Core 1.5.0 1.5.1 delta

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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 removed outdated warning from FeatureIO/gff for handling ### directives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 removed outdated warning from FeatureIO/gff for handling ### directives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 removed outdated warning from FeatureIO/gff for handling ### directives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 removed outdated warning from FeatureIO/gff for handling ### directives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 removed outdated warning from FeatureIO/gff for handling ### directives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 removed outdated warning from FeatureIO/gff for handling ### directives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 removed outdated warning from FeatureIO/gff for handling ### directives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
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