Core 1.2.2 1.2.3 delta

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

Bio::Align::DNAStatistics

Major addition of methods to study synonymous/non-synonymous codon changes

More error handling

Bug fixes to jk_var()

SYNOPSIS made runnable

Bio::AlignIO::fasta

Added support for writing out the sequence description too for MSA fasta format

Added description parsing as well

Bio::Cluster::UniGene

NCBI *.data files now have version numbers on the accession numbers in SEQUENCE lines. Parser now parses them correctly.

Should have used -seq_version (RichSeq) rather than version (Seq) - changed

Changes to allow SEQ line accession number and version to be correctly added to the Seq object.

Bio::ClusterIO::dbsnp

Whitespace cdata is now ignored -- don't try to parse it.

Some refsnp tags don't begin with NSE-rs

Migrating bugfix from main trunk

Bio::ClusterIO::unigene

NCBI *.data files now have version numbers on the accession numbers in SEQUENCE lines. Parser now parses them correctly.

A couple of fixes for NCBI format changes: - SEQ lines now have parsing of accession number and seq version no - SEQTYPE and TRACE added

Bio::CodonUsage::IO

initial commit

Minor changes

Bio::CodonUsage::Table

Initial commit of Bio::CodonUsage::Table

newmethods added

Improved constructor

Bio::DB::CUTG

Initial commit of Bio::DB::CUTG.pm

read/write methods removed

Bio::DB::Fasta

Fixed Bio::DB::Fasta so that it returns undef when get_Seq_by_id() is called on a nonexistent ID

Slightly more informative error message

Bio::DB::GFF

Fixed tables being created twice on GFF->initialize

Fixed documentation bug in Bio::DB::GFF

Added API for deleting GFF features and groups

Added the ability to delete features, groups, ranges and types

SEVERE bug squashed. The load_sequence_string routine (used by load_from_embl) first calls insert_sequene_chunk to load the initial chunks, then calls insert_sequene to load the last chunk, but expects a successful return value from the first call. insert_sequence_chunk did not return anything, so the last chunk of sequence was never loaded. This probably didn't affect anyone who was not using Oracle, since mysql doesn't necessarily require the sequence to be chunked to teh extent that Oracle does.

Quiet undef warnings that show up during tests

Added segment->delete() method; allow control of range type of features to delete

Removed the clone default from the aggregator

Added support for tied filehandles to GFF loading

Fixed support for tied filehandles in GFF loading

Generalized split_group() function

Folded GFF3 changes into branch

Fixed broken Bio::DB::GFF->load_gff() call -- I had broken it so that it worked on filehandles but not on file or directory names!

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

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

Returning hard-coded default values from 'guess_name' if the feature has no attributes at all. This is probably bad, but since the features are used for grouping it may be necessary to return at least something. This is just a temporary fix until someone with more knowledge fixes it

Adding versioning tag

Keeping biofetch and biofetch_oracle sync'ed

Miss-named a variable

Gff loaders now gff3 compatible

Changing tag translation in bp_genbank2gff.pl; unfortunately the dichotomy between CDS and exon features makes it difficult to be completely gff3 compatible; needs work

Bio::DB::GFF::Adaptor::biofetch_oracle

Biofetch_oracle inherits from the oracle adaptor rather than the mysql adaptor like biofetch.pm. I suppose this should be decided at run-time one day...

Allow preferred-tags hash, used to chose the gclass/gname of the feature, to be modified in the constructor so that it might make more sensible choices for viral genomes. Should not affect anyone else, as it is set to the old defaults if the argument is not present.

Use the rearrange function as I should have in the first place

Keeping biofetch and biofetch_oracle sync'ed

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

Added the ability to delete features, groups, ranges and types

Added segment->delete() method; allow control of range type of features to delete

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

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

Use the rearrange function as I should have in the first place

Remove debugging output to STDERR

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

Fixed updating of (DB)sequence when doing a bulk load

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

Added the ability to delete features, groups, ranges and types

Bio::Graphics::FeatureFile now has a very minimal set of Bio::DasI interfaces for use with Pauls freaky weird branch; Also tinkered with BioGraphics regression tests. Will need more regression tests added because position of glyphs on test 3 has shifted right by a pixel

Added segment->delete() method; allow control of range type of features to delete

Bio::DB::GFF::RelSegment

Silently fix data problems when someone has inadvertently said that feature coordinate stop < start

Doc fix, more fully implement Bio::SeqI by adding feature_count and get_SeqFeature get_allSeqFeature aliases

Added segment->delete() method; allow control of range type of features to delete

Made the segment->feature() call more configurable for range type

Bio::DB::GFF::Segment

Needs to full implement SeqI.pm interface - is_circular needs to be implemented

Seqname can be an alias for seq_id

Is circular bug fixed

Doc fix, more fully implement Bio::SeqI by adding feature_count and get_SeqFeature get_allSeqFeature aliases

Bio::DB::GFF::Util::Binning

The sprintf statement was assuming that the integer passed into it was positive. Though it doesnt make sense to pass a negative integer into this routine, at least now it wont croak if you do.

Bio::DB::MeSH

Initial commit

Bio::DB::NCBIHelper

Fix to REMOVE the 'gb|' prefix added from NCBIHelper [sigh]- this all keeps looking hackier than every

Add method to cache/handle DB::RefSeq handle creation, can be overriden now AND inherits retrieval type from the creator class to help with CGI running of Bio::DB code and the retrieval_type => 'pipeline'

Modifying the change Jason made this AM - there was a confusion between which arg was called retrieval_type and which was called retrievaltype. It now passes the argument correctly. THANKS JASON - it works great now.

Bio::DB::Query::GenBank

Fixed documentation errors in Bio::DB::Genbank

Fixed documentation errors in Bio::DB::Genbank

Bio::DB::Query::WebQuery

Issue #1463

Bio::DB::RefSeq

Fix to REMOVE the 'gb|' prefix added from NCBIHelper [sigh]- this all keeps looking hackier than every

Bio::DB::WebDBSeqI

Fix to REMOVE the 'gb|' prefix added from NCBIHelper [sigh]- this all keeps looking hackier than every

Bio::Expression::FeatureGroup

Copying bioperl-microarray dependencies to release branch

Check for data before calling in array context

Fixes for MAS 5.0 parsing. bioperl-microarray tests now passing

Bio::Expression::FeatureGroup::FeatureGroupMas50

Copying bioperl-microarray dependencies to release branch

Bad method names

Bad method fix migrated to release

Bio::Expression::FeatureSet

->featuregroup

Copying bioperl-microarray dependencies to release branch

Bio::Expression::ProbeI

Copying bioperl-microarray dependencies to release branch

Bio::Factory::FTLocationFactory

Issue #1487. Deal with case when end < start gracefully even though it is an error with the inputfile

Issue #1487. Deal with case when end < start gracefully even though it is an error with the inputfile

Let's make sure verbosity is really inherited so we can quiet things for a release

Let's make sure verbosity is really inherited so we can quiet things for a release

Insure that verbosity is inherited

Bio::Graphics

Updated changes file

Bio::Graphics::Feature

Added docs for url() and configurator() method

Bio::Graphics::FeatureFile now has a very minimal set of Bio::DasI interfaces for use with Pauls freaky weird branch; Also tinkered with BioGraphics regression tests. Will need more regression tests added because position of glyphs on test 3 has shifted right by a pixel

Solved the problem of outputting '.' in place of a strand whith features coming from plugins

Solved the problem of outputting '.' in place of a strand with gff string of features coming from plugins

Removing leftover debugging messages

Bio::Graphics::FeatureFile

Made Bio::Graphics::FeatureFile able to return an iterator across itself in a Bio::Das::SegmentI manner

Bio::Graphics::FeatureFile now has a very minimal set of Bio::DasI interfaces for use with Pauls freaky weird branch; Also tinkered with BioGraphics regression tests. Will need more regression tests added because position of glyphs on test 3 has shifted right by a pixel

Bio::Graphics::FeatureFile feature enhancements

Added GFF3 compatibility to Bio::Graphics::FeatureFile

Need to 'use Bio::DB::GFF' now to irely on it, also the method is called split_group not _split_group

Bio::Graphics::FeatureFile::Iterator

Added the iterator for Bio::Graphics::FeatureFile

Bio::Graphics::Glyph

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::alignment

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::anchored_arrow

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::arrow

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::box

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::cds

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::crossbox

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::diamond

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::dna

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::dot

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::ellipse

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::ex

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::generic

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::graded_segments

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::heterogeneous_segments

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::line

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::oval

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::pinsertion

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::processed_transcript

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::redgreen_box

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::segments

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::toomany

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::track

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::transcript

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::transcript2

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::translation

Added ability to toggle showing of amino acid sequence

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Glyph::xyplot

Added a highlight feature to Bio::Graphics so that individual features can be emphasized

Bio::Graphics::Panel

Fixed documentation bug in Bio::DB::GFF

Bio::Graphics::Pictogram

Default behavior now scales column height with information content. set normalize() for old behavior (all columns equal height)

Allowing -normalize option to constructor

Check for data before calling in array context

Bio::Location::Simple

Silence some warnings when strand is empty (should it be 0 instead of undef?)

Bio::Location::Split

Doc fix

Bio::Matrix::Generic

A generic matrix implementation for generalized cases when we want to store column/row data

Phylipdist parser ported to Matrix::IO

Bio::Matrix::IO

Parse PAM/BLOSUM matricies

Bio::Matrix::IO::phylip

Phylipdist parser ported to Matrix::IO

Bio::Matrix::IO::scoring

Parse PAM/BLOSUM matricies

Bio::Matrix::MatrixI

Basic matrix interface - realize this is limited for row/column data - when we derive PWM,PSSM try matricies we'll redo the interfaces

Phylipdist parser ported to Matrix::IO

Bio::Matrix::PhylipDist

More proper way to get the row pointer (IMHO) - previous was spewing warnings during tests

Phylipdist parser ported to Matrix::IO

Missing use stmts

Bio::Matrix::Scoring

Parse PAM/BLOSUM matricies

Bio::Ontology::SimpleGOEngine

Fixed and improved the simplehierarchy parser to better deal with a more recent edition of eVOC. Overrode close() in the dagflat parser to close the _defs_io too.

Bio::OntologyIO

Fixed and improved the simplehierarchy parser to better deal with a more recent edition of eVOC. Overrode close() in the dagflat parser to close the _defs_io too.

Check for data before calling in array context

Bio::OntologyIO::dagflat

Fixed and improved the simplehierarchy parser to better deal with a more recent edition of eVOC. Overrode close() in the dagflat parser to close the _defs_io too.

Bio::OntologyIO::simplehierarchy

Fill both name() and identifier() with name from a simple hierarchy file

Fixed and improved the simplehierarchy parser to better deal with a more recent edition of eVOC. Overrode close() in the dagflat parser to close the _defs_io too.

Bio::Phenotype::MeSH::Term

Initial commit

Bio::Phenotype::MeSH::Twig

Initial commit

Runnable synopsis

Bio::PopGen::IO

Interface to describe output of populations/individuals

Bio::PopGen::IO::csv

Support writing these formats as well

Bio::PopGen::IO::prettybase

Prettybase format parser (SeattleSNPs)

Support writing these formats as well

Support new option -convert_indel_states which if set to true will replace alleles which are > 1 character in length with an 'I' and will replace '-' alleles with 'D' to signify indel polymorphisms

Bio::PopGen::Individual

Slight API change and doc update

Add some debugging when we overwrite a genotype

Bio::PopGen::IndividualI

Slight API change and doc update

Bio::PopGen::MarkerI

Doc fix

Bio::PopGen::Population

Doc fix and more testing of the Stats objects reveal missing things

Bio::PopGen::PopulationI

Doc fix and more testing of the Stats objects reveal missing things

Bio::PopGen::Simulation::Coalescent

Migrating to properly named module - this will replace Bio::Tree::RandomTree (although I may leave it in place for building random topologies, need a phylogenetics expert to help with proper code for sampling random trees from treespace)

Doc fix

We traffic in genotypes now instead of name/allele pairs

Bio::PopGen::Simulation::GeneticDrift

Genetic drift simulation - to be built upon

Doc fix and more testing of the Stats objects reveal missing things

Runnable synopsis

Bio::PopGen::Statistics

Migrated Bio::Tree::Statistics to Bio::PopGen::Statistics since all the stats are related to the coalescent, proper tree statistics should (CI, etc) should be implemented in the old module

Pi and theta can be calculated from allele frequencies and thus from a Bio::PopGen::PopulationI object as well. Added heterozygosity method as well. Tests pass for pi and theta now

Missing ++ in my haste

Doc fix and more testing of the Stats objects reveal missing things

Changed over to calculate seg_sites from a shared method and tajima's D and Fu and Li D* now works

External mutations can now be estimated, Fu and Li's D works, F* and F still need fixing

Added method for calculating composite LD, still testing for correctness

Derived_mutations returns the number of external and internal (on the tree) mutations

Composite LD corrected

Fixed Issue #1498, documentation errors

Issue #1498 - added missing use stmt

Bio::PrimarySeq

Fixed a bug in seq() that would not invalidate length if it had been set without a sequence, and then a sequence was set.

Support desc as an alias for description

Bio::PrimarySeqI

Shift should be okay

Fixed translate

Bio::Restriction::Analysis

Added Analysis class, docs are more less correct

Doc fix

Runnable synopsis

Bio::Restriction::Enzyme

Initial commit

Added Analysis class, docs are more less correct

Cloning depends no longer of external module 'Storable'

Runnable synopsis

Bio::Restriction::Enzyme::MultiCut

Initial commit

Added Analysis class, docs are more less correct

Bio::Restriction::Enzyme::MultiSite

Initial commit

Bio::Restriction::EnzymeCollection

Initial commit

Added Analysis class, docs are more less correct

Bio::Restriction::EnzymeI

Initial commit

Bio::Restriction::IO

Initial commit

Bio::Restriction::IO::base

Initial commit

Added Analysis class, docs are more less correct

Bio::Restriction::IO::itype2

Initial commit

Bio::Restriction::IO::withrefm

Initial commit

Bio::Root::HTTPget

Runnable synopsis, methods are not exported so procedural calling is not possible

Bio::Root::Storable

Initial commit

Uses Data::Dumper if Storable not installed

Bio::Search::HSP::FastaHSP

Get start/end position properly for the get_aln which represents the pairwise alignment

Bio::Search::HSP::GenericHSP

Evalue of 0 is valid - only call pvalue alternative when it is undefined

SimpleAlign object will have sequences which still have their anchors in the original sequence via start/end in LocatableSeq

Doc update

Don't whine when type is undef

Bio::Search::HSP::HSPI

Doc update

Bio::Search::HSP::PSLHSP

Added PSL parser

Bio::Search::Hit::GenericHit

Don't rely on HSPs always being there, when we instantiate with a bits value

Bio::Search::Hit::HitI

Doc update

Bio::SearchIO

Issue #1469 - better guessing of format based on some regexps for filename

Add a more extensive regexp for format guessing from filename

Redundancy in the regexp

Arguments were not being passed to the Writer module

Bio::SearchIO::Writer::GbrowseGFF

A ResultWriter module that takes BLASTN (only, at the moment) and writes out Gbrowse-flavour GFF that can be imported to create DNA alignment features in Gbrowse.

Erroneously getting query name

'anchor' sequence on minus strand was assigned wrong strand

Writing wrong coordinates for anchor feature, but HSP's were correct

I didn't like all the little insignificant HSPs interfering with the 'real' HSPs that contribute to the alignment, so evaluate each HSP according to the evalue cutoff as well as the Hit.

Bio::SearchIO::Writer::HTMLResultWriter

First commit of Gary William's cleanup of the output

Some more code cleanup changes - BLASTX frames were reportedly wrong and fixed by Gary. I also added more documentation

Frame is really set correctly for all cases now. Frame needs to be +1 since bioperl stores frames as 0,1,2 but BLAST is 1,2,3. Also insure and ending

 after each HSP so that formatting is correct. Added commas to reported numbers for reported number of sequences and letters (from Perl cookbook) -private method _numwithcommas 

: One more place where numbers should have commas : Add revision string : Add revision string : Sigh - one more time - get revision stuck in there : Even more configurable, you can provide your own hit_link_desc hit_link_align, title, start_report, introduction methods. These fixes are done in part by Gary Williams as well as by Jason : Merge changes from main trunk to properly format HTML Result output - also add some documentation on the filter functions : FASTXY handled ; Bio::SearchIO::Writer::TextResultWriter : Bring TextResultWriter up to speed - commit to writing out in NCBI format for now : Bring TextResultWriter up to speed - commit to writing out in NCBI format for now ; Bio::SearchIO::axt : Missing use Factory stmts ; Bio::SearchIO::blast : Fix extra newline failing with getting query length - Gary Williams reported bug : Matrix is not a single value in WU-BLAST BLASTN, take the whole line : Fix for Wes Barris's reported issue with blastcl3 and integer overflow : Fix for Wes Barris's reported issue with blastcl3 and integer overflow : Fix {{Bugzilla|1484}} - don't match the N column from the hit signif list for gapped NCBI blast rps. Also don't match what we don't need. : Fix {{Bugzilla|1484}}, and also insure that evalues start with a number so they can be processed as numberic by Perl : Tiny change to not print warnings when Data is undef, the test needs to be before the reference to the value... : Tiny change to not print warnings when Data is undef, the test needs to be before the reference to the value... : Not complete, but much better statistics and parameter parsing for NCBI and WU-BLAST : Tests for a couple more of the parameters and stats : Added some more tests for the other paramaters - can now infer expected value cutoff from stats parsed at the end (ncbi format) ; Bio::SearchIO::blasttable : Parse NCBI BLAST -m8/-m9 format ; Bio::SearchIO::blastxml : Push newline onto the stack too ; Bio::SearchIO::fasta : Parse library name for mlib produced reports : Fix bug found in report by David Clark where percent Id is < 10 then we need to account for a possible space before the % number : Fix (on branch) bug found in report by David Clark where percent Id is < 10 then we need to account for a possible space before the % number : Go ahead and fix the mlib or SSEARCH parsing problem with getting the db name ; Bio::SearchIO::hmmer : Fix bug reported by Sophia which happens when a result does not have top level scores about the E value cutoff but does have individual domains and alignments : Make $_ local, have a default hmmidline s.t. we can parse non-headered data, capitalization fix ; Bio::SearchIO::psl : Added PSL parser : Make sure last hit makes it in, also parameterize better ; Bio::SearchIO::sim4 : Luc Gauthier's generous contribution of improvements to the parsing. Still need to design some more extensive tests. ; Bio::Seq::Meta::Array : Use the length of the sequence as defined by the object rather than testing the length of the sequence string : New altered to allow dynamic inheritance ; Bio::Seq::PrimedSeq : Porting Rob Edwards extension of Primer3 wrapper and parser : {{Bugzilla|1473}}, change ref($obj) eq "obj" to ref($obj) && $obj->isa("obj") : Runnable synopsis ; Bio::SeqFeature::AnnotationAdaptor : Added remove_Annotations() method to better comply with a mutable AnnotationCollectionI. ; Bio::SeqFeature::Collection : Deal with fact that Storable can't deal with the register_for_cleanup part : Throw away code refs and use Storable freeze/thaw instead ; Bio::SeqFeature::FeaturePair : Be even more explicit about our memory cleanup in an attempt to remove memory leaks from cycles ; Bio::SeqFeature::Gene::GeneStructure : Attempt to insure mem cycles are freed - should be a partial fix for {{Bugzilla|1431}} by using register_for_cleanup to insure that a cleanup method is properly called ; Bio::SeqFeature::Gene::Intron : We're passing in objects - test that ref is equal ; Bio::SeqFeature::Gene::Transcript : Attempt to insure mem cycles are freed - should be a partial fix for {{Bugzilla|1431}} by using register_for_cleanup to insure that a cleanup method is properly called : Be even more explicit about our memory cleanup in an attempt to remove memory leaks from cycles ; Bio::SeqFeature::Generic : Calling $sf->remove_Seqfeatures on a sf with an empty $self->{'_gsf_sub_array'} caused an error; fixed this by adding an || [] to teh array dereference : Protection in case strand is undef, won't spew warnings : Be even more explicit about our memory cleanup in an attempt to remove memory leaks from cycles : Need to change the order of the match so we don't get NaN warnings : Fixed failure of Bio::SeqFeature::Generic to set display_name properly in new() ; Bio::SeqFeature::Primer : Porting Rob Edwards extension of Primer3 wrapper and parser ; Bio::SeqFeature::Tools::TypeMapper : Fixed problem with resolving mRNA <-> CDS via splice sites ; Bio::SeqFeature::Tools::Unflattener : Added the -use_magic option to unflattener; see docs for details added a test and some test data for unflattener : Changed method of resolution of mRNA to CDS - should be more reliable : Fixed problem with resolving mRNA <-> CDS via splice sites : Improved problem reporting : Fixed problem reporting : Fixed warnings ; Bio::SeqFeatureI : Fixed bug in SYNPOSIS changed get_tag_value to get_tag_values : Fix the improper sorting of locations when they come from different remote locations, add a test for this as well : More tests, corrections, insure that remote DB handle is actually getting passed in : Remove debugging : Fix {{Bugzilla|1475}} on branch : Very, very strange fix to SeqFeatureI : This should take care of Ewan's wacky problem - test defined before initializing a InMemoryCache I think. Perhaps need to beef up InMemoryCache in the future... : This should take care of Ewan's wacky problem - test defined before initializing a InMemoryCache I think. Perhaps need to beef up InMemoryCache in the future... ; Bio::SeqIO : Solved the problem of outputting '.' in place of a strand with gff string of features coming from plugins : Sorry about that. I have to do this in my copy to prevent CGI.pm from complaining. : Guess gbk as genbank format : Guess gbk as genbank format : Match gbs : Gbs extenion matched to genbank format as well : Let's make sure verbosity is really inherited so we can quiet things for a release : Let's make sure verbosity is really inherited so we can quiet things for a release : Insure that verbosity is inherited ; Bio::SeqIO::bsml : {{Bugzilla|1490}} fixed on main trunk - and will more appropriately split up the keywords : On branch {{Bugzilla|1490}} and some code cleanup as well ; Bio::SeqIO::embl : Fix {{Bugzilla|1494}} as well as insure that KW lines wrap and the semicolons are only seen once per list by stripping them out properly from the parsed line : Fix {{Bugzilla|1494}} as well as insure that KW lines wrap and the semicolons are only seen once per list by stripping them out properly from the parsed line : Code cleanup and optimization : Code cleanup and optimization : Code cleanup and optimization, fix {{Bugzilla|1504}} : Avoid undef warnings when no KW are present ; Bio::SeqIO::fasta : Added preferred_id_type() to allow specification of what type of identifier to be used after the '>' when writing fasta output. Also added @SEQ_ID_TYPES containing list of allowable types. : Migrating version 1.41.2.3 to the main trunk. : Add a little docu describing preferred_id_type and the valid values ; Bio::SeqIO::genbank : {{Bugzilla|1489}} fixed on the branch : An implementation to fix request #1513 - parsing dates which are slighly malformed, added in a century guess as well : An implementation to fix request #1513 - parsing dates which are slighly malformed, added in a century guess as well : {{Bugzilla|1517}} fixed on branch - parse/write SEGMENT lines from genbank files - using AnnotationCollection rather than adding to the Seq object model : {{Bugzilla|1517}} fixed on main - parse/write SEGMENT lines from genbank files - using AnnotationCollection rather than adding to the Seq object model : {{Bugzilla|1515}} parse/store/write ORIGIN field from genbank parsing : Extra docs about where data goes after being parsed in Genbank module. {{Bugzilla|1515}} parse/store/write ORIGIN field from genbank parsing ; Bio::SeqIO::locuslink : Fixed locuslink parser to not slam lines together that it shouldn't. Also, removed duplicates from the dblinks and adjusted the test accordingly. ; Bio::SeqIO::swiss : Fixed missed eval() bugs really... : Fix {{Bugzilla|1504}} - plus some cleanup and code optimization - don't need to call top_SeqFeatures more than once. Some protection for writing non SeqI objects as well. : Code cleanup and optimization : Code cleanup and optimization, fix {{Bugzilla|1504}} ; Bio::SeqUtils : {{Bugzilla|1477}} - selenocystein abbr was wrong, Thanks to Matthew Betts for the spot : {{Bugzilla|1477}} - selenocystein abbr was wrong, Thanks to Matthew Betts for the spot ; Bio::SimpleAlign : Insure that seq ISA locatable seq : Doc fix : Debugging msg fix ; Bio::Structure::IO::pdb : Fixed 1485 : Tidying up... ; Bio::Symbol::README.Symbol : Describe state of Symbol code ; Bio::Taxonomy : This module is almost completely changed, to make a new system of Taxonomy. As discussed in bioperl mailing list. the new taxonomy is a hash as data structure. ; Bio::Taxonomy::FactoryI : The factory to fetch taxonomy. Bio:DB::Taxonomy and its children will be changed to implement this interface : Add the rich naming system. ; Bio::Taxonomy::Node : Add the rich naming system. ; Bio::Tools::Analysis::DNA::ESEfinder : Initial commit : Now returns ref to array of parsed data ; Bio::Tools::Analysis::Protein::Domcut : Initial commit : _result() altered to allow dynamic inheritance : More documentation ; Bio::Tools::Analysis::Protein::GOR4 : Initial commit : Use the fact the Bio::Tools::Analysis::SimpleAnalysisBase isa LWP::Useragent : More documentation ; Bio::Tools::Analysis::Protein::HNN : Initial commit : Minor bug fix : More documentation ; Bio::Tools::Analysis::Protein::Mitoprot : Initial commit of Mitpprot.pm : More documentation ; Bio::Tools::Analysis::Protein::NetPhos : Returns ref to array of predictions, passes tests : More documentation ; Bio::Tools::Analysis::Protein::Sopma : Initial commit : More documentation ; Bio::Tools::Analysis::SimpleAnalysisBase : Initial commit : Bio::Seq no longer valid input ; Bio::Tools::Genewise : Also parse HMM produced gene modules and get supporting information : Oops slightly tighter regexp fix : As usual Aaron knows way more than I do. Regexp optimization : Tag values a little more Gbrowse friendly and to a GFF standard ; Bio::Tools::Phylo::PAML : Parse NSSites output for multiple models, sites under selection, introduce additional result object to hold these values. The API will probably change some as I make sure that things are really labeled correctly. ; Bio::Tools::Phylo::PAML::ModelResult : Parse NSSites output for multiple models, sites under selection, introduce additional result object to hold these values. The API will probably change some as I make sure that things are really labeled correctly. ; Bio::Tools::Phylo::PAML::Result : Parse NSSites output for multiple models, sites under selection, introduce additional result object to hold these values. The API will probably change some as I make sure that things are really labeled correctly. ; Bio::Tools::Phylo::Phylip::ProtDist : Doc fix ; Bio::Tools::Primer::Assessor::Base : Added in start of primer design framework ; Bio::Tools::Primer::AssessorI : Added in start of primer design framework ; Bio::Tools::Primer::Feature : Added in start of primer design framework ; Bio::Tools::Primer::Pair : Added in start of primer design framework ; Bio::Tools::Primer3 : Porting Rob Edwards extension of Primer3 wrapper and parser ; Bio::Tools::PrositeScan : parser for the result of prosite scan. ; Bio::Tools::QRNA : QRNA parser ; Bio::Tools::Run::RemoteBlast : {{Bugzilla|1500}} - Remote BLAST RID line parsing is more forgiving s.t. NCBI internal changes do not cause problems : {{Bugzilla|1500}} - Remote BLAST RID line parsing is more forgiving s.t. NCBI internal changes do not cause problems ; Bio::Tools::Run::StandAloneBlast : Better tests to catch things - StandAloneBlast now supports SearchIO by default : Feature from Paul to allow multiple databases to be used : Added support for WU-Blast, still experimental : Treat switches differently : Allow quiet/silent mode ; Bio::Tools::SeqPattern : Doc improvements ; Bio::Tools::SeqStats : Added selenocysteine ; Bio::Tree::AlleleNode : Now is the intersection of PopGen::Individual and Tree::Node : Remove the add_Genotype overriding because it doesn't work with multiple inheritance (without NEXT) : Inherits from Tree::Node, implements IndividualI plus the methods which modify the data -not my ideal soln since I copy+pasted all the lines, but works : Proper containment implementation ; Bio::Tree::Node : Doc update : {{Bugzilla|1380}}, fix memory leaks : Register for cleanup to remove mem leaks : Boostrap is folded into same tag/val field for NHX and Generic nodes so we can read in newick and write NHX. Some cleanup to the regexps so we can parse in protml trees and extract the bootstrap value in the node object. : Resistance is futile - must merge main trunk changes to branch to not have nhx format fall over ; Bio::Tree::NodeI : Doc fix : Resistance is futile - must merge main trunk changes to branch to not have nhx format fall over ; Bio::Tree::NodeNHX : Boostrap is folded into same tag/val field for NHX and Generic nodes so we can read in newick and write NHX. Some cleanup to the regexps so we can parse in protml trees and extract the bootstrap value in the node object. : Resistance is futile - must merge main trunk changes to branch to not have nhx format fall over ; Bio::Tree::RandomFactory : I've remove add_Mutations as this was only appropriate for coalescent simulations and is not part of Bio::PopGen::Simluation::Coalescent. I've left the random tree generation in place but note the caveats that they aren't really appropriate for phylogenetic analyses ; Bio::Tree::Statistics : All the stats were appropriate for coalescent simluation results and for allele data not phylogenetic trees so I've moved these over to PopGen ; Bio::Tree::Tree : {{Bugzilla|1380}}, fix memory leaks : Make sure Nodes are not cleaned up when we specify -nodelete : Make sure Nodes are not cleaned up when we specify -nodelete : Merge main trunk changes - nodelete support ; Bio::Tree::TreeFunctionsI : Using Ramiro's rerooting implementation - this hasn't been fully tested though and doesn't yet solve Daniel's reported problem(s) : Daniel Barker's changes to make rerooting correct : Make sure Nodes are not cleaned up when we specify -nodelete : Make sure Nodes are not cleaned up when we specify -nodelete : Handle case when no clade root can be found ; Bio::Tree::TreeI : Support getting the leaves of the tree directly : Get_leaf_node methd ported over - it is simple API addition ; Bio::TreeIO::TreeEventBuilder : Merged changesfor internal node label parsing to branch from main trunk ; Bio::TreeIO::newick : Fixing over-zealous whitespace removal from node labels. we do this by not tampering with " quoted strings. i'm not sure if newick allows " to be escaped within these labels... if so, there may be a bug here. : Removed unnecessary escap char in space removing regex. added regex to remove quotes and leading/trailing spaces from node labels as necessary. : Merged changesfor internal node label parsing to branch from main trunk : Resistance is futile - must merge main trunk changes to branch to not have nhx format fall over ; Bio::TreeIO::nexus : A parser for PAUP produced NEXUS format trees ; Bio::TreeIO::nhx : Resistance is futile - must merge main trunk changes to branch to not have nhx format fall over : Slightly simpler logic ; FAQ : Location and subseq() : Added Q/A on BLAST HTML parsing. Neat solution! : Version 1.2.3, HMMER domains using SearchIO, Genbank/protein bug : Wrong error message : Last copy was empty ; Makefile.PL : Change version number ; biodatabases.pod : Changed bpindex, bpfetch to bp_index, bp_fetch for consistency. Update bioperl-db section. : Correct and simplify : Add mention of bioperl-db's loading scripts ; bioscripts.pod : Added mention of standaloneblast.pl : Added mention of popgen/parse_calc_stats.pl : Added new scripts/utilities scripts : Added mention of heterogeneity.PLS : Added mention of mutate.PLS : Changed bpindex, bpfetch to bp_index, bp_fetch for consistency : Added mention of composite_LD.PLS : A simple script to display hit overview, much like NCBI overview in BLAST report page ; bptutorial.pl : SearchIO is default object for StandAloneBlast, changed example code : Bl2seq in SearchIO : Albert's patch : Must commit this new text on Bio::Restriction before I can update - not done yet : New Bio::Restriction section and script section replace old : New Annotation::Collection section, separate LiveSeq and LargeSeq, correcting internal links, editing : Added mention of Biosql, editing : Changed bpindex, bpfetch to bp_index, bp_fetch for consistency : Added HOWTO link, corrected graphics scripts locations, fixed some internal links : Add links to FAQ, update SeqIO formats, and edits : Fixed missed eval() bugs really... : A bit on Location, more Pise, update OBDA, edits : - removed testing for "Storable" - restriction fragment code now works (analysis object knows about enzymes in its collection, fragments() can be called by enzyme name rather than passing it an enzyme object) : Bptutorial examples now die more gracefully when t/data isn't found : #2 : Add gbs and gbk as Genbank suffixes ; examples/db/dbfetch : Lost track of this one as well ; examples/generate_random_seq.pl : New version by Richard Adams : Added option to generate 1 to n random sequences ; examples/popgen/parse_calc_stats.pl : Initial commit of examples ; examples/tools/standaloneblast.pl : I misplaced this... ; models/bio_restriction.dia : Initial commit; created with Dia 0.91 ; models/coordinatemapper.dia : Polished with dia 0.91 ; scripts/Bio-DB-GFF/bp_genbank2gff.PLS : Fixed documentation bug in Bio::DB::GFF : Added a couple of new ways to get the data into this script, including piping accession numbers from another script (e.g. a query script) or having a folder full of GB files ready to process : Adding -adaptor as an argument to hopefully enable it to connect to an oracle adaptor : Oops. made some modifications to the .pl file that didnt' make it into the .PLS file. It now calls biofetch_stdout by defaut, or whatever adaptor you send it as an argument. : Modified to make more sensible tag/value choices for viral genomes where the products come from post-translational processing (thus they all have the same transcript, but different products). This takes advantage of a change I have just made to Bio::DB::GFF:Adaptor::biofetch_oracle that allows the default preferred_tags hash to be modified by arguments to the constructor. : Gff loaders now gff3 compatible : Changing tag translation in bp_genbank2gff.pl; unfortunately the dichotomy between CDS and exon features makes it difficult to be completely gff3 compatible; needs work ; scripts/Bio-DB-GFF/bp_genbank2gff.pl : Added genbank converter and postgres bulkloader ; scripts/Bio-DB-GFF/bulk_load_gff.PLS : Gff loaders now gff3 compatible : Added support for tied filehandles to GFF loading : Generalized split_group() function ; scripts/Bio-DB-GFF/bulk_load_gff.pl : Folded GFF3 changes into branch ; scripts/Bio-DB-GFF/fast_load_gff.PLS : Gff loaders now gff3 compatible : Added support for tied filehandles to GFF loading : Generalized split_group() function ; scripts/Bio-DB-GFF/fast_load_gff.pl : Folded GFF3 changes into branch ; scripts/Bio-DB-GFF/generate_histogram.pl : Folded GFF3 changes into branch ; scripts/Bio-DB-GFF/load_gff.pl : Folded GFF3 changes into branch ; scripts/Bio-DB-GFF/load_ucsc.pl : Support for unigene features added. ; scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS : Fixed updating of (DB)sequence when doing a bulk load ; scripts/Bio-DB-GFF/pg_bulk_load_gff.pl : Added genbank converter and postgres bulkloader ; scripts/Bio-DB-GFF/process_gadfly.pl : Folded GFF3 changes into branch ; scripts/Bio-DB-GFF/process_ncbi_human.pl : Folded GFF3 changes into branch ; scripts/Bio-DB-GFF/process_sgd.pl : Folded GFF3 changes into branch ; scripts/Bio-DB-GFF/process_wormbase.pl : Folded GFF3 changes into branch ; scripts/graphics/search_overview.PLS : A simple script to display hit overview, much like NCBI overview in BLAST report page : Add revision stuff ; scripts/index/bp_fetch.PLS : Changed bpindex, bpfetch to bp_index, bp_fetch for consistency ; scripts/index/bp_index.PLS : Changed bpindex, bpfetch to bp_index, bp_fetch for consistency ; scripts/index/bpfetch.PLS : Changed bpindex, bpfetch to bp_index, bp_fetch for consistency ; scripts/index/bpindex.PLS : Changed bpindex, bpfetch to bp_index, bp_fetch for consistency ; scripts/install_bioperl_scripts.pl : Added usage information to the script because I can never remember the arguments : And it must also be run from the parent directory ; scripts/popgen/composite_LD.PLS : Composite LD calculator : Document 2 more options : Do the indel states conversion - more docs : Remove slash : Doc update ; scripts/popgen/heterogeneity_test.PLS : Matt's Heterogeneity test : We can id internal/external (to the tree) mutations based on an outgroup which has no mutations ; scripts/seq/seqtools.pl : Bug fix: added missing -fmt option in GetOptions() call. Also added -idtype option for use when outputting fasta formatted streams. ; scripts/utilities/TAG : Expanded the def ; scripts/utilities/bp_sreformat.PLS : Exit quietly ; scripts/utilities/mask_by_search.PLS : A script to mask sequences based on their overlaps with known sequence as identified in a SearchIO parseable report : Doc updates ; scripts/utilities/mutate.PLS : Added script/utilities/mutate.PLS : Simplify... ; scripts/utilities/search2alnblocks.PLS : Script to turn SearchIO parseable report (with alignments) into alignment blocks - suitable for input to QRNA