Core 1.0.1 1.0.2 delta

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

Bio::Align::Utilities
Place to put various utilities which operate on Bio::Align::AlignI object - for now just 1 method to convert aa alignments to their corresponding DNA alignments much like mrtrans
Can't rely on self methods
No use of self in function
Bio::AlignIO
Added missing supported formats
New suffixes in _guess_format
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::AlignIO::clustalw
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::AlignIO::emboss
Subtle bug in emboss parsing which was adding extra gaps at the beginning of global alignment sequences after parsing
Bio::AlignIO::fasta
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::AlignIO::mega
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::AlignIO::msf
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::AlignIO::nexus
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::AlignIO::pfam
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::AlignIO::phylip
Strip any trailing _'s
Parameterize id_length to avoid hardcoded 10 in the module
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::AlignIO::psi
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::AlignIO::selex
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::Cluster::UniGene
NCBI format changed, module now handles multiple locuslink ids
Documentation changes, next_unigene() should be next_cluster(). ClusterIO now includes Cluster::Unigene, so you don't need to include it in the calling package.
Was calling Bio::Seq::SeqFactory::create_sequence() instead of create()
Bio::Cluster::UniGeneI
NCBI format changed, module now handles multiple locuslink ids
Bio::Cluster::dbSNP
Adding a functional but incomplete dbSNP xml parser. needs docs!
Bio::ClusterIO
Added dbsnp as a valid format
Documentation changes, next_unigene() should be next_cluster(). ClusterIO now includes Cluster::Unigene, so you don't need to include it in the calling package.
Bio::ClusterIO::dbsnp
Adding a functional but incomplete dbSNP xml parser. needs docs!
Fixed an EOF problem
Bio::ClusterIO::unigene
Removed Parse::RecDescent, used regexes instead.
Documentation changes, next_unigene() should be next_cluster(). ClusterIO now includes Cluster::Unigene, so you don't need to include it in the calling package.
Was calling Bio::Cluster::Unigene instead of Bio::Cluster::UniGene
Bio::Coordinate::Collection
First commit of coordinate mapper modules
Mappers in a collection are now sorted
True many-to-many or many-to-one mapping now possible
Bio::Coordinate::ExtrapolatingPair
First commit of coordinate mapper modules
Bio::Coordinate::MapperI
First commit of coordinate mapper modules
Deleted unnecessary methods
Putting back in() and out()
Bio::Coordinate::Pair
First commit of coordinate mapper modules
Fixed coordinate mapping to reverse strand
Added synopsis
Doc fixes
Bio::Coordinate::Result
First commit of coordinate mapper modules
Bio::Coordinate::Result::Gap
First commit of coordinate mapper modules
Bio::Coordinate::Result::Match
First commit of coordinate mapper modules
Bio::DB::Biblio::biofetch
One too many printings of the content str
Bio::DB::Biblio::soap
Fixed: looking for keywords with numeric values
Bio::DB::GFF
Made changes for compatibility with Generic Genome Browser 1.44
Doc type - Bio::DB::Aggregator->Bio::DB::GFF::Aggregator
Changes to Bio::DB::GFF to allow retrieval of segments that do not have genomic coordinates (not listed as features relative to themselves)
Adjusted the dna() method so that it returns full length of the dna if start and end are undefined
Bio::DB::GFF::Adaptor::biofetch
Made changes for compatibility with Generic Genome Browser 1.44
Bio::DB::GFF::Adaptor::dbi::mysql
Removed stupid mysql assumptions from the connect() call
Fixed 3-frame translation glyph to accomodate 6-frame translation; improved the "what I wanted, not what I said" behavior of the mysql DBGFF adaptor
Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights
Changes to Bio::DB::GFF to allow retrieval of segments that do not have genomic coordinates (not listed as features relative to themselves)
Adjusted the dna() method so that it returns full length of the dna if start and end are undefined
Adjusted the dna() method so that it returns full length of the dna if start and end are undefined
Added an index to the attribute_value field, causing vast improvement in performance on alias searches
Added an index to the attribute_value field, causing vast improvement in performance on alias searches
Bio::DB::GFF::Adaptor::dbi::mysqlopt
Adjusted the dna() method so that it returns full length of the dna if start and end are undefined
Bio::DB::GFF::Adaptor::memory
Made changes for compatibility with Generic Genome Browser 1.44
Adjusted the dna() method so that it returns full length of the dna if start and end are undefined
Adjusted the dna() method so that it returns full length of the dna if start and end are undefined
Bio::DB::GFF::Adaptor::memory_iterator
Made changes for compatibility with Generic Genome Browser 1.44
Adjusted the dna() method so that it returns full length of the dna if start and end are undefined
Bio::DB::GFF::Feature
Made changes for compatibility with Generic Genome Browser 1.44
Adding SeqFeatureI method seqname which points to the hashkey 'sourceseq'
Adjusted the dna() method so that it returns full length of the dna if start and end are undefined
Bio::DB::GFF::RelSegment
Made changes for compatibility with Generic Genome Browser 1.44
Return from overlaps/contains when item is not a RelSegment
Return from overlaps/contains when item is not a RelSegment
Changes to Bio::DB::GFF to allow retrieval of segments that do not have genomic coordinates (not listed as features relative to themselves)
Adjusted the dna() method so that it returns full length of the dna if start and end are undefined
Bio::DB::GFF::Segment
Segment implements SeqI now
Bio::DB::GenBank
Migrate to Eutils
Bio::DB::GenPept
Migrate to Eutils
Bio::DB::NCBIHelper
Migrate to Eutils
Bio::DB::RefSeq
Support embl-> embl
Bio::DB::WebDBSeqI
Migrate to Eutils
Quieter warnings - they show up in the 'throw' which can be trapped
Bio::Factory::EMBOSS
Added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero
Bio::Factory::ObjectFactoryI
New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects
Bio::Factory::Pise
Added id
Bio::Factory::SequenceFactoryI
Move to more general factory type
Bio::Graphics::Feature
Made changes for compatibility with Generic Genome Browser 1.44
Added a decent 6-frame translation glyph
Added spliced cds and 3-frame translation glyphs
Bio::Graphics::FeatureFile
Made changes for compatibility with Generic Genome Browser 1.44
Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.
Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.
Better bump control in the render() call
Better bump control in the render() call
Reenabled ability of feature2label to detect type/subtype relationships
Folded recent bug fixes from release branch into dev branch
POX fixes
Updated Bio::Graphics::FeatureFile to allow glyph-specific settings in configuration files to be set programmatically. For example: [named genes] glyph = arrow fgcolor = blue height = sub { shift->source eq 'GenBank' ? 20 : 10 } The power of perl. You can't help loving it.
Added spliced cds and 3-frame translation glyphs
Bio::Graphics::Glyph
Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.
Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.
Algorithm improvements to bump algorithm give 5x speedup for complex images
Algorithm improvements to bump algorithm give 5x speedup for complex images
The group glyph will now refuse to do simple bumping because it is unattractive
Improved behavior of segmented glyphs when they go off the edges
Improved behavior of segmented glyphs when they go off the edges
Cleaned up the boundaries of graphic elements so that adjacent features exactly abut at the nucleotide level (this problem always occurs when numbering nucleotides rather than numbering spaces between nucleotides)
Off-by-one error in glyph coordinates -- only apparent at nucleotide-level resolution
Added 6-frame translation and cds glyphs
Added spliced cds and 3-frame translation glyphs
Bio::Graphics::Glyph::Factory
Added 6-frame translation and cds glyphs
Added spliced cds and 3-frame translation glyphs
Bio::Graphics::Glyph::alignment
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::anchored_arrow
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::arrow
Made changes for compatibility with Generic Genome Browser 1.44
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::box
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::cds
Updated Bio::Graphics::FeatureFile to allow glyph-specific settings in configuration files to be set programmatically. For example: [named genes] glyph = arrow fgcolor = blue height = sub { shift->source eq 'GenBank' ? 20 : 10 } The power of perl. You can't help loving it.
Added spliced cds and 3-frame translation glyphs
Fixed a problem in cds glyph that caused first methionine to be skipped on forward cds
Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights
Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::crossbox
Made changes for compatibility with Generic Genome Browser 1.44
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::diamond
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::dna
Rename s/Ace::Graphics/Bio::Graphics/ where applicable
Made changes for compatibility with Generic Genome Browser 1.44
Updated regression tests to accomodate earlier changes to Glyph coordinate mapping
Added a decent 6-frame translation glyph
Added 6-frame translation and cds glyphs
Added spliced cds and 3-frame translation glyphs
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::dot
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::ellipse
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::ex
Made changes for compatibility with Generic Genome Browser 1.44
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::extending_arrow
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::generic
Made changes for compatibility with Generic Genome Browser 1.44
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::graded_segments
Made changes for compatibility with Generic Genome Browser 1.44
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::group
The group glyph will now refuse to do simple bumping because it is unattractive
The group glyph will now refuse to do simple bumping because it is unattractive
Bio::Graphics::Glyph::heterogeneous_segments
Made changes for compatibility with Generic Genome Browser 1.44
Added 6-frame translation and cds glyphs
Added spliced cds and 3-frame translation glyphs
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::line
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::oval
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::pinsertion
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::primers
Made changes for compatibility with Generic Genome Browser 1.44
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::rndrect
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::ruler_arrow
Rename s/Ace::Graphics/Bio::Graphics/ where applicable
Made changes for compatibility with Generic Genome Browser 1.44
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::segmented_keyglyph
Made changes for compatibility with Generic Genome Browser 1.44
Added spliced cds and 3-frame translation glyphs
Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::segments
Added 6-frame translation and cds glyphs
Added spliced cds and 3-frame translation glyphs
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::span
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::toomany
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::track
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::transcript
Made changes for compatibility with Generic Genome Browser 1.44
Added spliced cds and 3-frame translation glyphs
Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::transcript2
Made changes for compatibility with Generic Genome Browser 1.44
Added spliced cds and 3-frame translation glyphs
Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::translation
Updated Bio::Graphics::FeatureFile to allow glyph-specific settings in configuration files to be set programmatically. For example: [named genes] glyph = arrow fgcolor = blue height = sub { shift->source eq 'GenBank' ? 20 : 10 } The power of perl. You can't help loving it.
Added spliced cds and 3-frame translation glyphs
Fixed 3-frame translation glyph to accomodate 6-frame translation; improved the "what I wanted, not what I said" behavior of the mysql DBGFF adaptor
Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights
Added arrowheads for start codons to three-frame translation, and added settings to change colors and heights
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::triangle
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Glyph::wormbase_transcript
Removed wormbase_transcript.pm glyph; this is properly part of gbrowse
Bio::Graphics::Panel
Added the much-requested color_name_to_rgb() method
Added the much-requested color_name_to_rgb() method
Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.
Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.
Added 6-frame translation and cds glyphs
Added spliced cds and 3-frame translation glyphs
Complete documentation of all glyphs
Complete documentation of all glyphs
Bio::Graphics::Util
Updated Bio::Graphics::FeatureFile to allow glyph-specific settings in configuration files to be set programmatically. For example: [named genes] glyph = arrow fgcolor = blue height = sub { shift->source eq 'GenBank' ? 20 : 10 } The power of perl. You can't help loving it.
Added spliced cds and 3-frame translation glyphs
Bio::Index::Blast
For best results "use strict"
Bio::Index::EMBL
For best results "use strict"
Bio::Index::Fasta
For best results "use strict"
Bio::Index::Fastq
For best results "use strict"
Bio::Index::GenBank
For best results "use strict"
Bio::Index::SwissPfam
For best results "use strict"
Bio::Index::Swissprot
For best results "use strict"
Bio::LocatableSeq
Refactoring Locations so that 22^23 is valid for Bio::Location::Simple. Fuzzy throws an error if given this location.
Updated to full name of parameter as required
Bio::Location::Atomic
This is the old Simple.pm
Added each_Location() to Location/Atomic.pm and removed it from Simple.pm (it inherits from Atomic). This also fixes Fuzzy.pm since that one also inherits from Atomic.
Bio::Location::Fuzzy
Changed 'loc_type' into 'location_type' everywhere
Changed 'loc_type' into 'location_type' everywhere
Refactoring Locations so that 22^23 is valid for Bio::Location::Simple. Fuzzy throws an error if given this location.
Doc fix and update
Make sure SEQ_ID method exists for fuzzy
Undo braindead duplicate parameter parsing -- read the inheritance first jason!
Bio::Location::Simple
Doc fixes. cleaner default value setting for strand()
Doc fixes. cleaner default value setting for strand()
Allowed setting seq_id() in the contructor
Enabled setting seq_id in the constructor
Refactoring Locations so that 22^23 is valid for Bio::Location::Simple. Fuzzy throws an error if given this location.
Fixed setting location_type('\^')
Removed a debugging statement
Fixed location_type() when given '^' as an argument
Addition of method each_Location(), which will return an array of locations for either a Simple or Split locations. Called on Simple, it will just return itself in a one-element array. Called on Split, will return an array with all sub_Locations (recursively checked).
Added each_Location() to Location/Atomic.pm and removed it from Simple.pm (it inherits from Atomic). This also fixes Fuzzy.pm since that one also inherits from Atomic.
Bio::Location::Split
Allowed setting seq_id() in the contructor
Enabled setting seq_id in the constructor
Refactoring Locations so that 22^23 is valid for Bio::Location::Simple. Fuzzy throws an error if given this location.
Addition of method each_Location(), which will return an array of locations for either a Simple or Split locations. Called on Simple, it will just return itself in a one-element array. Called on Split, will return an array with all sub_Locations (recursively checked).
Doc fix and update
Cleanup params
Bio::LocationI
Addition of method each_Location(), which will return an array of locations for either a Simple or Split locations. Called on Simple, it will just return itself in a one-element array. Called on Split, will return an array with all sub_Locations (recursively checked).
Bio::PrimarySeq
Issue #1211
Report the offending characters in the throw string
Bio::Range
Minor doc format fixes
Minor doc format fixes
Bio::Root::Err
Fixed name
Bio::Root::Exception
Migrating fix 1.14 to branch-1-0-0
Bio::Root::IO
Made tempfile() respect an (UNLINK => 0) parameter
UNLINK now behaves properly and is tested
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Moved flush trait up to Root::IO
Bio::Root::Root
Modifications to throw() - Better test for key-value pairs and passing original @args through if not. Bio::Root::Exception can deal with raw args now. - Added leading newline to the output string to ensure that the output doesn't start on a partial line.
Migrated changes into branch-1-0-0 from the trunk version 1.12.
Fixed %args in scalar context bug
Fixed my %args || @args fix
Bio::Root::RootI
Modifications to _rearrange(): Added the mod test to ensure we have key-value pairs. Fixes bug where a single string parameter beginning with '-' gets lost. This tends to happen in error messages such as: $obj->throw("-id not defined") Modifications to throw() and warn(): Added leading newline to the output string to ensure that the output doesn't start on a partial line.
Migrated changes in 1.47.2.5 and 1.47.2.4 to the trunk (BIOPERLDEBUG stuff)
Migrated changes from trunk version 1.50
Bio::Search::HSP::BlastHSP
New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects
Bio::Search::HSP::GenericHSP
New method seq_inds as part of migration from BlastHSP to GenericHSP, will also perform properly on FASTA HSPs by trimming the context sequence first
POX fixes
Strip '\' and '/' splicing indicator and remove contextual sequence before building an Align::AlignI object with get_aln
Handle empty sequence names when preping for get_aln
Changes to calculate alignment and HSP trimming better
Trim out the splice chars from fasta HSPs - but trunc both query and sbjct sequence
New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects
Better fasta parsing merged from main trunk
Yet another fix for gawd-awful parsing of FastA
Merged FastA changes from trunk to branch, <whew> think it is right now
Strand and length are now properly matched up to the 'hit'/'subject', 'query', 'total'/'hsp' values through hsp->strand('query') or hsp->length('hit')
Small changes to improve generic nature of these objects
Supidity abounds! left off the lefthand side in eq comparison, wonder why it always true
Bio::Search::HSP::HMMERHSP
New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects
POX fixes
Bio::Search::HSP::HSPFactory
New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects
Bio::Search::HSP::HSPI
New method seq_inds as part of migration from BlastHSP to GenericHSP, will also perform properly on FASTA HSPs by trimming the context sequence first
Override strand method to delegate to query or hit/subject
Override start/end to work with named start/end components params, added tests for these
Small changes to improve generic nature of these objects
Bio::Search::HSP::WABAHSP
Parse waba output as an alignment
Bio::Search::Hit::GenericHit
Iteration supported as a data field
New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects
POX fixes
Bio::Search::Hit::HMMERHit
New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects
POX fixes
Bio::Search::Hit::HitFactory
New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects
Bio::Search::Hit::HitI
Teeny addition to the SYNOPSIS
Small changes to improve generic nature of these objects
Bio::Search::Result::GenericResult
Result can store the lit reference for the algorithm
Bio::Search::Result::HMMERResult
New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects
POX fixes
Bio::Search::Result::ResultFactory
New factories to create the various needed objects like Result,Hit, HSP in a dynamic fashion - for SearchIO plug-and-play of objects
Bio::Search::Result::WABAResult
Parse waba output as an alignment
Bio::SearchIO::EventHandlerI
Plug in new Result/Hit/HSP factory interface
Bio::SearchIO::SearchResultEventBuilder
Query,name,accession split into separate fields properly
Use object specific tags for the fields so we can strip them out in the event-builder without having to know what the arguments to the object are - this simplifies the event builder
Plug in new Result/Hit/HSP factory interface
Take either specified algorithm_name or the requested type
Bio::SearchIO::Writer::HTMLResultWriter
Fix bugs exposed by double checking
Use object specific tags for the fields so we can strip them out in the event-builder without having to know what the arguments to the object are - this simplifies the event builder
Bio::SearchIO::Writer::TextResultWriter
Dump a text BLAST format report out from a SearchIO object
Use object specific tags for the fields so we can strip them out in the event-builder without having to know what the arguments to the object are - this simplifies the event builder
Bio::SearchIO::blast
Use object specific tags for the fields so we can strip them out in the event-builder without having to know what the arguments to the object are - this simplifies the event builder
Plugin auto-writer
Modified start_element() to prevent lots of uninitialized warnings when type isn't defined.
Bio::SearchIO::blastxml
Query,name,accession split into separate fields properly
Use object specific tags for the fields so we can strip them out in the event-builder without having to know what the arguments to the object are - this simplifies the event builder
Bio::SearchIO::fasta
More intelligently handle FASTA 'context' sequence
Use object specific tags for the fields so we can strip them out in the event-builder without having to know what the arguments to the object are - this simplifies the event builder
More robust FastA parsing -- toaddress bug illustrated by Robin Emig
Changes to better parse fasta (merged from trunk)
Better fasta parsing merged from main trunk
Default ID size is actually 6 -- and allow it to be automagically adjusted (not-well-tested)
Yet another fix for gawd-awful parsing of FastA
Merged FastA changes from trunk to branch, <whew> think it is right now
Handle another stupid case
Handle another stupid case
Another bug thanks to Robin Emig's excellent testsuite of FASTA reports
Another bug thanks to Robin Emig's excellent testsuite of FASTA reports
Bio::SearchIO::hmmer
Parse HMMER reports with SearchIO
POX fixes
Bio::SearchIO::psiblast
Add doc for write_result
Bio::SearchIO::waba
Parse waba output as an alignment
Bio::Seq
Expanded doc, more methods are documented now with lovely L<> links
Bio::Seq::SeqFactory
Move to more general factory type
Bio::SeqFeature::Collection
Fixed boundary bug that was exposed on MacOS X, us for loop instead of while to insure initial key value is retrieved. Fun with BDB and DB_File interface
Properly set the tmpname- was getting the filehandle there previously
Added feature_count method to return number of features contained in the collection
Bio::SeqFeature::Computation
Warning when initializing strangely
Bio::SeqFeature::Gene::Transcript
Add_utr and add_exon now return true which makes tests possible
Bio::SeqFeature::SimilarityPair
Undo deprecation of subject() in similarityPair - both hit and subject will work
Bio::SeqI
Expanded doc, more methods are documented now with lovely L<> links
Fix stupid copy+paste error
Bio::SeqIO
Added fastq to valid formats
Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)
Preload staden::read (via eval, so safe if not installed) - not entirely happy about having to do this, but load_format() for the staden::read-using formats doesn't seem to do the trick
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Moved flush trait up to Root::IO
Bio::SeqIO::FTHelper
Refactoring Locations so that 22^23 is valid for Bio::Location::Simple. Fuzzy throws an error if given this location.
Named parameter needs to change from seqid to seq_id
Used named parameter location_type instead of old shorthand loc_type
Bio::SeqIO::abi
Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)
Fixed a few warning-bugs
Made new formats not throw on loading, but usage (allowing future pure Perl methods to work)
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::ace
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::alf
Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)
Fixed a few warning-bugs
Made new formats not throw on loading, but usage (allowing future pure Perl methods to work)
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::bsml
Bsml module calling a bunch of methods that are not part of primarySeqI or SeqI, so I put an eval{} around them. Also changed molecule() call to alphabet(); this module is still producing a major number of "odd numbered elements in hash assignment" warnings; could someone put it out of its misery?
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::ctf
Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)
Fixed a few warning-bugs
Made new formats not throw on loading, but usage (allowing future pure Perl methods to work)
Messed up the SeqFactory settings - reset
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::embl
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::exp
Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)
Fixed a few warning-bugs
Made new formats not throw on loading, but usage (allowing future pure Perl methods to work)
Messed up the SeqFactory settings - reset
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::fasta
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::fastq
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::game
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::game::seqHandler
The method 'create' now since we are dealing with a more generalized factory
Bio::SeqIO::gcg
Removed upper-casing of sequence.
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::genbank
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::largefasta
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::phd
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::pir
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::pln
Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)
Fixed a few warning-bugs
Made new formats not throw on loading, but usage (allowing future pure Perl methods to work)
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::qual
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::raw
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::scf
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::swiss
The method 'create' now since we are dealing with a more generalized factory
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SeqIO::ztr
Added new SeqIO formats supported by the Staden io_lib read library, available in bioperl_ext; Pure perl versions left as an exercize for the reader ;)
Fixed a few warning-bugs
Made new formats not throw on loading, but usage (allowing future pure Perl methods to work)
Messed up the SeqFactory settings - reset
Added -flush option to SeqIO constructor; defaults to 1, 'flush on write'; SeqIO/*.pm modules updated to conform
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::SimpleAlign
Handle missing ids a bit more gracefully
Bio::Tools::Blast
Doc fix
Bio::Tools::Eponine
wrapper for Eponine - a mammalian TSS predictor(written by Thomas Down - Sanger)
parser for Eponine..updated description. (wrapper on it's way)
Bio::Tools::HMMER::Results
Remove debugging
Bio::Tools::HMMER::Set
Insure that each added domain is unique
Insure that each added domain is unique
Bio::Tools::Phylo::PAML
Added ISA for AnalysisResultI
Initial parsing setup; everything should work (but return empty objects)
Fixed bug with io not being initialized
Get the ISA correct
Bio::Tools::Phylo::PAML::Codeml
Bare bones object for Aaron and Jason to expand
Proposed usage documented in the SYNOPSIS - open for discussion, of course
PAML parser and result objects
Bio::Tools::Phylo::PAML::Result
PAML parser and result objects
Initial parsing setup; everything should work (but return empty objects)
Fixed bug with io not being initialized
Bio::Tools::Run::EMBOSSApplication
Added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero
Removed Run wrappers -- they are in bioperl-run repository
Bio::Tools::Run::EMBOSSacd
Added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero
Removed Run wrappers -- they are in bioperl-run repository
Bio::Tools::Run::Genscan
Wrapper for Genscan executable
POX fixes
Removed Genscan from main - moved to bioperl-run
Bio::Tools::Run::PiseApplication
Removed Run wrappers -- they are in bioperl-run repository
Bio::Tools::Run::PiseJob
Removed Run wrappers -- they are in bioperl-run repository
Bio::Tools::Run::PiseJobParser
Removed Run wrappers -- they are in bioperl-run repository
Bio::Tools::Run::Pseudowise
Removed Run wrappers -- they are in bioperl-run repository
Bio::Tools::Run::RemoteBlast
Removed Run wrappers -- they are in bioperl-run repository
Bio::Tools::Run::RepeatMasker
Use the determined path to RP when attempting to find the version
Doc fix
POX fixes
Removed Run wrappers -- they are in bioperl-run repository
Bio::Tools::Run::StandAloneBlast
Removed Run wrappers -- they are in bioperl-run repository
Bio::Tools::Run::TribeMCL
Wrapper for tribemcl program for protein family clustering using markov flow simulation based on blast scores
Modified the way input is fed.
Removed Run wrappers -- they are in bioperl-run repository
Bio::Tools::SeqAnal
Doc fix
Bio::Tools::SeqPattern
Doc fix
Http://bioperl.org/Core/Examples no longer exists
Bio::Tools::Sigcleave
Doc fix
Bio::Tools::WWW
Doc fix
Bio::Tools::pSW
Noted protein-only. Removed IN_DEVELOPMENT comment
Bio::Tree::Node
Changes to fix problems described by Howard Ross including reading/writing newick format without branch lengths and storing nodes in proper read-in order (for clarity).
Eliminate stupid double-recursion when getting nodes in-order based on height in tree, this fixes Issue #1218 reported by Howard Ross
Eliminate stupid double-recursion when getting nodes in-order based on height in tree, this fixes Issue #1218 reported by Howard Ross
Bio::Tree::NodeI
Changes to fix problems described by Howard Ross including reading/writing newick format without branch lengths and storing nodes in proper read-in order (for clarity).
Eliminate stupid double-recursion when getting nodes in-order based on height in tree, this fixes Issue #1218 reported by Howard Ross
Eliminate stupid double-recursion when getting nodes in-order based on height in tree, this fixes Issue #1218 reported by Howard Ross
Bio::Tree::Tree
Changes to fix problems described by Howard Ross including reading/writing newick format without branch lengths and storing nodes in proper read-in order (for clarity).
Bio::TreeIO
Verbosity persists with the event based tree builder too
Bio::TreeIO::TreeEventBuilder
Changes to fix problems described by Howard Ross including reading/writing newick format without branch lengths and storing nodes in proper read-in order (for clarity).
Bio::TreeIO::newick
Changes to fix problems described by Howard Ross including reading/writing newick format without branch lengths and storing nodes in proper read-in order (for clarity).
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::TreeIO::tabtree
New output only module for displaying a tree as an ASCII drawing
POX fixes
Set autoflush to only be called if a valid fh existed too, moved the _flush_on_write up to the Root::IO object and utilized it in AlignIO and TreeIO
Bio::Variation::SNP
Adding a functional but incomplete dbSNP xml parser. needs docs!
Forgot to SNP to inherit from Allele, cleaned up test file, added more tests.
More docs
Bio::Variation::VariantI
Doc fix
Doc fix
FAQ
Generated FAQ update with new questions baout features and annotations
Added mention of NP_
Makefile.PL
Added BioGraphics dependency to Text::Shellwords
Added DIR option to WriteMakefile for future need
bioperl.pod
Added mention of BioPerlBlast.pl
Added mention of dbsnp.pl and feature_draw.pl
bptutorial.pl
Note on -readmethod and RemoteBlast
Revcom->trunc() becomes trunc()->revcom
Georg's suggestions
Added mention of HMMER parsing by SearchIO
Added phylip to AlignIO's I/O list
Updated supported AlignIO formats, updated EMBOSS sections, minor stuff...
For best results "use strict" with Bio::Index
examples/BioPerlBlast.pl
Script from Simon Chan
scripts/bpindex.pl
Uncomment "use strict", script works
scripts/feature_draw.pl
Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.
Added regression tests and more documentation for Bio::Graphics. Also made the Bio::Graphics::Panel::bump method more flexible by allowing EnsEMBL-style simple bumping.
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