Core 1.5.0 1.5.1 delta

These are detailed notes on changes made between bioperl-release-1-5-0 and bioperl-release-1-5-1.

Bio::Align::DNAStatistics

Return -1 when the distance is not computable (to avoid div by 0 faults)

Bio::AlignIO

Tidying _guess_format sub

Bio::AlignIO::emboss

Issue #1651

Issue #1651 on 1.5.1 branch

Bio::AlignIO::fasta

Parameterize this so we can override when I want to encode numbers in the alignment

Bio::AlignIO::largemultifasta

Less spam, more ham

Bio::AlignIO::phylip

Tag length doc

Bio::AlignIO::psi

Via the Web

Bio::AnalysisI

Default location for SOAP analysis services at EBI has changed

Bio::AnnotatableI

Fixes to bugs argument handling in get_Annotations() and in populating the type map. The rest is whitespace formatting.

Bio::Annotation::Collection

Fixes to deal with string-overloaded annotation classes that may evaluate to an empty string.

Bio::Annotation::Comment

Killed Issue #1742 by introduction of Bio::Annotation::* stringification and cmp/eq overloading. removed outdated warning from FeatureIO/gff for handling ### directives

Bio::Annotation::DBLink

Killed Issue #1742 by introduction of Bio::Annotation::* stringification and cmp/eq overloading. removed outdated warning from FeatureIO/gff for handling ### directives

Added url method to DBLink

Added documentation. Changed tagname accessor to new format to allow unsetting.

Bio::Annotation::OntologyTerm

Killed Issue #1742 by introduction of Bio::Annotation::* stringification and cmp/eq overloading. removed outdated warning from FeatureIO/gff for handling ### directives

Bio::Annotation::Reference

Killed Issue #1742 by introduction of Bio::Annotation::* stringification and cmp/eq overloading. removed outdated warning from FeatureIO/gff for handling ### directives

Bio::Annotation::SimpleValue

Killed Issue #1742 by introduction of Bio::Annotation::* stringification and cmp/eq overloading. removed outdated warning from FeatureIO/gff for handling ### directives

Bio::Annotation::StructuredValue

Killed Issue #1742 by introduction of Bio::Annotation::* stringification and cmp/eq overloading. removed outdated warning from FeatureIO/gff for handling ### directives

Bio::Annotation::Target

Killed Issue #1742 by introduction of Bio::Annotation::* stringification and cmp/eq overloading. removed outdated warning from FeatureIO/gff for handling ### directives

Bio::Assembly::Contig

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bio::Assembly::IO::ace

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Wes Barris patch

Bio::Assembly::Scaffold

Fix get_nof_contigs() to always to call get_contig_ids() in list context. Cudos to Wes Barris.

Bio::Assembly::Singlet

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bio::Biblio

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::Article

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::BiblioBase

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::Book

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::BookArticle

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::IO

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::IO::medline2ref

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::Journal

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::JournalArticle

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::MedlineArticle

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::MedlineBook

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::MedlineBookArticle

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::MedlineJournal

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::MedlineJournalArticle

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::Organisation

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::Patent

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::Person

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::Proceeding

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::Provider

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::PubmedArticle

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::PubmedBookArticle

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::PubmedJournalArticle

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::Ref

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::Service

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::TechReport

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::Thesis

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Biblio::WebResource

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::Cluster::UniGene

Added support for restr_expr line and peripheral value in seq lines Added further species to species map

Whitespace formatting only.

Bio::Cluster::UniGeneI

Added support for restr_expr line and peripheral value in seq lines Added further species to species map

Bio::ClusterIO::unigene

Added support for restr_expr line and peripheral value in seq lines Added further species to species map

Fixed parser to tolerate // in the description (TITLE) line. Yes, NCBI does this (although only a single record in Mm.data - but still.).

Bio::CodonUsage::Table

extra error handling /detection

Bio::Coordinate::Result

Warn and return on an empty location value

Bio::DB::Ace

Changed syntax to prevent rpmbuild from detecting Ace.pm dependency. this should still work as advertised, but can someone with an Ace install please test and verify?

Bio::DB::Biblio::eutils

Mention example code

Bio::DB::Biblio::pdf

Woo

Moving from crawl to if/else block for recognizing publisher sites.

Bio::DB::Biblio::soap

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::DB::BiblioI

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

Bio::DB::CUTG

extra error handling /detection

Bio::DB::Fasta

Retain header for description

Undocumented limitation on fasta line lengths is now documented and trapped

Fixed binmode() related issue on windows platforms

Bio::DB::GFF

Bio::DB::GFF loading now correctly handles cases of features with multiple parents (e.g. spliced exons)

The attributes "Name" and "Synonym" in GFF3 files now treated as equivalent to Alias

Multiple tweaks to make glyphs and aggregators more SO compliant

Gff3 loading respects the group-tags hint

Fixed off-by-one error in height of panel - under some circumstances the last pixel could get cut off from the bottom

The berkelydb adaptor will now work with plain old DB_File

Added verbose progress reports to bp_load_gff loader

Documentation enhancements

Fixed off-by-one reporting error in verbose progress messages

Progress reporting should work better now

Improved loading status messages and made it possible for bp_load_gff.pl to create new databases when given the -c flag

For mysql adaptor only, disable keys during loading -- this should lead to a performance boost

Bio::DB::GFF::Adaptor::berkeleydb

Added Simon's BerkeleyDB GFF database - full functionality is not confirmed

The berkelydb adaptor will now work with plain old DB_File

Berkeleydb adaptor now passes all 138 regression tests

Type and attribute-fetching optimizations now work properly

Berkeley adaptor no longer requires in-memory sorting for iterator to work; normalized names of the memory_iterator to memory::iterator

Fixed bug in types request; notes search is quite slow

Rebuild indices automatically when source files changed

Improved performance and storage characteristics

Added verbose progress reports to bp_load_gff loader

Documentation enhancements

Search_notes() is working, but it is too slow -- will need an optimized index for this

Keyword searching should be fast now

Removed extraneous newlines in keyword index

Made the temporary directory selectable; clarified documentation

Added basic error checking during database updating to catch filesystem errors, etc

Improved loading status messages and made it possible for bp_load_gff.pl to create new databases when given the -c flag

Removed warning

Implement classes() function

Fixed synopsis error and killed undef variable warnings in serializer

Bio::DB::GFF::Adaptor::berkeleydb::iterator

Berkeley adaptor no longer requires in-memory sorting for iterator to work; normalized names of the memory_iterator to memory::iterator

Improved performance and storage characteristics

Fetching features with an iterator was completely broken; now fixed

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

Get_features_by_name() now searches the aliases as well

Multiple tweaks to make glyphs and aggregators more SO compliant

Due to poor documentation, the new() method will now accept any of -password -passwd or -pass

Speculative changes to prevent some versions of mysql from "missing" features due to mysql floating point comparison problems

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

Found and killed more places where GD::SVG will break

For mysql adaptor only, disable keys during loading -- this should lead to a performance boost

Disable keys did not have anticipated performance boost, so commented out

Back to full text search method

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

This module reads from a database adapted to serve both CMap and GBrowse.

Added a link creation method for CMap.

Needed to overwrite another method to get the regular loader to work properly.

Found and killed more places where GD::SVG will break

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

Making searches case insensitive in pg adaptor. The oracle adaptor should probably be modified in the same way if it hasn't already.

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

Fixed a problem involving memory.pm not being able to cope with empty feature classes

GFF memory adaptor is now case-insensitive

Fixed undefined variable warning

Added Simon's BerkeleyDB GFF database - full functionality is not confirmed

The berkelydb adaptor will now work with plain old DB_File

Berkeleydb adaptor now passes all 138 regression tests

Type and attribute-fetching optimizations now work properly

Berkeley adaptor no longer requires in-memory sorting for iterator to work; normalized names of the memory_iterator to memory::iterator

Improved performance and storage characteristics

Documentation enhancements

Keyword searching should be fast now

Implement classes() function

Bio::Perl imports Bio::Root::VERSION so that MakeMaker can pick up the release version correctly

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

Improved performance and storage characteristics

Fixed synopsis error and killed undef variable warnings in serializer

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

Berkeley adaptor no longer requires in-memory sorting for iterator to work; normalized names of the memory_iterator to memory::iterator

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

Berkeley adaptor no longer requires in-memory sorting for iterator to work; normalized names of the memory_iterator to memory::iterator

Bio::DB::GFF::Aggregator::processed_transcript

Multiple tweaks to make glyphs and aggregators more SO compliant

Bio::DB::GFF::Aggregator::so_transcript

Added so_transcript glyph and aggregator; they are identical to processed_transcript glyph and aggregator, but are easier to remember

Bio::DB::GFF::Feature

Added a method to create a cmap link from a feature.

Bio::DB::GFF::RelSegment

Intersections between Features should generate RelSegments, not new Features (and besides, the two new() APIs don't match, so the previous code caused a bug)

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

Speculative changes to prevent some versions of mysql from "missing" features due to mysql floating point comparison problems

Bio::DB::NCBIHelper

Quote IDs for seq retrieval from NCBI to avoid mistaking accession which start with numbers for GI numbers

Bio::DB::RandomAccessI

Bugs by Web

Bio::DB::SeqHound

Initial commit

Bio::DB::Taxonomy

Flatfile, not localfile

Bio::DB::Taxonomy::entrez

Get the full information from Eutils TaxonomyDB XML and now can create full Taxonomy::Node objects from the Web-CGI

Support query by GI number; better handling of non-species nodes esp nodes which are actually subspecies/strain designations

Bio::Factory::AnalysisI

Default location for SOAP analysis services at EBI has changed

Bio::Factory::FTLocationFactory

Issue #1765 - now does proper hierarchical parsing and returns the sub-locs in same order as parsed in by resorting the sections before building the final SplitLocation

A semi-hack to deal with something that seems weird with perl. Rebuild the match string with the previous match string before continuing the oparg matching fun. Matching inner paren sets needs to include complement as well. This should be independent of the improved Split location to_FTstring writing which dumps more compacted location strings

Bio::FeatureIO::gff

Killed Issue #1742 by introduction of Bio::Annotation::* stringification and cmp/eq overloading. removed outdated warning from FeatureIO/gff for handling ### directives

Only get SOFA if the validate flag is set

Removed caching of every feature that is seen, which resulted effectively in a memory leak when it runs with a largish gff file. Instead, only the IDs are cached.

Modified gff.pm to allow multiple instances of the same tag, for example: Ontology_term=GO:0007155,GO:0005194;Ontology_term=GO:0005578 which is valid GFF3. Also modified the knownGene.gff3 test data file to test this.

Bio::Graph::IO::dip

Changed write() not to fail tests

Bio::Graph::ProteinGraph

Bug removed from union() to allow faster merging

Add subgraph() which overrides that in SimpleGraph.pm, articulation_points returns array ref, not array

Nodes can now be any objects that implement Bio::IdentifiableI and Bio::AnnotatableI interfaces

Cleanup warnings and remove STDERR printing to debug statements

Bio::Graph::SimpleGraph

Alter edges() and has_edge() to work with Bio::GRaph::Edge objects as well as simple edges

Cleanup warnings and remove STDERR printing to debug statements

Bio::Graph::SimpleGraph::Traversal

Make SYNOPSIS runnable

Bio::Graphics::Feature

Fixed problem in which portions of tracks would randomly disappear

Added whiskerplot for displaying statistical data

Bio::Graphics::FeatureFile

Killed two uninitialized variable warnings

Added a callback to featurefile->render so that individual tracks can be suppressed

Anonymous subroutines now in the package as init_code

Added so_transcript glyph and aggregator; they are identical to processed_transcript glyph and aggregator, but are easier to remember

When a callback fails, warning code now identifies the callback more specifically

Check in the file that defines _callback_complain()

Fixed off-by-one error in height of panel - under some circumstances the last pixel could get cut off from the bottom

Fixed a bug which prevented link and title callbacks from being evaluated within feature files

Fixed an artefact that was causing extra undef keys to appear in the FeatureFile object

Fixed problems that occur when someone changes $/ from underneath us

Added whiskerplot for displaying statistical data

Bio::Graphics::Glyph

Killed two uninitialized variable warnings

Fixed inheritance of Bio::Graphics::Panel so that it can be inherited from (bug reported by Philippe Cote)

Bio::DB::GFF loading now correctly handles cases of features with multiple parents (e.g. spliced exons)

Multiple tweaks to make glyphs and aggregators more SO compliant

Fixed a bug in the box calculation of the processed_transcript glyph which will cause a crash when the -box_subparts option is true

Added crossed connector lines and improved font loading performance

Filter out off-scale features before they are added to track; also fixed an issue with the module crashing if the image generator class not brought in before populating tracks

Fixed various problems relating to generalization of GD/GD::SVG constants

Added an option to disable searching for subfeatures; this can speed up operations when you know in advance that no features contain subfeatures

Xyplot now handles negative points correctly, though the scale could do with more work; found and corrected a bug in Glyph which causes extra bottom padding to be applied in some circumstances

Corrected a layout bug that I introduced yesterday; there is something wrong with the padding of the xyplot glyph

Handling of scales much improved; now possible to color individual boxes or points according to score or other criteria

Fixed off-by-one error in height of panel - under some circumstances the last pixel could get cut off from the bottom

Fixed bug involving the -no_subparts option

Fixed problem in which portions of tracks would randomly disappear

Added a way to number the individual exons of a transcript

Fixed a clipping bug that crops up when displaying a Bio::Das::Segment; and made the 'color' option take precedence over the 'fgcolor' option

For mysql adaptor only, disable keys during loading -- this should lead to a performance boost

Added option to display track categories after track descriptions

Added whiskerplot for displaying statistical data

Added a fudge to bump routine to correct for GD rounding errors

Bio::Graphics::Glyph::Factory

Fiddled with arrow glyph to fix off-by-one errors that appear at base pair scales

When a callback fails, warning code now identifies the callback more specifically

Bio::Graphics::Glyph::arrow

Fiddled with arrow glyph to fix off-by-one errors that appear at base pair scales

Fixed aesthetic problem in the arrow glyph

Bio::Graphics::Glyph::cds

Modified the cds glyph to support a 'sub_part' option. This is important for chado objects, because mRNA objects may contain UTRs and introns and they should not be drawn in the cds glyph, so in a gbrowse/chado contect, the option 'sub_part = CDS' can be used.

Bio::Graphics::Glyph::dna

Added gc sliding window comparison contributed by Pete Ashton

Bio::Graphics::Glyph::generic

Added a way to number the individual exons of a transcript

Back to full text search method

Bio::Graphics::Glyph::graded_segments

Migrated semantic zooming methods from merged_alignment.pm to a base class "merge_parts.pm" to be used by graded_segments.pm and other glyphs that inherit from it. Changed map_gap to be calculated relative to the sequence segment rather than the merged subfeatures.

Bio::Graphics::Glyph::heterogeneous_segments

Corrected a problem with dna sequence not being draw at high magnification

Bio::Graphics::Glyph::merge_parts

Added merge_parts.pm a base class for graded_segments and related glyphs

Small fix to max_gap method

Bio::Graphics::Glyph::merged_alignment

Added the merged_alignment glyph. It: 1) allows user-specified background colors for alignment features based on binned scores 2) supports semantic (un)zooming of dense alignment features at lower resolution. The glyph for high density alignment features is simplified by merging adjacent parts and calculatiung a weighted average score.

Documentation fix.

Migrated semantic zooming methods from merged_alignment.pm to a base class "merge_parts.pm" to be used by graded_segments.pm and other glyphs that inherit from it. Changed map_gap to be calculated relative to the sequence segment rather than the merged subfeatures.

Corrected a problem with dna sequence not being draw at high magnification

Bio::Graphics::Glyph::minmax

Added merge_parts.pm a base class for graded_segments and related glyphs

Bio::Graphics::Glyph::processed_transcript

Added code to processed_transcript that will make it easier to draw features in which exons are colinear with utrs

Multiple tweaks to make glyphs and aggregators more SO compliant

Quenched lots of bugs in the procedures that create implied UTRs and clip exons for drawing

Fixed a bug in the box calculation of the processed_transcript glyph which will cause a crash when the -box_subparts option is true

Fiddled with arrow glyph to fix off-by-one errors that appear at base pair scales

Bio::Graphics::Glyph::segmented_keyglyph

Added option to display track categories after track descriptions

Bio::Graphics::Glyph::segments

Added a way to number the individual exons of a transcript

Bio::Graphics::Glyph::so_transcript

Sequence-ontology compatible transcript

Added so_transcript glyph and aggregator; they are identical to processed_transcript glyph and aggregator, but are easier to remember

Bio::Graphics::Glyph::track

Fixed problem in which portions of tracks would randomly disappear

Fixed a clipping bug that crops up when displaying a Bio::Das::Segment; and made the 'color' option take precedence over the 'fgcolor' option

Improved appearance of xyplot scale, and created a documented extension method for the glyph

Bio::Graphics::Glyph::transcript

Added a way to number the individual exons of a transcript

Bio::Graphics::Glyph::translation

Added 'triletter_code' option to draw 3-letter code amino acids (if asked, and there's room)

Oops, forgot valine!

Bio::Graphics::Glyph::triangle

Stretch fix for triangle glyph suggested by Horvath Tamas

Bio::Graphics::Glyph::whiskerplot

Added whiskerplot for displaying statistical data

Increased flexibility of whiskerplot configuration

Bio::Graphics::Glyph::xyplot

Xyplot now handles negative points correctly, though the scale could do with more work; found and corrected a bug in Glyph which causes extra bottom padding to be applied in some circumstances

Handling of scales much improved; now possible to color individual boxes or points according to score or other criteria

Improved appearance of xyplot scale, and created a documented extension method for the glyph

Added whiskerplot for displaying statistical data

Increased flexibility of whiskerplot configuration

Bio::Graphics::Panel

Fixed inheritance of Bio::Graphics::Panel so that it can be inherited from (bug reported by Philippe Cote)

Added crossed connector lines and improved font loading performance

Filter out off-scale features before they are added to track; also fixed an issue with the module crashing if the image generator class not brought in before populating tracks

Calls to set_pen() were failing because of a GD symbol that needed to be imported

Fixed handling of gdBrushed constant that broke compatibility with GD::SVG

Fixed various problems relating to generalization of GD/GD::SVG constants

Found and killed more places where GD::SVG will break

Added the ability to tile an image or callback into the panel

Fixed off-by-one error in height of panel - under some circumstances the last pixel could get cut off from the bottom

Added a Bio::Graphics api_version() call in order to detect version skew

Fixed an artefact that was causing extra undef keys to appear in the FeatureFile object

Fixed problem in which portions of tracks would randomly disappear

Keyword searching should be fast now

Fixed problems that occur when someone changes $/ from underneath us

Added a way to number the individual exons of a transcript

Added option to display track categories after track descriptions

Added whiskerplot for displaying statistical data

Increased flexibility of whiskerplot configuration

Bio::Index::Blast

Documenting default keys

Runnable SYNOPSIS

Somewhere along the line I broke t/BlastIndex.t, now it passes

Bio::Index::EMBL

Documenting default keys

Bio::Index::Fasta

Example is incomplete

Bio::Index::Fastq

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bio::Index::GenBank

Add id_parser method

Runnable SYNOPSIS

Bio::Index::Swissprot

Comment

Runnable SYNOPSIS

Bio::LiveSeq::IO::SRS

BEGIN{'eval "require srsperl;";'} in place of 'use srsperl'. same effect, but removes srsperl from RPM-detected module dependencies, and srsperl.pm is not freely available.

Bio::LocatableSeq

Checking for presence of strand to avoid falling apart without warning

Bio::Location::Atomic

Throw via a class we already have access to

Move coordinate policy implementation to Location::Atomic and add flip_strand API

Bio::Location::Split

Splitloc with a single sub-location shouldn't have 'join' wrapped around it

Nicely compacted split location strings for rev-complement features

Bio::LocationI

New method 'flip_strand'

Move coordinate policy implementation to Location::Atomic and add flip_strand API

Remanents removed

Bio::Matrix::Generic

Protection

Paul Wieserma's changes, this obj is zero based

Changed

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

Write_psm method implemented

Bio::Matrix::PSM::IO::masta

Add raw gapless sequence alignment as an input/output to convert to/from Bio::Matrix::PSM::SiteMatrix object

Already some bug fixes. To do: add writing in seq format (not implemented yet)

SEQ output added

Fixed check that fires warnings wih -w renamed next_matrix to next_psm as IO requires

Tests pass and remove debugging

Bio::Matrix::PSM::InstanceSite

Annotation and species methods added

Bio::Matrix::PSM::SiteMatrix

Tests pass and remove debugging

Bio::Ontology::Ontology

Documented the new() method's parameters.

Remove unnessecarily use'd SimpleGOEngine - this gets rid of the default dependency on Graph.pm. Can you believe it. Also, nonetheless instantiate engine instance only when demanded.

Bio::Ontology::SimpleGOEngine

Added the GraphAdaptor modules by Nat Goodman that make SimpleGOEngine work with Graph.pm versions 0.2x and 0.5x. Thank's Nat.

Aside from documentation reformatting, a small one-line change that fixes the bug of relationships seeming lost under certain versions of Graph.pm.

Bio::Ontology::SimpleGOEngine::GraphAdaptor

Added the GraphAdaptor modules by Nat Goodman that make SimpleGOEngine work with Graph.pm versions 0.2x and 0.5x. Thank's Nat.

Added CVS Id lines. "Obfuscated" email.

Bio::Ontology::SimpleGOEngine::GraphAdaptor02

Added the GraphAdaptor modules by Nat Goodman that make SimpleGOEngine work with Graph.pm versions 0.2x and 0.5x. Thank's Nat.

Added CVS Id lines. "Obfuscated" email.

Bio::Ontology::SimpleOntologyEngine

White space formatting only.

Bio::Ontology::Term

Fixed the dblink storing and retrieval. I'm surprised that only the bioperl-db tests caught this, not bioperl itself. Also, moved the category() decorator into the interface.

Bio::Ontology::TermI

Re-arranged. Consider it a no-change.

Bio::Perl

Bio::Perl imports Bio::Root::VERSION so that MakeMaker can pick up the release version correctly

Bio::PopGen::IO::csv

Literal \\s+ was being used to write output file

Bio::PopGen::IO::hapmap

= 11 as of Dec 2004

Allow starting column to be specified - example date has start col at 10 although rich was hardcoding things to 11

Bio::PopGen::IO::phase

Fixing description

Bio::PopGen::IO::prettybase

Fix bug that caused last iteration of next_population to still return a population rather than undef even if there are no individuals left.

Bio::PopGen::PopStats

Docu fix

Bio::PopGen::Statistics

Docu fix

Bio::PrimarySeq

Parameterize the valid character pattern so it can be augmented when numbers are allowed to be encoded in a sequence string

Edits

Bio::PrimarySeqI

Translate() can used with named parameters

Additional argument to translate, -orf, that instructs translate() to find 1st ORF

Bio::RangeI

Uninitialized overlap values

Calling static methods on interfaces deprecated in RangeI - deprecated to Range. See mail list for details type mapper - mapping genbank scaffolds to SO:databank_entry removed; use contig instead

Bio::Search::HSP::BlastHSP

Doc fix

Bio::Search::HSP::FastaHSP

Doc fix

Bio::Search::HSP::GenericHSP

Doc fix

Handle S-W SSEARCH results here as well

Bio::Search::HSP::HMMERHSP

Doc fix

Bio::Search::HSP::HSPFactory

Doc fix

Bio::Search::HSP::HSPI

Doc fix

Bio::Search::HSP::PSLHSP

Doc fix

Bio::Search::HSP::PsiBlastHSP

Doc fix

Bio::Search::HSP::WABAHSP

Doc fix

Bio::Search::Hit::Fasta

Old module but updated emails

Bio::SearchIO

Table of SearchIO formats and what they map to

Bio::SearchIO::SearchResultEventBuilder

Adding code to push data into seqdesc for hsp query/hit objects

Bio::SearchIO::Writer::GbrowseGFF

Susan Miller's changes, plus my own to allow modification of Prefix and separation of match and HSP fields. Can't remember what is SO compliant but this is easily customized now

Bio::SearchIO::blast

Issue #1739; match scientific notation in score and possible e+ values

Match full db path

More wu-blast stats and params parsing

Bernd Brandt bug that webblast NCBI 2.2.10 does not have ':' after Query/Subject in alignment. Tests and bugfix

Enforce \n for expected line feed

Bio::SearchIO::blasttable

Enforce \n for expected line feed

Bio::SearchIO::exonerate

Parse Hit and Query Features from VULGAR properly

Only parse vulgar or cigar but not both

Add documentation for the new options

Bio::SearchIO::hmmer

Fixing Sean O'Keeffe's bug wrt -A0 hmmpfam files

Bio::SearchIO::psl

Allison Lee PSL help in fixing coordinate bug problem

Enforce \n for expected line feed

Bio::Seq::BaseSeqProcessor

Changed default behaviour of write_seq(). process_seq() is called first passing the object into the stream

Bio::Seq::LargeLocatableSeq

Less spam - more ham

Bio::Seq::LargeSeqI

Less spam - more ham

Bio::Seq::Meta

Documentation changes

Remove automatic padding, can be re-enabled by force_flush()

Bio::Seq::Meta::Array

Documentation changes

Doc fixes

Remove automatic padding, can be re-enabled by force_flush()

Bio::Seq::MetaI

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Remove automatic padding, can be re-enabled by force_flush()

Bio::Seq::PrimaryQual

Handle zero as a quality value, fix Issue #1824

Bio::Seq::PrimedSeq

Cleanup a little bit of empty warnings when no -left or -right or -both is provided, default is to return both if no argument is provided

Assign correct coordinates for the start and end of the primer sequences in the SeqFeature

Bio::Seq::Quality

New implementation of Bio::Seq::SeqWithQuality

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Remove automatic padding, can be re-enabled by force_flush()

Bio::Seq::SeqBuilder

Formatting

Bio::Seq::SeqWithQuality

Fixed an oddball situation in which a reference was passed to the seq argument of the constructor

Handle zero as a quality value, fix Issue #1824

Fix synopsis

Add deprecated warning

Bio::Seq::SequenceTrace

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bio::Seq::TraceI

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bio::SeqFeature::Annotated

Don't need this!

Fixed to use @ISA instead of use base (problems on 5.6.0 otherwise). Throw exception instead of semi-silently ignoring calls.

Bio::SeqFeature::AnnotationAdaptor

Only whitespace/tab formatting.

Bio::SeqFeature::Gene::GeneStructure

Partial solution for Issue #1778 - weaken references. This only works in perl 5.8.0+ so we will have to see about the other workaround solution.

Bio::SeqFeature::Gene::Transcript

Partial solution for Issue #1778 - weaken references. This only works in perl 5.8.0+ so we will have to see about the other workaround solution.

Fix Oliver Burren's reported bug about adding exons/features not-in-order causes problems. So insure features are sorted and include strand in the sorting equation

Bio::SeqFeature::Gene::TranscriptI

Partial solution for Issue #1778 - weaken references. This only works in perl 5.8.0+ so we will have to see about the other workaround solution.

Bio::SeqFeature::Generic

Just get start,end,strand instead of a range object, removing the need for an additonal new call that will just get thrown away

Issue #1720 fix, delete a key from hash in the generic_cleanup function, even though we are really just derefering which should be enough

Bio::SeqFeature::Tools::FeatureNamer

Added DESCRIPTION

Bio::SeqFeature::Tools::IDHandler

Changed policy for autogenerated feature IDs the source rather than the type is now the first thing in the ID before the ':' this should not affect any code, as these IDs are not intended to be stable outside any particular chaos document, code should not rely on the ID being structured in any particular way also this only affects code for which IDs are autogenerated this does make the ID easier to treat as a URI; the part preceeding the ':' is equivalent to the namespace

Bio::SeqFeature::Tools::TypeMapper

Calling static methods on interfaces deprecated in RangeI - deprecated to Range. See mail list for details type mapper - mapping genbank scaffolds to SO:databank_entry removed; use contig instead

Typemapper is now complete

Bio::SeqFeature::Tools::Unflattener

Typemapper is now complete

Unflattener: now less strict about ordering of exons in a transcript - this allows us to process the trans-spliced transcripts in NC_001284 (if exons are not in order a severity-3 problem is thrown, which can be ignored by user if their threshold is high enough) chaos.pm: uses derives_from instead of produced_by for mRNA to pp relation seqconvert: added chaos and chadoxml as file formats

Bio::SeqFeature::TypedSeqFeatureI

Added TypedSeqFeature

Bio::SeqIO

Tidying _guess_format sub

Correction

Bio::SeqIO::FTHelper

Bugs at bugzilla

Bio::SeqIO::MultiFile

Bugs at bugzilla

Bio::SeqIO::abi

Documented to return a Bio::Seq::SeqWithQuality - not sure why it hasn't before, but it does now

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bugs at bugzilla

Bio::SeqIO::ace

Bugs at bugzilla

Bio::SeqIO::agave

Bugs at bugzilla

Bio::SeqIO::alf

Bugs at bugzilla

Bio::SeqIO::asciitree

Bugs at bugzilla

Bio::SeqIO::bsml

Bugs at bugzilla

Bio::SeqIO::chadoxml

Bugs at bugzilla

Bio::SeqIO::chaos

Changed policy for autogenerated feature IDs the source rather than the type is now the first thing in the ID before the ':' this should not affect any code, as these IDs are not intended to be stable outside any particular chaos document, code should not rely on the ID being structured in any particular way also this only affects code for which IDs are autogenerated this does make the ID easier to treat as a URI; the part preceeding the ':' is equivalent to the namespace

Unflattener: now less strict about ordering of exons in a transcript - this allows us to process the trans-spliced transcripts in NC_001284 (if exons are not in order a severity-3 problem is thrown, which can be ignored by user if their threshold is high enough) chaos.pm: uses derives_from instead of produced_by for mRNA to pp relation seqconvert: added chaos and chadoxml as file formats

Bugs at bugzilla

Bugzilla only

Bio::SeqIO::chaosxml

Bugs at bugzilla

Bio::SeqIO::ctf

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bugs at bugzilla

Bio::SeqIO::embl

Alex's patch

Fix ID line parsing: the molecule string can have spaces in it. Like: "genomic DNA"

Changed regexp for ID line. The capturing parentheses are the same, the difference is an optional repeated-not-semi-colon expression following the captured \S+. This means the regexp works when the division looks like /PRO;/ or when the division looks like /ANG ;/ - the latter is from EMBL repbase

Bio::SeqIO::entrezgene

Entrezgene parser Still not implemented: convert to locuslink and STS

Conversion to locuslink (backcompatibility), gene status, generifs are now stored as DBLinks with additional info (ref gene, ref pubmed id), some bugs eliminated. Also the parser now uses Bio::ASN1::EntrezGene

Now the Seq objects, contained in the cluster will know their namespace and authority for example: namespace Reference, authority genomic

Fixed the CDD data parsing+minor fixes

Parsing the service record (generifs for gene with no entrez gene records) is disabled by default use -service_record=>'yes' if you want to get this record +fix for the different specie format in this record

Few bug fixes:entrez gene status, database links

Few fixes for some warnings Annie Law observed

Trimopt removed...

Fixing warnings....

Bio::SeqIO::exp

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bugs at bugzilla

Bio::SeqIO::fastq

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bugs at bugzilla

Bio::SeqIO::game

Made lack on annotations non-fatal

Bugs at bugzilla

Bio::SeqIO::game::featHandler

Made lack on annotations non-fatal

Bio::SeqIO::game::gameHandler

Made lack on annotations non-fatal

Bio::SeqIO::game::gameSubs

Made lack on annotations non-fatal

Bio::SeqIO::game::gameWriter

Made lack on annotations non-fatal

Bio::SeqIO::game::seqHandler

Made lack on annotations non-fatal

Bio::SeqIO::gcg

Bugs at bugzilla

Bio::SeqIO::genbank

Add capacity to read and write the DBSOURCE line

Parse swissprot fields in genpept file (dbsource)

Fix genbank.pm so it treats multi-line SOURCE sections correctly, this defect broke both common_name() and classification(). Unfortunately the fix is an unattractive hack - I believe that re-writing genbank.pm to accomodate N lines per section would be a substantial amount of work.

Issue #1871; some indented fun too. The action was in the 'REFLOOP' parsing loop, I changed the pattern to expect at least 9 spaces at the beginning of a line to indicate line wrapping. This was the problem, the regexp wanted to make ' PUBMED' a line wrap because the pattern matched \s{3,} in the REMARK regexp. It should be tighter now

Bio::SeqIO::kegg

Bugs at bugzilla

Bio::SeqIO::largefasta

Bugs at bugzilla

Bio::SeqIO::locuslink

Bugs at bugzilla

Bio::SeqIO::metafasta

Remove automatic padding, can be re-enabled by force_flush()

Needs to use Bio::Seq::Meta, I think. Also needs SYNOPSIS.

Bio::SeqIO::phd

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bugs at bugzilla

Bio::SeqIO::pir

Bugs at bugzilla

Bio::SeqIO::pln

Bugs at bugzilla

Bio::SeqIO::qual

Not sure why this thing dumpValued during write_seq.

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bugs at bugzilla

Bio::SeqIO::raw

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bugs at bugzilla

Bio::SeqIO::scf

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bugs at bugzilla

Bio::SeqIO::swiss

Guido's fixes for Issue #1727

Bugs at bugzilla

Bio::SeqIO::tab

Remove uninit warnings

Bugs at bugzilla

Bio::SeqIO::tigr

Bugs at bugzilla

Bio::SeqIO::tigrxml

Bugs at bugzilla

UTR calculations improved, make SO compliant so gene->mRNA->{exon,CDS,five_prime_UTR,three_prime_UTR}

Bio::SeqIO::tinyseq

Bugs at bugzilla

Bio::SeqIO::ztr

Removing Bio:Seq::SeqWithQuality in favour of Bio::Seq::Quality

Bugs at bugzilla

Bio::SimpleAlign

Alex Brown's bug report about residue count

Alex Brown's bug report about residue count

Doc fix

Remove_gaps() did not use the passed gap_char argument. Enabled it but added a note to use gap_char() and remove_columns. Resolves Issue #1868

Bio::SimpleAnalysisI

Default location for SOAP analysis services at EBI has changed

Bio::Structure::Atom

Bugs at bugzilla

Bio::Structure::Chain

Bugs at bugzilla

Bio::Structure::Entry

Bugs at bugzilla

Bio::Structure::IO

Bugs at bugzilla

Bio::Structure::Model

Bugs at bugzilla

Bio::Structure::Residue

Bugs at bugzilla

Bio::Structure::SecStr::DSSP::Res

Added residues() method which is an iterator over all real residues of all chains or just of a specified chain. Also, fixed two bugs: 1. Problem with DSSP chain termination codes encountered when resolving residue ids. 2. Problem parsing excess blank lines at EOF.

Bio::Structure::StructureI

Bugs at bugzilla

Bio::Taxonomy::Node

Get the full information from Eutils TaxonomyDB XML and now can create full Taxonomy::Node objects from the Web-CGI

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

Debugged, URL's changed

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

Species now put in 'userSpecies' field

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

'site' tag added to features

Bio::Tools::CodonTable

NCBI's Codon Table page has changed

Bio::Tools::GFF

The script was silently broken by a change to the default behaviour of the Bio::FeatureHolderI::get_all_SeqFeatures method. I also: 1) made some changes to how shared exons are handled in response to the updated GFF3 spec. 2) dealt with labelling problem in gene containment hierarchies derived from third-party (non-refseq) annotations. I think more testing is required.

Bio::Tools::GuessSeqFormat

There might be more than one space between numseq and seqlength

Add a space after >

Seqname in second line of possibly_phylip

Fixed phylip to pass the tests

Bio::Tools::HMM

Hidden Markov Model module

Fixed a silly bug at line 449

Fixed a bug in HMM::likelihood

Bio::Tools::Hmmpfam

Allow parse of multiple records in stream

Make e-value default score displayed in gff, rather than raw score

Bio::Tools::Lucy

Fixed, from Philip

Apply patch

Added doc

The deepest cut... remove double cut

Bio::Tools::Phylo::Molphy::Result

SPAM-B-gone and bugs only via web

Bio::Tools::Phylo::PAML

Updated for parsing branch-specific parameters. These are now added to the Tree objects. Example SYNOPSIS code and script coming

Slight doc cleanup -- still need a better SYNOPSIS for all the options

Parse input params

Parse RST files, thanks to Albert Vilella for contributing start of the anc seq parsing. This does not full capture the rst file but gets close, things left to do are in the TODO

Get rid of empty lines while parsing dnds_site_classes

Docu fix -- API is get_trees() not get_tree()

Less spam - more ham

Bio::Tools::Phylo::PAML::ModelResult

Return an empty array where appropriate

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

Parse input params

Parse RST files, thanks to Albert Vilella for contributing start of the anc seq parsing. This does not full capture the rst file but gets close, things left to do are in the TODO

Less spam - more ham

Bio::Tools::Primer3

George's patch

Make SYNOPSIS runnable

Fixed Issue #1827

Handle parsing of primer3 output when only 1 primer is requested

Bio::Tools::Promoterwise

Handle different versions of promoterwise

Bio::Tools::Pseudowise

Rewritten parser

Bio::Tools::RestrictionEnzyme

Fat fingers

Bio::Tools::Run::RemoteBlast

Issue #1864 fixed, test for STATUS line in the report

Support for XML and blasttable

Env_proxy when initing UserAgent

Bio::Tools::Run::WrapperBase

Tempdir can now be set

Fixing self messing

Bio::Tools::SeqStats

Issue #1738

Made it possible to silence warning about ambiguous bases wih verbose() < 0

Force count_codons() to count everything in upper case. Otherwise results do not make sense if the sequence is in mixed case.

Bio::Tools::Spidey::Exon

Latest

Bio::Tools::Spidey::Results

Ryan's fixes

Latest

Make SYNOPSIS runnable

Bio::Tools::dpAlign

Fixed some wrong comments. Not change to code

Set score for SimpleAlign

Bio::Tools::ipcress

Added a parser for the oputput of ipcress, part of Guy Slater's exonerate package. This module is analogous to EPCR.pm

Bio::Tools::isPcr

Added a parser for the output of Jim kent's isPcr (in silico PCR). This module is analogous to EPCR.pm

Fixed filehandle support

Added a parser for the oputput of ipcress, part of Guy Slater's exonerate package. This module is analogous to EPCR.pm

Bio::Tools::tRNAscanSE

Better SYNPOSIS doc

Bio::Tree::AlleleNode

No bug email

Bio::Tree::Compatible

Testing compatibility of phylogenetic trees with nested taxa

Bio::Tree::DistanceFactory

Respect interface design

Bio::Tree::Draw::Cladogram

A Cladogram and Tanglegram drawing module

Use branch lengths to draw phylograms

Added aspect ratio parameter, default to golden ratio

Added option to ignore branch lengths

Bio::Tree::Node

Play nice with wantarray

Bug fixes for node height

Join two nodes into one if node only has one child: per bug from Niv Sabath

Hmm, this code should be for a Node not a Tree

Bio::Tree::NodeI

Bug fixes for node height and depth

Bio::Tree::TreeFunctionsI

Assign branchlength to outgroup after reroot in the same fashion as PHYLIP retree reroot() function by splitting the difference

Reroot is consistent with retree from PHYLIP now

Hmm, this code should be for a Node not a Tree

Bio::TreeIO

No bug emailaddr

Bio::TreeIO::TreeEventBuilder

Fix for Issue #1852

Bio::TreeIO::nexus

Issue #1854, now process everything from a single line newline is just another whitespace char

FAQ

Change version

1.5.1

Makefile.PL

Made changes to remove pg_bulk_load_gff.PLS because it's functionality has been aquired by bulk_load_gff.PLS. A symlink is created (from bp_pg_bulk_load_gff.pl to bp_bulk_load_gff.pl) on install using the script install_util/symlink_scripts.PLS.

Rolling back changes until discussed.

Since the bp_bulk_load_gff.pl has been replaced with a script that takes the place of both itself (mysql version) and bp_pg_bulk_load_gff.pl (postgresversion), we want to create a symbolic link from postgresversion to bp_bulk_load_gff.pl on install. This will make the change transparent to people who have been using the postgres version. On make, an external script maintenence/symlink_scripts.pl gets created with all the necessary path info. In the postamble of Makefile.PL, a line was inserted to call the symlink_scripts.pl file. Then on install, symlink_scripts.pl is run and creates the symbolic link. The Perl symlink function was used to create the link, so that on systems where symlink doesn't work, it catches the error and prints a note tothe user. That is untested though.

Bio::SeqIO::entrezgene depends on GI::Parser::EntrezGene

Dependancy changed to Bio::ASN1::EntrezGene now

Fixed requirements

Modified the symlink script to take an argument indicating where the script will be installed. Previously, it assumed the system-wide location as the default (eg, /usr/local/bin), making non-priv install impossible (though it failed quitely, so the non-priv person didn't know anything happened). Modified Makefile.PL to provide the arg where scripts will be installed. This was not tested on Windows but it should work there as well.

Entrezgene added to changes Bio::ASN1::EntrezGene added as a dependency for Bio::SeqIO::entrezgene

biodatabases.pod

Updated bioperl-db related documentation.

1.5.1

biodesign.pod

1.5.1

bioperl.pod

Fix the version number

1.5.1

bioscripts.pod

More on scripts/ scripts

New script

Describe newly added script

Remove duplicate

Seqret added

Add classify hits on taxonomy script

1.5.1

bptutorial.pl

Default location for SOAP analysis services at EBI has changed

Change URL

Edit

Change documentation of translate()

Correct URL

Edits, correct URLs, more on translate().

examples/Bio-DB-GFF/load_ucsc.pl

Fixed so that gff files are written to individual files as intended, rather than to STDOUT

examples/align/align_on_codons.pl

New API

examples/align/clustalw.pl

Format

examples/biblio/biblio-eutils-example.pl

Split script into soap and eutils examples

examples/biblio/biblio-soap-example.pl

Split script into soap and eutils examples

examples/biblio/biblio_examples.pl

Split script into soap and eutils examples

examples/biographics/render_sequence.pl

Render fixed for current 1.5.x API

examples/root/lib/Bio/PrimarySeqI.pm

New API

examples/tools/parse_codeml.pl

Correct

maintenance/modules.pl

Ignore the synopsis of Bio::Tools::HMM which has the functional code in bioperl-ext

Less spam - more ham

maintenance/symlink_scripts.PLS

Since the bp_bulk_load_gff.pl has been replaced with a script that takes the place of both itself (mysql version) and bp_pg_bulk_load_gff.pl (postgresversion), we want to create a symbolic link from postgresversion to bp_bulk_load_gff.pl on install. This will make the change transparent to people who have been using the postgres version. On make, an external script maintenence/symlink_scripts.pl gets created with all the necessary path info. In the postamble of Makefile.PL, a line was inserted to call the symlink_scripts.pl file. Then on install, symlink_scripts.pl is run and creates the symbolic link. The Perl symlink function was used to create the link, so that on systems where symlink doesn't work, it catches the error and prints a note tothe user. That is untested though.

The PLS suffix has a specific meaning in Bioperl, this should have the suffix pl instead

No, I was wrong, Ben wants this to be installed and not just run

Modified the symlink script to take an argument indicating where the script will be installed. Previously, it assumed the system-wide location as the default (eg, /usr/local/bin), making non-priv install impossible (though it failed quitely, so the non-priv person didn't know anything happened). Modified Makefile.PL to provide the arg where scripts will be installed. This was not tested on Windows but it should work there as well.

maintenance/symlink_scripts.pl

The PLS suffix has a specific meaning in Bioperl, this should have the suffix pl instead

No, I was wrong, Ben wants this to be installed and not just run

scripts/Bio-DB-GFF/bulk_load_gff.PLS

Added much functionallity. This now can use both the mysql and mysqlcmap adaptors. It also can be a replacement for pg_bulk_load_gff.PLS. When called as *pg_bulk_gff.pl it will function the same as pg_bulk_load_gff.pl

Bio::DB::GFF loading now correctly handles cases of features with multiple parents (e.g. spliced exons)

Quashed spurious warnings about embedded sequences

The attributes "Name" and "Synonym" in GFF3 files now treated as equivalent to Alias

Fixed off-by-one error in height of panel - under some circumstances the last pixel could get cut off from the bottom

Removing the comment that deletes the temp files

Made bulk and fast loaders robust to FASTA sequence distributed throughout file

Fix DREADFUL bug which deleted FASTA files regardless of whether or not they were temporary, this should take care of it

scripts/Bio-DB-GFF/fast_load_gff.PLS

Bio::DB::GFF loading now correctly handles cases of features with multiple parents (e.g. spliced exons)

Quashed spurious warnings about embedded sequences

Multiple tweaks to make glyphs and aggregators more SO compliant

Fixed off-by-one error in height of panel - under some circumstances the last pixel could get cut off from the bottom

Made bulk and fast loaders robust to FASTA sequence distributed throughout file

scripts/Bio-DB-GFF/genbank2gff3.PLS

The script was silently broken by a change to the default behaviour of the Bio::FeatureHolderI::get_all_SeqFeatures method. I also: 1) made some changes to how shared exons are handled in response to the updated GFF3 spec. 2) dealt with labelling problem in gene containment hierarchies derived from third-party (non-refseq) annotations. I think more testing is required.

Fix regexp

Some changes to use the locus_tag attribute when no gene name is found and (hopefully) properly unflatten unlabelled genes.

Repaired the way the path to -o is resolved.

scripts/Bio-DB-GFF/load_gff.PLS

Fixed off-by-one error in height of panel - under some circumstances the last pixel could get cut off from the bottom

Added verbose progress reports to bp_load_gff loader

Improved loading status messages and made it possible for bp_load_gff.pl to create new databases when given the -c flag

Fixed synopsis error and killed undef variable warnings in serializer

scripts/Bio-DB-GFF/load_ucsc.pl

This script is in examples/

scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS

Made changes to remove pg_bulk_load_gff.PLS because it's functionality has been aquired by bulk_load_gff.PLS. A symlink is created (from bp_pg_bulk_load_gff.pl to bp_bulk_load_gff.pl) on install using the script install_util/symlink_scripts.PLS.

scripts/DB/biofetch_genbank_proxy.PLS

Obscure emails, standardize perl at header

scripts/DB/bioflat_index.PLS

Obscure emails, standardize perl at header

Correct

scripts/DB/biogetseq.PLS

Obscure emails, standardize perl at header

scripts/DB/flanks.PLS

Obscure emails, standardize perl at header

scripts/README

Add README

scripts/biblio/biblio.PLS

Biblio modules updated to reflect the new location and API changes in the OpenBQS service at EBI

scripts/biographics/bp_glyphs1-demo.PLS

Demo of new glyphs.

scripts/index/TAG

Seqret added

scripts/index/bp_seqret.PLS

Seqret added

More permissive filename extensions and have to create a new seq object to properly write out/override description and display_id as seq objs from DB::Fasta don't include description

Support start/end (sbegin,send) options

scripts/searchio/README

Update related documentation

scripts/searchio/TAG

Update related documentation

scripts/searchio/fastam9_to_table.PLS

Fix header

Deal with TFASTX [f] or [r] fields, properly report querylen as well for these

scripts/searchio/hmmer_to_table.PLS

Superfast HMMER to table parsing

scripts/seq/extract_feature_seq.PLS

Obscure emails, standardize perl at header

scripts/seq/make_mrna_protein.PLS

Obscure emails, standardize perl at header

New API

scripts/seq/seqconvert.PLS

Obscure emails, standardize perl at header

Unflattener: now less strict about ordering of exons in a transcript - this allows us to process the trans-spliced transcripts in NC_001284 (if exons are not in order a severity-3 problem is thrown, which can be ignored by user if their threshold is high enough) chaos.pm: uses derives_from instead of produced_by for mRNA to pp relation seqconvert: added chaos and chadoxml as file formats

scripts/seq/split_seq.PLS

Obscure emails, standardize perl at header

Mauricio Herrera Cuadra changes to make script more robust

Correct

scripts/seq/translate_seq.PLS

Obscure emails, standardize perl at header

scripts/seq/unflatten_seq.PLS

Obscure emails, standardize perl at header

scripts/taxa/classify_hits_kingdom.PLS

Add classify hits on taxonomy script

scripts/taxa/query_entrez_taxa.PLS

Example script to use taxonomy db and query for name, gi number, etc

scripts/utilities/bp_sreformat.PLS

Support line-length specification on the cmdline