string

Fixes to ontology regex to parse a greater subset of DAG-Edit files. i have tracked down the files where DAG-Edit IDs are validated: GOFlatFileAdapter.java the regex still only matches a subset of the allowed characters in an identifier. identifiers can be any non-whitespace, non ;$,:!\? characters > length 1 on either side of a : separator. i've opted to match \w+:\w+, hopefully we don't need to go beyond this.

Bio::SeqIO::pir

Warn if whitespace in display_id()

Bio::SeqIO::swiss

Better parsis of virus names

Resoving Issue #1519 1. fixed sprintf bug sometimes leading to extra space after ID tag 2. OS line output for viri now contains all the information after species name. The complex strain/abbreviation/common name list is stored in sub_species() which was previously not in use for viri. This is a hack but the (first) OS line now makes a perfect round trip.

Warn if whitespace in display_id()

Bio::SeqIO::tigr

Adding TIGR XML parser

Bio::SeqUtils

Translate_6frames() failed on sequences where bioperl would guess that the sequence string is protein. Streamlined coding of the method to avoid guessing.

Bio::SimpleAlign

Adding a parser and tests for UCSC maf (multiple alignment format) format. added a method SimpleAlign::splice_by_seq_pos to allow splicing of all sequences based on the gap locations of one sequence within the alignment. this could in principle be called repeatedly to remove all gaps from the MSA.

Cleaned up unit test spurious warnings. bugfix in maf parser for detecting last record in file. added functionality to trim gaps from a MSA for a given sequence to SimpleAlign. trimming allowed implementation of exporting Seq and SeqFeatures from SimpleAlign. the api here is still rough, comments appreciated.

Run clean with -w on

Offset location of new seq with features by location of original seq requested to build from. added rudimentary key/value parsing for maf 'a' lines

Bio::Species

Commented out internal calls to methods not doing anything

Bio::Structure::IO

Fixed email

Bio::Structure::IO::pdb

Append to the hash rather than allocate to objects for this

Bio::Taxonomy

Clean up the rank sets

Bio::Tools::Analysis::DNA::ESEfinder

Bulletproof the code some more, report warnings from POST events - now require HTML::HeadParser to be installed

Bio::Tools::Analysis::Protein::Domcut

Improvedfeature parsing

Tests fail better without network access

Added source tags to features

Bio::Tools::Analysis::Protein::ELM

INitial commit of ELM.pm, a wrapper around the EMBL functional peptide motif prediction server

Made printing "." to indicate waiting depend on verbosity. Unconditional printing messed up the test suite. An altenative would be to print to STDERR, instead.

Added source tags to features

Bulletproof code some more

Bio::Tools::Analysis::Protein::GOR4

Tests fail better without network access

Added source tags to features

Bio::Tools::Analysis::Protein::HNN

Tests fail better without network access

Added source tags to features

Bio::Tools::Analysis::Protein::NetPhos

Necessary change to result parser for non-standard sequence names

Added source tags to features

Bio::Tools::Analysis::Protein::Scansite

Wrapper arounf Scansite phosphorylation site server

White space fixes to make code easier to read

Bio::Tools::Analysis::Protein::Sopma

Tests fail better without network access

Added source tags to features

Bio::Tools::Analysis::SimpleAnalysisBase

New method - clear() allows multiple anlyses using the same object

Bio::Tools::BPlite

Issue #1542 - improper detection of end of Query regexp

Bio::Tools::BPlite::Iteration

Have be set to instead of undef - perhaps this is not entirely the best thing - are we screwing up in the parsing instead? use Bio::SearchIO instead I guess

Bio::Tools::CodonTable

New method add_table() if you know what you are doing you can add custom codon table

Bio::Tools::EMBOSS::Palindrome

Parsing and tests for 'palindrome'

Bio::Tools::GFF

GFF3 parsing and writing support

Include a header line describing that this is GFF3 per spec.

Hack-y support for writing out FeaturePairs, but a start. We need to support the notion of Feature themselves generating attribute section

Fix slightly brain dead code to use arrays instead of chop;chop;

Adding support for parsing GFF ##sequence-region header lines. these are transformed into featureless Bio::LocatableSeq objects, available via the next_segment method.

Needed to move header parsing outside of next_feature, as it may be useful to handle sequences before sequence features (think database inserts).

Changed GFF3 parse to split on spaces and added a note about not supporting sequences

Fixed to deal with split locations for GFF3 output. Should probably do the same for GFF2 and GFF1 but that code makes my head hurt.

Bio::Tools::GuessSeqFormat

Guessing sequence and align formats by looking into file

Remove line(), replace with text() which takes in multi line texts

Changed GuessSeqFormat to return undef

Fix game format guess

1) updated game XML parser/writer to deal more effectively with mRNA/CDS pairs and retain UTR splice info and play nicely with Bio::SeqFeature::Tools::Unflattener 2) moved game XML tests from SeqIO.t to game.t; added new tests 3) updated Bio::Tools::GuessSeqFormat for new game format

Bio::Tools::Phylo::PAML

Silenced a warning reported in Issue #1560

George Hartzell fixes

Bio::Tools::Phylo::PAML::Result

Doc fix

Bio::Tools::Primer3

Removed global $version

Bio::Tools::Prints

Prints now returns FeaturePair, rather than previously SeqFeature.

Bio::Tools::RandomDistFunctions

Utility module for generating random variates according to different distributions

Docu update

Bio::Tools::Run::RemoteBlast

Set an agent string per request from NCBI G. Coulouris

Bio::Tools::Run::StandAloneBlast

Allow SearchIO to be used for all output format types now with _READMETHOD set

Bio::Tools::SeqWords

New method: count_overlap_words() feature enhancement from Issue #1554

Bio::Tools::Signalp

Add the SignalP-HMM result. $feat->score; # Signal peptide probability $feat->get_tag_values('peptideProb')->[0]; # signalp peptide probability $feat->get_tag_values('anchorProb')->[0]; # signalp anchor probability

Bio::Tree::Node

Sort as advertised

Simpler way to add children with descendents all at once, add documentation for the feature, left/right was never an options, just specify an array of descendents

Throw if we pass in a hash reference too

Bulletproofing for length 0 branch lengths

Bio::Tree::NodeI

Default doesn't need to print out leaf status

Merge of NHX parsing changes to the branch - just in case and to provide diffs for people working with 1.2.3

Bio::Tree::RandomFactory

Re-implementation which is more in line with generating phylogenetically proper trees - using Mike Sanderson's suggestions based on his r8s code. Still needs some more work and some tests

Still probably some errors in assigning the tree weights, Mike assigns time slighly differently than I do so I need to figure out if distributions are really correct and/or if the normalization technique is really working.

Simpler way to add children with descendents all at once, add documentation for the feature, left/right was never an options, just specify an array of descendents

Bio::Tree::TreeFunctionsI

Bulletproofing for length 0 branch lengths

Bio::TreeIO

Adding support to output SVG::Graph trees via TreeIO subsystem. svggraph.pm module courtesy of Brian O'Connor <boconnor@ucla.edu>

Some docs

Extension support for lintree

Bio::TreeIO::TreeEventBuilder

Some debugging and better detection of when we need to pop off the stack

Merge of NHX parsing changes to the branch - just in case and to provide diffs for people working with 1.2.3

Some docs

Bio::TreeIO::lintree

Lintree parser and tests

Bio::TreeIO::newick

Bulletproofing for length 0 branch lengths

Issue #1570, support multi-lined newick files again. Strip \n and \r as they mean nothing and should not be converted to _ with Allen's WS handler regexp

Bio::TreeIO::nexus

Some docs

Bio::TreeIO::nhx

Fix problems with parsing, better detectiono of 'leafstatus' now, rebless Nodes to NodeNHX for NHX writing - this could cause problems later, but works as is right now

A cheating way, but fixing Issue #1471

Merge of NHX parsing changes to the branch - just in case and to provide diffs for people working with 1.2.3

Bio::TreeIO::svggraph

Adding support to output SVG::Graph trees via TreeIO subsystem. svggraph.pm module courtesy of Brian O'Connor <boconnor@ucla.edu>

Bio::TreeIO::tabtree

First attempt at making tabtree more useful

Makefile.PL

Removed dependency on Data::Stag - no longer required by new chadoxml code

An experiment - let's enable Makefile.PL pre-reqs (dependancies)

Added SVG dependency

Update prereqs

Add DG::SVG to (optional) dependencies

It's 'GD', not 'DG'

bioscripts.pod

Add mention of filter_search.PLS

Add mention of rnai_finder.cgi

Add back bioflat

New directory

Move from examples/ to scripts/

Added mention of all_glyphs.pl

bptutorial.pl

Issue #1527, fix on branch for consistency, even if we don't do another release off this branch

Add some URLs

Old URLs

Hard return breaks link

Hard return breaks link

PAML HOWTO

Tests fail better without network access

Edits

Better discussion of sequence objects. Edits.

examples/biblio/biblio_examples.pl

Add another useful bit

A couple more examples

examples/biographics/all_glyphs.pl

New script that displays all glyphs; enabled SVG output from other example scripts

Removed some extraneous internal notes on glyph compatability

Added a shaded arrow

examples/biographics/dynamic_glyphs.pl

Added support for SVG output

New script that displays all glyphs; enabled SVG output from other example scripts

examples/biographics/lots_of_glyphs.pl

Added support for SVG output

New script that displays all glyphs; enabled SVG output from other example scripts

examples/db/bioflat_index.pl

Add back bioflat

Binarysearch and flat are the same

Move from examples/ to scripts/

examples/rnai_finder.cgi

Initial check-in of cgi script for RNAi reagent design

Moved rnai_finder.cgi from examples to examples/sirna

examples/sirna/TAG

Moved rnai_finder.cgi from examples to examples/sirna

examples/sirna/rnai_finder.cgi

Moved rnai_finder.cgi from examples to examples/sirna

maintenance/authors.pl

Helper script to keep AUTHORS file up to date

models/popgen.dia

Bio::PopGen classes by Albert Vilella

scripts/Bio-DB-GFF/bp_genbank2gff.PLS

Changes making genbank2gff.pl use SOFA terms for type names in generated GFF3

Removed dependency on having a running mysql database when writing converted GFF3 files to stdout

This biofetch adaptor and genbank2gff are better than before, but not yet perfect. Fixed: - Gets right the parentage of CDSs (belong to mRNAs) and exons (belong to chromosomes or other regions). - variation features are now clasified as SNPs (if the length is 1), else chromosome_variation. - no longer creates CDS lines that span introns. Remaining problems: - with multiple transcript genes, it can get confused as to which CDSs go with which mRNA (solution: reimplement with Unflattener) - SNP features can all get assigned the same ID, which is illegal in GFF3, though I don't think it will cause problems with gbrowse (though it probably will with chado).

Slight adjustment to genbank2gff script to handle fly gene records right

scripts/Bio-DB-GFF/bulk_load_gff.PLS

Added minor workarounds for Bio::DB::GFF roundtripping to artemis

Fixed overly-promiscuous regexp for detecting FASTA files

Added option to set MAX_BIN, and updated the postgres loader to deal with gff3 (note that the gff3 stuff is completely untested though)

Added support for bulk loading from a local gff source to a remote db server

Added support for dsn strings in the form of "dbi:mysql:database=xxx;host=xxx"

Fixed a minor gff3 bug

scripts/Bio-DB-GFF/fast_load_gff.PLS

Added minor workarounds for Bio::DB::GFF roundtripping to artemis

Fixed overly-promiscuous regexp for detecting FASTA files

Added an option for setting MAX_BIN

Fixed a minor gff3 bug

scripts/Bio-DB-GFF/load_gff.PLS

Fixed overly-promiscuous regexp for detecting FASTA files

Added an option to set MAX_BIN

scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS

Added option to set MAX_BIN, and updated the postgres loader to deal with gff3 (note that the gff3 stuff is completely untested though)

Fixed a minor gff3 bug

scripts/DB/bioflat_index.PLS

Move from examples/ to scripts/

scripts/graphics/frend.PLS

Bio::Graphics::FeatureFile: remove uninit variable warning when calling features() without arguments; fixed frend web-based feature renderer to accomodate recent changes in FeatureFile API

scripts/graphics/search_overview.PLS

Prevent barfing when Hit doesn't have any HSPs

scripts/popgen/composite_LD.PLS

Fix to deal with newer API

Print with new API

scripts/searchio/filter_search.PLS

Added in simple filtering script using SearchIO - useful for me, and could be useful to others over time

scripts/utilities/search2gff.PLS

Allow overriding of the source tag as parsed by SearchIO

Output 'match' and 'component' lines for GFF dumping