Core 0.6.2 0.7.0 delta

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These are detailed notes on changes made between release-06-2 and release-0-7-0.

Bio::AlignIO
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
RootI compliance and some documentation reformatting
Quoted unquoted string literals used as hash keys.
Changed to new RootI chained new structure
Cleanup to support 5.00404
Corrected error in documentation (SYNOPSIS)
Bio::AlignIO::bl2seq
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
RootI compliance
Quoted unquoted string literals used as hash keys.
Changed to new RootI chained new structure
Cleanup to support 5.00404
BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes
Bio::AlignIO::clustalw
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
RootI compliance
Changed to new RootI chained new structure
Fixed clustalw alignIO module to honor input file order
Bio::AlignIO::fasta
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
RootI compliance
Changed to new RootI chained new structure
Bio::AlignIO::mase
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
RootI compliance
Changed to new RootI chained new structure
Bio::AlignIO::msf
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
RootI compliance
Changed to new RootI chained new structure
Changed code needing a checksum to use SeqIO::gcg->GCG_checksum().
Bio::AlignIO::pfam
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
RootI compliance
Changed to new RootI chained new structure
Bio::AlignIO::prodom
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
RootI compliance
Changed to new RootI chained new structure
Bio::AlignIO::selex
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
RootI compliance
Changed to new RootI chained new structure
Bio::AlignIO::stockholm
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
RootI compliance
Changed to new RootI chained new structure
Cleanup to support 5.00404
Bio::Annotation
Got annotation objects up to 0.7 spec. Made tests more robust to non present modules
Changed to new RootI chained new structure
Corrected syntax error in documentation (SYNOPSIS)
Corrected documentation (SYNOPSIS) Bio::Pfam::Annotation -> Bio::Annotation
Added add/remove/each_gene_name(). Made gene_name() deprecated.
Bio::Annotation::Comment
Got annotation objects up to 0.7 spec. Made tests more robust to non present modules
Changed to new RootI chained new structure
Bio::Annotation::DBLink
Got annotation objects up to 0.7 spec. Made tests more robust to non present modules
Changed to new RootI chained new structure
Bio::Annotation::Reference
Got annotation objects up to 0.7 spec. Made tests more robust to non present modules
Changed to new RootI chained new structure
Bio::DB::Ace
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Bio::DB::GDB
Changed to new RootI chained new structure
Length set properly and include HTML::Parser explictly
Length is really in kilobases
Removed reference to bioperl-guts-l list.
Documentation cruft fix
Fail gracefully on no network connection
Bio::DB::GenBank
Migrated to use LWP
Some bulletproofing
Added a swissprot lookup via web expasy can be customized to be used on a local expasy
Changed IO::String creation to OO style. Would not work otherwise.
Even though we are going to revamp this module, missing a 'use IO::String' causes it to fail
Centralized common code in Bio::DB::WebDBSeqI and Bio::DB::NCBIHandler This reorganized Bio::DB::GenPept and Bio::DB::GenBank to use a centralized module and LWP
Fixed the documentation of several methods.
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Bio::DB::GenPept
Added a swissprot lookup via web expasy can be customized to be used on a local expasy
Centralized common code in Bio::DB::WebDBSeqI and Bio::DB::NCBIHandler This reorganized Bio::DB::GenPept and Bio::DB::GenBank to use a centralized module and LWP
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Bio::DB::NCBIHelper
Added Bio::DB::NCBIHelper to centralize code for communicating with NCBI web sequence databases
Fixed request_method() not to ignore a value it doesn't find in the table of predefined formats. Fixed documentation of this method.
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Bio::DB::SRS
Added experimental SRS module for sequence retrieving
Hilmar told me to delete this
Bio::DB::SwissProt
Added a swissprot lookup via web expasy can be customized to be used on a local expasy
Did not need Batch request for swissprot
Corrected include stmt
Changed IO::String creation to OO style. Would not work otherwise.
Updated to use Bio::DB::WebDBSeqI interface
Quoted unquoted string literals used as hash keys.
Suppressed one-at-a-time warning for array refs if array has only one element.
Changed to new RootI chained new structure
Bio::DB::WebDBSeqI
Removed TEMPDIR in DESTROY
Quoted unquoted string literals used as hash keys.
Fixed get_Seq_XXX() methods to delegate to get_Stream_XXX() methods. Fixed a bug in a get_Stream_XXX() method (-mode not specified). Fixed documentation of request_method().
Changed to new RootI chained new structure
Removed File::Spec dependancy, tempfile creation is handled in Bio::Root::RootI now
Changed to adopt Bio::Root::IO.
Bio::DBLinkContainerI
RootI compliance and some documentation reformatting
Removed reference to bioperl-guts-l list.
Bio::Factory::DriverFactory
Initial revision.
Added driver_table() and more documentation.
Fixed _load_module() to construct the module's pathname platform independently (hopefully).
Use Root::IO to do catfile in file loading methods rather than File::Spec of DriverFactory
Bio::Factory::SeqAnalysisParserFactory
Initial revision.
Added hmmer and blast (bplite as a synonym) to supported methods.
Added GFF and Sim4.
Bio::Factory::SeqAnalysisParserFactoryI
Initial revision.
Added documentation. Corrected documentation bugs.
Bio::Index::Abstract
RootI compliance and some documentation reformatting
Changed to new RootI chained new structure
Accidentially removed use DB_File, caused a bug also removed routine verbose as this is handled by upstream Bio::Root::RootI behaviour is to print msgs to STDERR when verbose > 0
Bug #860 fixed Index now supports dynamic including of dbm_package
Removed reference to bioperl-guts-l list.
Update to RootI
Updated to work with File::Spec from perl 5.00503 which does not have cwd or rel2abs
Fixed new location of FILESPECLOADED.
Bio::Index::AbstractSeq
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Update to RootI
Bio::Index::EMBL
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Bio::Index::Fasta
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Bio::Index::GenBank
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Bio::Index::SwissPfam
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
†corrected documentation error (SYNOPSIS)
Bio::Index::Swissprot
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Fixed bug #874. (Needed also code to reset @acc and $id.)
Bio::LiveSeq::AARange
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Fixed LiveSeq for 5.0004 compatbility
Quoted unquoted string literals used as hash keys.
Bio::LiveSeq::Analyser
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Bio::LiveSeq::Chain
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Slight modifications done when creating the tests.
Fixed LiveSeq for 5.0004 compatbility
Quoted unquoted string literals used as hash keys.
->label_exists gave a warning as a side effect when label did not exist
Bio::LiveSeq::ChainI
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
Bio::LiveSeq::DNA
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Quoted unquoted string literals used as hash keys.
Bio::LiveSeq::Exon
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Quoted unquoted string literals used as hash keys.
Bio::LiveSeq::Gene
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Fixed LiveSeq for 5.0004 compatbility
Quoted unquoted string literals used as hash keys.
Method delete_Obj added to all LiveSeq objects. Since they contain circular references, memory was not freed properly after losing the $gene (top level) reference. Thanks to Arne for help on this.
Fixed small Issue #1215 /Bio/LiveSeq/Gene.pm: lines 380, 385, 393
All tests pass on 5.0004 except GDB.t! Hurray!
Bio::LiveSeq::IO::BioPerl
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Fixed LiveSeq for 5.0004 compatbility
Quoted unquoted string literals used as hash keys.
Changed EMBL-feature loading code to use the new SplitLocation
Fixed call of deprecated each_secondary_accessions().
$featlocation->isa('Bio::Location::FuzzyLocationI') code added. Tests pass again.
LocationI and Coordinate Polisy now in place, I could remove the code added to take FuzzyLocations into account. In effect reverted to version 1.7.
Bio::LiveSeq::IO::Loader
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
Restructured Mutator.pm. Added Mutation.pm to hold mutation information. Tests for both. Example script.
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Slight modifications done when creating the tests.
No more warnings. $exoncount and $introncount array index variables were not initialized to 0 before using.
Quoted unquoted string literals used as hash keys.
Default to 0 if element is undef in 'rangeofarray'
Added 'use Bio::Tools::CodonTable'. This wasn't expected to and indeed doesn't fix the errors triggered in t/LiveSeq.t.
Bio::LiveSeq::IO::SRS
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Quoted unquoted string literals used as hash keys.
Bio::LiveSeq::Intron
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Bio::LiveSeq::Mutation
Restructured Mutator.pm. Added Mutation.pm to hold mutation information. Tests for both. Example script.
Corrected a minor bug that denied mutation inputs with length==0
Bio::LiveSeq::Mutator
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
Restructured Mutator.pm. Added Mutation.pm to hold mutation information. Tests for both. Example script.
Moved the pre CVS history away from the module: # Version history: # Thu Apr 13 18:09:55 BST 2000 v 1.0 begun # Thu Apr 13 19:15:28 BST 2000 v 1.1 first tentative version, to be tested # Fri Apr 14 03:13:18 BST 2000 v 1.2 deIssue #2000 v.2.75 complete rewrite into a class
Fixed some errors that were causing messages in make test
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Quoted unquoted string literals used as hash keys.
Coded the workaround to understand if rna is affected in the case where some new labels have been inserted (requiring the use of the method follow() instead than the faster but errorprone use of < and >). Introduced an "RNApostlabel" to fix the problems of "end of exon" mutations when retrieveing the RNAdownstreamsequences.
Bio::LiveSeq::Prim_Transcript
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Bio::LiveSeq::Range
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Bio::LiveSeq::Repeat_Region
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Bio::LiveSeq::Repeat_Unit
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Bio::LiveSeq::SeqI
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
Fixed some errors that were causing messages in make test
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Fixed LiveSeq for 5.0004 compatbility
Quoted unquoted string literals used as hash keys.
Method delete_Obj added to all LiveSeq objects. Since they contain circular references, memory was not freed properly after losing the $gene (top level) reference. Thanks to Arne for help on this.
Fixed small Issue #1215 /Bio/LiveSeq/Gene.pm: lines 380, 385, 393
Removed DOS LFs
Bio::LiveSeq::Transcript
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
Fixed some errors that were causing messages in make test
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Slight modifications done when creating the tests.
Fixed some more warnings.
Fixed LiveSeq for 5.0004 compatbility
Quoted unquoted string literals used as hash keys.
Fixed doc format bug.
Bio::LiveSeq::Translation
1st commitment of LiveSeq modules inside BioPerl - 11 Dec 00 LiveSeq works with BioPerl 0.6.2 or SRS 6.0.6 (the modules in the IO subdirectory take care of the input sequences exploting these two packages). Test files and application programs will be added. This is LiveSeq 1.0b - by Joseph A.L. Insana
- slight cleaning of the code to keep -w happy Jason commited his fixes quicker! - removed a few prime characters to keep emacs fontifier happy - added 1; into module ends.
Quoted unquoted string literals used as hash keys.
Bio::LocatableSeq
RootI compliance and some documentation reformatting
Moved PrimarySeq and Seq to RootI style news. Fixed the knock on effects. LargeSeq/LargeFasta fail - cant fix them
Bio::Location::AvWithinCoordPolicy
Initial revision.
Bio::Location::CoordinatePolicyI
Initial revision.
Documentation update (more precide about return type).
Bio::Location::Fuzzy
Split, Fuzzy Location
Separate method for range fuzziness (not just start/end fuzziness)
Current solution to Fuzziness, still needs to be worked on to handle more cases
Complete fuzzy feature cycle of in fuzzy feature -> out fuzzy feature via SeqIO::genbank works
Handle SNP variations more properly and better SplitLocation handling -- handle 'order' and 'join'
More robustness for Location handling -- especially better handling of Fuzziness
Correct location behavior to return min_start == max_start when start is defined SplitLocation->start will return the value of the 1st (sorted) contained location Location.t was updated to test for this as well
Start/end default to '0' when start/end are fuzzy -- this is instead of undef
Corrected to handle Location start/end as '0' when point is fuzzy
Changed _fuzzyencode to _fuzzydecode. Made sure this returns proper type/min/max, setting the right end possibly to undef. Adapted hash of patterns accordingly. Changed way of storing/setting coordinates, is now fully overridable. Works with coord policy.
Fixed missing check for reverse strand feature location string should include complement and fixed Fuzzy::to_FTstring to properly return fuzzified location string
More fixes to Fuzzy location string generation and extra tests to help
Location output strings corrected for fuzzy
Corrected documentation
Bio::Location::FuzzyLocationI
Moved to Location object
Added some documentation to the interfaces
Split, Fuzzy Location
Separate method for range fuzziness (not just start/end fuzziness)
Current solution to Fuzziness, still needs to be worked on to handle more cases
Complete fuzzy feature cycle of in fuzzy feature -> out fuzzy feature via SeqIO::genbank works
Handle SNP variations more properly and better SplitLocation handling -- handle 'order' and 'join'
Corrected documentation for _fuzzypointencode() and _fuzzyrangeencode().
More robustness for Location handling -- especially better handling of Fuzziness
Corrected a doc bug.
Corrected documentation
Bio::Location::NarrowestCoordPolicy
Initial revision.
Corrected doc bug.
Removed 'use Bio::LocationI': not needed and may cause a loop (due to the BEGIN block in Bio::LocationI).
Bio::Location::Simple
Moved to Location object
Added some documentation to the interfaces
Current solution to Fuzziness, still needs to be worked on to handle more cases
More robustness for Location handling -- especially better handling of Fuzziness
Revised way of storing the coordinates. min/max now don't call start/end. Improved documentation.
Fixed missing check for reverse strand feature location string should include complement and fixed Fuzzy::to_FTstring to properly return fuzzified location string
Bio::Location::Split
Split, Fuzzy Location
Max_end/min_start added
Handle SNP variations more properly and better SplitLocation handling -- handle 'order' and 'join'
More robustness for Location handling -- especially better handling of Fuzziness
Correct location behavior to return min_start == max_start when start is defined SplitLocation->start will return the value of the 1st (sorted) contained location Location.t was updated to test for this as well
DB.t now skips tests correctly
Corrected to handle Location start/end as '0' when point is fuzzy
Added implementation of is_single_sequence(). Revised several methods to work with coord policy. Revised sorting in sub_Location() (now also deals with sublocs on more than one seq). Added documentation.
Fixed missing check for reverse strand feature location string should include complement and fixed Fuzzy::to_FTstring to properly return fuzzified location string
Corrected documentation
Bio::Location::SplitLocationI
Moved to Location object
Added some documentation to the interfaces
Split, Fuzzy Location
Max_end/min_start added
Handle SNP variations more properly and better SplitLocation handling -- handle 'order' and 'join'
More robustness for Location handling -- especially better handling of Fuzziness
Removed method that forced SplitLocationI implementations to be mutable
Added is_single_sequence().
Corrected documentation
Bio::Location::WidestCoordPolicy
Initial revision.
Removed 'use Bio::LocationI': not needed and causes a loop (due to the BEGIN block in Bio::LocationI).
Bio::LocationI
Moved to Location object
Added some documentation to the interfaces
Seq_id method added
More robustness for Location handling -- especially better handling of Fuzziness
Added coordinate_policy().
Corrected documentation
Bio::PrimarySeq
Added id() method (copy from Seq.pm)
Removed debugging cruft
Safer length call
Fixed regex bug in _guess_type
Moved PrimarySeq and Seq to RootI style news. Fixed the knock on effects. LargeSeq/LargeFasta fail - cant fix them
Doc bug
Changed to new RootI chained new structure
Added capability of initializing to an empty sequence.
Changed hash access to method seq() call in substr(), length(), and _guess_type().
Moved initialization stuff to the top for better maintenance.
Bio::PrimarySeqI
Interface should define desc - even as abstract
Added PrimarySeqI->translate fixes from Alex Bateman that speed up translating 2x. Unambiguous two character codons at the end of the sequence [like 'AC' (ACN > T) and 'GT' (GTN > V)] did not translate to an amino acid when PrimarySeqI->translated! Fixed that. Added tests.
The last option to translate (throw or warn when errors in fullCDS translating) was implemented wrong way round. Added testing for terminator codons inside CDS.
Removed documentation for deprecated methods. Reorganized ordering of methods to move private and deprecated ones to the end. Changed way of object creation in trunc(), translate(), and revcom().
Reverted to choosing class of sequence to be instantiated in trunc/revcom/translate, based on can_call_new().
Removed GCG_checksum() (now in SeqIO::gcg).
Bio::Range
Corrected documentation (-end instead of -stop) and fixed _new() to allow also 0 as coordinate.
RootI compliance and some documentation reformatting
Quoted unquoted string literals used as hash keys.
Changed to new RootI chained new structure
Clean up of Bio::Range and Bio::RangeI. Attributes can now be set one by one in Bio::Range. Doc fixes. Methods now check that attributes are set before doing operations. Important: Interface for methods 'union' and 'intersection' redifined. Both now return an object.
Bio::RangeI
Corrected documentation (-end instead of -stop).
RootI compliance and some documentation reformatting
Corrected copy-paste errors in documentation. Added documentation for strand option.
Slightly safer check to be sure it is a range object in contains()
Clean up of Bio::Range and Bio::RangeI. Attributes can now be set one by one in Bio::Range. Doc fixes. Methods now check that attributes are set before doing operations. Important: Interface for methods 'union' and 'intersection' redifined. Both now return an object.
Bio::Root::Err
Bugs 855 857 863
This test will only work from bioperl-live/
Removed reference to bioperl-guts-l list.
Fixing :std bug again
Bio::Root::IO
Initial revision.
A couple of fixes. Added $FILESPECLOADED (redundant to !$PATHSEP, though). Added recognition of -input.
Changed to be literal string rather than doubled quote to prevent interpretation of \T in C:\TEMP
Tests to verify tempfiles are being removed
Removed some debugging cruft and theoretically added protection for case when File::Spec is installed but tempdir is not included (perl 5.004)
Too many ')'
Test to see that 'can' call 'tempfile' even when File::Temp is loaded
Correct 'can' syntax to make 5.005 happy. Sigh
Added automatic registration of _io_cleanup(). Added _io_cleanup(), which simply delegates to DESTROY.
For unkown reasons the loop to DESTROY ended up in recursion, even though I thought I prevented this. Moved functionality to _io_cleanup(), removed DESTROY.
Bio::Root::IOManager
Removed reference to bioperl-guts-l list.
Bio::Root::Object
Removed reference to bioperl-guts-l list.
Added note about deprecation to documentation. Added warning to _initialize().
Bio::Root::RootI
Fix in Bio::Root::RootI::_rearrange
Beginning the migration to RootI only
Got annotation objects up to 0.7 spec. Made tests more robust to non present modules
RootI new changed to check if caller is a reference or a class
Added correction for storing verbose value A more correct solution to all the (verbose,strict) needs to be implemented in the new RootI code
Tempfile and tempdir capability added
Removed debugging code
Always remove tmp files even if created by File::Temp
Better tempfile/tempdir handling
Quoted unquoted string literals used as hash keys.
Refactored RootI to handle chained new instead of chained _initialize left an empty _initialize for backwards compatibility verbose, strict, should work now
Fixed doc format bug.
Refactored (heavily) RootI. Alot of code removal. I think it is short and sweet now
Test LargeSeq, added better inheritance model
Lost comma, uncessary use
Cleanup to support 5.00404
Changed verbose() to resort to default $VERBOSITY if called as a class method. The consequence is that warn() and throw() are now callable as class methods (which is convenient, isn't it).
Moved tempfile() etc to Bio::Root::IO. Also moved loading attempts of File::Spec and friends.
Added a toplevel (empty) DESTROY so that all objects have a DESTROY method (was causing IUPAC tUPAC, which uses AUTOLOAD, to complain)
Properly removing tempfiles
Added DESTROY and _register_for_cleanup().
Bio::Root::Utilities
Removed reference to bioperl-guts-l list.
Copied code from IOManager to ignore alarm() if it's not provided in the runtime system.
Changed inheritance to RootI. Changed date_format() to accept also a epoch time to be formatted. Changed file_date() to use stat instead of 'ls -gla'; the date will be taken from the mtime field.
Bio::Root::Vector
Removed reference to bioperl-guts-l list.
Corrected ambiguity due to Vector.pm's shift() sub
Bio::Root::Xref
Removed reference to bioperl-guts-l list.
Bio::Search::Hit::Fasta
Likely meaningless changes as we will probably chuck these modules
Removed premature and currently unmaintained modules.
Bio::Search::Hit::HitI
Removed premature and currently unmaintained modules.
Bio::Search::Processor
Likely meaningless changes as we will probably chuck these modules
Removed premature and currently unmaintained modules.
Bio::Search::Result::Fasta
Likely meaningless changes as we will probably chuck these modules
Removed premature and currently unmaintained modules.
Bio::Search::Result::ResultI
Likely meaningless changes as we will probably chuck these modules
Removed premature and currently unmaintained modules.
Bio::SearchDist
RootI compliance and some documentation reformatting
Migrate to chained new with new Bio::Root::RootI
Fixed RootI-transition related bugs. Fixed other bugs consisting of calling non-existent functions etc. Did this module ever work? The call to fit_EVD() still needs to be fixed, because the C-function expects one additional parameter.
Fix compile time error; now have a run-time error for SearchDist
Fixed searchdist stuff. Not a numerically sensible test, but ensures you can actually call the routines
Bio::Seq
Changed documentation for display_id() (get/set) Made id() a real synonym for display_id (get/set) Removed unused variable declarations in primary_id()
Commented out fetch_SeqFeature. Is not required by any interface, and is not implemented.
RootI compliance and some documentation reformatting
Moved PrimarySeq and Seq to RootI style news. Fixed the knock on effects. LargeSeq/LargeFasta fail - cant fix them
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Added documentation to {top,all}_SeqFeature() methods. Removed unnecessary code and documentation.
Added RichSeq implementation - converted genbank/embl/swiss to use this - all tests pass. LiveSeq calls some deprecated methods
Made SeqI interface broader to include some methods from Seq
Added an empty DESTROY method to keep the autoloader from IUPAC.pm happy -- I know this is stupid, but I caused tempfile cleanup problems adding a blank DESTROY to RootI.pm
Bio::Seq::LargePrimarySeq
SeqIO support for largge sequence files in fasta format
Corrected where I used same variable name twice
Added better fallbacks for temp dir and next_seq returns a SeqI compliant object
Updated to use File::Temp
Moved PrimarySeq and Seq to RootI style news. Fixed the knock on effects. LargeSeq/LargeFasta fail - cant fix them
Changed over to IO::File for wrapping tempfile handle
Use Bio::Root::RootI for tempfile creation
Unlink file on object destruction don't wait on program to exit (File::Temp's behavior)
Test LargeSeq, added better inheritance model
Changed to adopt Bio::Root::IO.
Switched filehandle from IO::File to GLOB.
Bio::Seq::LargeSeq
Added better fallbacks for temp dir and next_seq returns a SeqI compliant object
Moved PrimarySeq and Seq to RootI style news. Fixed the knock on effects. LargeSeq/LargeFasta fail - cant fix them
Test LargeSeq, added better inheritance model
Lost comma, uncessary use
Fixed mailing lists.
Bio::Seq::RichSeq
Added RichSeq implementation - converted genbank/embl/swiss to use this - all tests pass. LiveSeq calls some deprecated methods
Corrected mailing lists and removed documentation for deprecated methods.
Added documentation (return types) (still insufficient).
Added some documentation and implementation of pid().
Somebody forgot a semicolon in Bio::Seq::RichSeq, which was screwing up GenBank imports
Bio::Seq::RichSeqI
Rich seq interface - 1st attempt
Initial revision.
Completed RichSeqI interface
Added pid() and improved some documentation.
Added returning TRUE at the end of the module.
Bio::SeqAnalysisParserI
RootI compliance and some documentation reformatting
Removed method parse(). Added documentation. Added documentation about expected new() parameters.
Made sure user does not explictly call new on Bio::SeqAnalysisParserI
Bio::SeqFeature::Computation
Generic object for a computation
Changed to take advantage of OO inheritance
Make 1 error message go away
Fixed doc format bug.
Removed due to design changes pending (will be incompatible with the current).
Bio::SeqFeature::FeaturePair
Migrated to RootI compliance
Migrated to new RootI
Moved to Location object
Delegate location to feature1
Bio::SeqFeature::Gene::Exon
Initial revision.
Added is_coding().
Fixed bug in cds().
Improved documentation.
Bio::SeqFeature::Gene::ExonI
Initial revision.
Added is_coding().
Improved documentation.
Bio::SeqFeature::Gene::GeneStructure
Initial revision.
Fixed and improved documentation.
Added warning about experimental status to promoter methods.
Bio::SeqFeature::Gene::GeneStructureI
Initial revision.
Added method introns().
Added warning about experimental status to promoter methods.
Bio::SeqFeature::Gene::Transcript
Initial revision.
Fixed forgotten $self at several places. Added sorting of exon types to exons() if strand is unambiguous. Now passes t/Genpred.t.
Fixed and improved documentation. UTR objects must now also implement Bio::SeqFeature::Gene::ExonI. Changed _make_cds() to omit phase/frame correction at exon boundaries if the next exon doesn't have a valid frame.
Added warning about experimental status to promoter methods.
Bio::SeqFeature::Gene::TranscriptI
Initial revision.
Added warning about experimental status to promoter methods.
Bio::SeqFeature::GeneStructure
Fixed wrong spelling of promoter.
Migrated to RootI compliance
Migrated to new RootI
Obsoleted by Bio::SeqFeature::Gene::* interfaces and stuff.
Bio::SeqFeature::Generic
Corrected passing on arguments to base class in _initialize().
Added mailing lists and author.
Standardization of doc, code layout, and adding explict call to CORE::length over local length routine
Migrated to RootI compliance
Migrated to new RootI
Moved to Location object
The two _from_gff_string routines now handle frame of '.', and also fixed a bug in the import of the attributes field in _from_gff2_string where I originally mis-read the GFF2 docs and was requiring an '=' sign between the tag and the value, which is not correct for GFF2.
Changed location() to check its parameter for implementing Bio::LocationI.
Added documentation for seq method
Added method gff_format() for get/set of the GFF interpreter. Removed _from_gff2_string(). Rewrote _from_gff_string() to delegate to the GFF interpreter. Removed -gff2_string initialization parameter, this is now the default. Added -gff1_string, which automatically installs a GFF1-format interpreter.
Frame of undef means no frame information, using undef rather than '.', however method to reset the frame to 'undef' for an instantiated object
Allow frame to be '.'
Reset frame to undef when user specifies a '.'
Switched BPpl test to == from eq (I guess) for expectation value to deal with formatting changes in expectation 5.0004 <=> 5.6.0
Moved seq formatter to run-time static function rather than compile time loading (which was looped as well)
Fixed a doc bug.
Bio::SeqFeature::Similarity
Migrated to RootI compliance
Migrated to new RootI
Bio::SeqFeature::SimilarityPair
Corrected _initialize().
Migrated to RootI compliance
Migrated to new RootI
Moved to Location object
Bio::SeqFeatureI
Added new method gff2_string, which outputs the feature in GFF2 format as described on the Sanger website. Attribute fields are now semicolon delimited, tags may have more than one space delimited value, free text is quoted and newline and tab characters are translated into their textual equivalents. Please contact me if you find errors in this routine. Mark
RootI compliance and some documentation reformatting
Fix doc so code snippet works (missing comma)
SeqFeature supports location
The gff2_string dumping routine for Features now dumps the attributes in ACeDB tag value format, without an '=' sign between them. This corrects my mis-reading of the GFF2 specs a couple of months ago. sorry.
Added variable $GFF_FORMATTER, initialized to a Bio::Tools::GFF instance with -gff_version set to 2. Removed gff2_string(). Rewrote gff_string(), it now simply delegates to $GFF_FORMATTER.
Moved seq formatter to run-time static function rather than compile time loading (which was looped as well)
Removed left-over GFF_FORMATTER variable.
Bio::SeqFeatureProducer
Added simplified helper class for adding analysis results as features to sequence objects through the SeqAnalysisParserI interface Only MZEF and Genscan were added through the initialize method but GFF and GAME should be considered
Quoted unquoted string literals used as hash keys.
Migrate to chained new with new Bio::Root::RootI
Modules phased out. Functionality moved to Bio::Factory::*.
Bio::SeqFeatureProducerI
Modules phased out. Functionality moved to Bio::Factory::*.
Bio::SeqI
Made SeqI interface broader to include some methods from Seq
Bio::SeqIO
Removed RootI dependence
Quoted unquoted string literals used as hash keys.
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Added warn/exception documentation to next_seq(). Changed validation in moltype() (deferred to Bio::PrimarySeq).
Changed to adopt Bio::Root::IO. Kept _filehandle() as a synonym to _fh().
Bio::SeqIO::FTHelper
Removed RootI dependence
Changed to new RootI chained new structure
FTHelper migrated to use Location::Split & Location::Fuzzy
Separate method for range fuzziness (not just start/end fuzziness)
Current solution to Fuzziness, still needs to be worked on to handle more cases
Complete fuzzy feature cycle of in fuzzy feature -> out fuzzy feature via SeqIO::genbank works
Handle SNP variations more properly and better SplitLocation handling -- handle 'order' and 'join'
Removed reference to bioperl-guts-l list.
Write items in sorted order
Updated to handle new LocationI syntax location of the type (5.12)..20 are still not parsed properly by FTHelper and are ignored
More robust regexp for getting more complicated features into location parsing
Regexp corrections
Bug #246 couldn't parse lines of complement(join(....)) since pattern expected only one 'word' directive before location info, remove complement string after assigning strandedness in _parse_loc
Bio::SeqIO::GAMEHandler
Corrected indication of module name in doc.
Removed RootI dependence
Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.
Bio::SeqIO::MultiFile
Removed RootI dependence
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Bio::SeqIO::ace
Removed RootI dependence
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Added use statements.
Bio::SeqIO::bioxml
Small correction in the comment header.
Removed RootI dependence
Quoted unquoted string literals used as hash keys.
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Added use statement.
Emoved bioxml.pm. bioxml users should switch to game.pm.
Bio::SeqIO::embl
Removed RootI dependence
Changed to new RootI chained new structure
Verbosity is shared now so can set verbosity at the top (Bio::SeqIO) level and will have messages silenced when verbosity= -1
Id generation func now takes a paramter for supporting different embl and genbank lines
Removed reference to bioperl-guts-l list.
Added RichSeq implementation - converted genbank/embl/swiss to use this - all tests pass. LiveSeq calls some deprecated methods
Bio::SeqIO::fasta
Commented out buggy lines
Removed multiple fasta parsing bug
Elia bug redux This should allow handling of both files with multiple fasta seqs and single fasta files and lines with >description >> 0.1
Removed RootI dependence
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Added capability of reading and writing empty sequences.
Added use statement.
Bio::SeqIO::featureHandler
Checking in game.pm into SeqIO. Helper classes are idHandler.pm, seqHandler.pm, and featureHandler.pm. Test script is t/game.t. Test data is t/test.game. Enjoy. Brad
Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.
Bio::SeqIO::game
Checking in game.pm into SeqIO. Helper classes are idHandler.pm, seqHandler.pm, and featureHandler.pm. Test script is t/game.t. Test data is t/test.game. Enjoy. Brad
Modifications to handle new RootI setup
Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.
Doc formatting fix
Made arguments SeqIO like
More revisions to not complain when certain things are null
This test will only work from bioperl-live/
Updated Bio::SeqIO::game. It now deals with filehandles and supports the 'chunkable' notation discussed on the mailing list. Brad
Fixed initializiation errors that were making noise in make test
Quoted unquoted string literals used as hash keys.
Changed to new RootI chained new structure
Bio::SeqIO::game::featureHandler
Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.
More revisions to not complain when certain things are null
Quoted unquoted string literals used as hash keys.
Changed to new RootI chained new structure
Added use statement.
Bio::SeqIO::game::idHandler
Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.
Quoted unquoted string literals used as hash keys.
Changed to new RootI chained new structure
Bio::SeqIO::game::seqHandler
Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.
Not using global variables
More revisions to not complain when certain things are null
Removing debugging code
Made it possible to import multiple sequences in one game file
Fixed initializiation errors that were making noise in make test
Quoted unquoted string literals used as hash keys.
Changed to new RootI chained new structure
Added use statement.
Bio::SeqIO::gcg
Removed RootI dependence
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Added use statement.
Moved GCG_checksum here from PrimarySeqI.
Bio::SeqIO::genbank
Removed RootI dependence
Changed to new RootI chained new structure
Verbosity is shared now so can set verbosity at the top (Bio::SeqIO) level and will have messages silenced when verbosity= -1
Id generation func now takes a paramter for supporting different embl and genbank lines
Bug that caused Title to smoosh words from second line
Removed reference to bioperl-guts-l list.
Added RichSeq implementation - converted genbank/embl/swiss to use this - all tests pass. LiveSeq calls some deprecated methods
Fixes for ensembl dumps. approved by Ewan :)
Removed semicolons from LOCUS line (for ensembl dumping)
Fix to deal with writing non richseqs out to genbank, still need to create and store the default date
Made LOCUS line parsing more robust (if it's genbank, get at the ID as a minimum. Some entries lack the molecule although they are nucleotide.
Fixed bug introduced by previous change (wrong syntax).
Fixes for ensembl dumps
Fixed parsing and writing of PID. Fixed parsing and writing of secondary accessions and seq version. Fixed print of too many spaces after REFERENCE. Now prints "residues" if it's protein.
Fixed problem with possible HTML tags in SOURCE/ORGANISM lines. Fixed unawareness of organelle in input and output.
Fixed missing handling of EOF in the middle of parsing.
Bio::SeqIO::idHandler
Checking in game.pm into SeqIO. Helper classes are idHandler.pm, seqHandler.pm, and featureHandler.pm. Test script is t/game.t. Test data is t/test.game. Enjoy. Brad
Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.
Bio::SeqIO::largefasta
SeqIO support for largge sequence files in fasta format
Added write support for large fasta and some more doc
Added better fallbacks for temp dir and next_seq returns a SeqI compliant object
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Bio::SeqIO::pir
Removed RootI dependence
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Added use statement.
Bio::SeqIO::raw
Removed RootI dependence
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Added use statement.
Bio::SeqIO::scf
Removed RootI dependence
Changed to new RootI chained new structure
Removed reference to bioperl-guts-l list.
Added use statement.
Bio::SeqIO::seqHandler
Checking in game.pm into SeqIO. Helper classes are idHandler.pm, seqHandler.pm, and featureHandler.pm. Test script is t/game.t. Test data is t/test.game. Enjoy. Brad
Modifications to handle new RootI setup
Updates to game.pm including feature recursion. game.pm's handler's moved to Bio/SeqIO/game. GAMEHandler.pm removed.
Bio::SeqIO::swiss
Removed RootI dependence
Changed to new RootI chained new structure
Verbosity is shared now so can set verbosity at the top (Bio::SeqIO) level and will have messages silenced when verbosity= -1
Added use statement.
Added RichSeq implementation - converted genbank/embl/swiss to use this - all tests pass. LiveSeq calls some deprecated methods
Simplified DBLink parsing code.
Fixed using RichSeq::seq_version() instead of sv().
Fixed bug #900: multiple gene names, separated by " OR ". Please someone check on a real example.
Bio::SeqUtils
Holder class for miscellaneous sequence methods. Created with seq3 and seq3in methods for handling three letter IUPAC amino acid code output and input.
Added a noncoded amino acid selenocystein which has one and three letter symbols.
Bio::SimpleAlign
Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl
RootI compliance and some documentation reformatting
Quoted unquoted string literals used as hash keys.
Migrate to chained new with new Bio::Root::RootI
Fixed clustalw alignIO module to honor input file order
Removed reference to bioperl-guts-l list.
Bio::Species
Named parameter for classification and migrate to new Bio::Root:RootI chained new
Bio::Tools::AlignFactory
Migrated to new Bio::Root::RootI chained new
Fixed to be RootI dependant
Fixed pSW bugs
Bio::Tools::Alignment::Clustalw
Added clustal.pl; also minor bug fixes
Minor code cleanup - Clustalw, AlignIO
Fixed passing of arguments to base class in _initialize(). Fixed exists_clustal() to return false upon missing program even though $@ is empty. Moved returning true to the end of the module (looks weird if in the middle). Fixed mailing lists in docs.
Fixed bug in Clustalw.pm sub exists_clustal
Did some doc and code formatting
Corrections and standardizations
Simplier way to unlink
Seqfiles are now created as tempfile rather than hardcoded names
Migrated to Bio::Tools::Run::Alignment
Bio::Tools::Alignment::TCoffee
Added TCoffee alignment
Simplier way to unlink
Seqfiles are now created as tempfile rather than hardcoded names
Migrated to Bio::Tools::Run::Alignment
Bio::Tools::AnalysisResult
Fixed wrong spelling of promoter.
Doc changes for standardization
Root I compliance
Migrated to new Bio::Root::RootI chained new
Commented out documentation for parse() (was required by Bio::SeqAnalysisParserI, but is now discouraged).
Changed to adopt Bio::Root::IO.
Bio::Tools::BPbl2seq
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
Removed RootI dependence and added some standardization
Quoted unquoted string literals used as hash keys.
Migrated to new Bio::Root::RootI chained new
Some cleanup to support 5.00404
BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes
Corrected documentation.
Fixed queryname field to not override -query line for Similarity, tagname is now -queryname
Changed to adopt Bio::Root::IO.
Bio::Tools::BPlite
Added documentation of functions
Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl
Aesthetics and removal of uneeded variables, some bulletproofing
Removed RootI dependence and added some standardization
Cleaned up BPpsi stuff, in particular for 5.00004
Quoted unquoted string literals used as hash keys.
Migrated to new Bio::Root::RootI chained new
BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes
Changed to adopt Bio::Root::IO.
Bio::Tools::BPlite::HSP
Added documentation of functions
Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl
Removed RootI dependance and some standardization
Quoted unquoted string literals used as hash keys.
Migrated to new Bio::Root::RootI chained new
Bug #885; tblastn parsing supported now, added a method 'frame' to BPlite::HSP to store this value
Corrected to use frame method from Bio::SeqFeature::Generic
Frame map from blast frame to gff frames
Handle frame mapping from BLAST to GFF
Frame of undef means no frame information, using undef rather than '.', however method to reset the frame to 'undef' for an instantiated object
Bio::Tools::BPlite::Iteration
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl
Removed RootI dependance and some standardization
Cleaned up BPpsi stuff, in particular for 5.00004
Quoted unquoted string literals used as hash keys.
Migrated to new Bio::Root::RootI chained new
Small fixes in -fh handling. Fixed nextSbjct to return undef instead of 0 on failure.
Bio::Tools::BPlite::Sbjct
Added documentation of functions
Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl
Removed RootI dependance and some standardization
Cleaned up BPpsi stuff, in particular for 5.00004
Quoted unquoted string literals used as hash keys.
Migrated to new Bio::Root::RootI chained new
BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes
Bug #885; tblastn parsing supported now, added a method 'frame' to BPlite::HSP to store this value
Bio::Tools::BPpsilite
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
Added example script standaloneblast.pl. Also some mods to StandAloneBlast.pm and BPpsilite.pm
Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl
Doc formatting
Removed RootI dependence and added some standardization
Cleaned up BPpsi stuff, in particular for 5.00004
Quoted unquoted string literals used as hash keys.
Migrated to new Bio::Root::RootI chained new
Some cleanup to support 5.00404
BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes
Tiny and purely cosmetic change.
Changed to adopt Bio::Root::IO. Tempfiles for iterations are not multi cpu-safe yet and need to be fixed.
Properly removing tempfiles
Bio::Tools::Blast
Documentation formatting
Bio::Tools::CodonTable
Migrated to new Bio::Root::RootI chained new
Added code #23: Thraustochytrium Mitochondrial
Bio::Tools::ESTScan
Fixed bugs in annotation of insertions/deletions, and others, too.
Migrated to new Bio::Root::RootI chained new
Added documentation to synopsis section.
Fixed to use _fh() instead of fh().
Bio::Tools::GFF
Added the GFF module that both reads and writes GFF formatted features. It is minimaly documented, and the GFF2 version doesn't seem to parse its own output.
Made a small change to the _gff2_string subroutine to fix the problem of fusing together multiple values of a single tag
Added close method, and proper testing of fields
Added a bunch of documentation. Made next_feature() safe. Some other very small changes.
Added gff_string() and from_gff_string() (version independent).
Changed to adopt Bio::Root::IO.
Added a 'chomp' to the from_gff2_string routine because frame information was being recorded with the newline character trailing. This is not required in the _from_gff_string method as this routine insists (wrongly) that a valid frame of 0,1, or 2 should be present, and defaults it to 0 if it doesn't see one of these options.
Added use Bio::SeqFeature::Generic, which is called by the next_feature method...
Bio::Tools::Genscan
Fixed wrong spelling of promoter.
Doc changes for standardization
Migrated to new Bio::Root::RootI chained new
Added frame recognition for each individual exon.
Added documentation to synopsis section.
Changed to use the new parent classes of Prediction::{Gene,Exon}.
Bio::Tools::HMMER::Domain
Migrated to new Bio::Root::RootI chained new
Added revision-Id line. Commented out documentation for deprecated methods. Changed initialization of feature1 and feature2 in new() to allow for parameter parsing.
Bio::Tools::HMMER::Results
Migrated to new Bio::Root::RootI chained new
Move from start_hmm to hstart & from end_hmm to hend
Made HMMER::Results SeqAnalysisParserI compliant
Changed to adopt Bio::Root::IO.
Bio::Tools::HMMER::Set
Migrated to new Bio::Root::RootI chained new
Added revision-Id line.
Bio::Tools::IUPAC
Migrated to new Bio::Root::RootI chained new
Fixed to be RootI dependant
Fixed to use named parameter -seq (is backward compatible though).
Bio::Tools::MZEF
Doc changes for standardization
Migrated to new Bio::Root::RootI chained new
Added documentation to synopsis section.
Changed to use the new parent classes of Prediction::{Gene,Exon}.
Bio::Tools::OddCodes
Migrated to new Bio::Root::RootI chained new
Added $Id$ line
Fixed to use named parameter -seq (is backward compatible though).
Bio::Tools::Prediction::Exon
Doc changes for standardization
Migrated to new Bio::Root::RootI chained new
Changed inheritance to SeqFeature::Gene::Exon. Fixed new(), no special primary_tag by default.
Bio::Tools::Prediction::Gene
Doc changes for standardization
Migrated to new Bio::Root::RootI chained new
Changed inheritance to SeqFeature::Gene::Transcript.
Bio::Tools::RestrictionEnzyme
Corrected mailing lists in doc.
Migrated to new Bio::Root::RootI chained new
Fixed bug introduced by chained new migration, added routined called cut_locations which reports the locations enzyme would cut rather than returning an htmlified seq str
Refactored (heavily) RootI. Alot of code removal. I think it is short and sweet now
Removed reference to bioperl-guts-l list.
Bio::Tools::Run::StandAloneBlast
Migrated code that runs tools to Bio::Tools::Run
Renaming packages for new dir structure
Fixed to PROPER usage of tempfile
Migrated to new Bio::Root::RootI chained new
Fixed several doc format bugs. (Why is an unprotected -p in the DESCRIPTION section disallowed and somewhere else it is not? Anyway, perldoc is quiet now.)
Fixed inclusion of 'use Bio::Root::RootI' instead of Bio::Root::Object. Fixed exists_blast() (didn't work due to missing braces).
Updated bptutorial and other documentation
BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes
Changed to adopt Bio::Root::IO.
Bio::Tools::SeqAnal
Corrected mailing lists.
Bio::Tools::SeqPattern
Aesthetics and removal of uneeded variables, some bulletproofing
SeqPattern.pm fixes and revisions
Fixed to be RootI dependant
Bio::Tools::SeqStats
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
Migrated to new Bio::Root::RootI chained new
Doc cleanup - variable initialization moved to BEGIN block
Fixed bugs and cleaned up code in SeqStats.pm and SeqStats.t
SeqStats clean up
Code cleanup, BEGIN block established, -seq supported as arg to new
Fixed documentation to use named parameter notation.
Bio::Tools::SeqWords
Fixed mailing lists. Fixed documentation to require arguments to new() in named parameter style for consistency. Changed inheritance to RootI, added a proper new(), which still allows for the argument being passed unnamed. Fixed count_words() to allow call as class method as the documentation promised.
Bio::Tools::Sigcleave
per request of Sanger Center webteam I've removed a dead URL that used to point to the EGCG docs. cdagdigian
Moved PrimarySeq and Seq to RootI style news. Fixed the knock on effects. LargeSeq/LargeFasta fail - cant fix them
Quoted unquoted string literals used as hash keys.
Bio::Tools::Sim4::Exon
Added 'use Bio::SeqFeature::SimilarityPair'.
Migrated to new Bio::Root::RootI chained new
Bio::Tools::Sim4::Results
Corrected a bug (wrong method name in call) in parse_next_alignment().
Migrated to new Bio::Root::RootI chained new
Explict call of fileparse needed to support 5.00404
Removed a left-over variable.
Bio::Tools::StandAloneBlast
Initial commits of StandAloneBlast- local blast module- and BPpsilite and BPbl2seq - psiblast and bl2seq report parsers- as well as related t files and supporting modules Iteration.pm and AlignIO/bl2seq.pm. Also minor documentation corrections (eg mailing list names)
Added example script standaloneblast.pl. Also some mods to StandAloneBlast.pm and BPpsilite.pm
Documentation reformat
Doc changes for standardization
Changed to use temporary files
Use tempfile creation from RootI
Migrated to Bio::Tools::Run
Bio::Tools::WWW
Fixed to be RootI dependant
Bio::Tools::pSW
Moved BEGIN block before use statements Now uses die when require fails so that the exception can be catched
Fixed pSW bugs
Bio::UnivAln
Quoted unquoted string literals used as hash keys.
Migrate to chained new with new Bio::Root::RootI
Bio::Variation::AAChange
Added $id$ lines, checked that modules end in 1;
Outdated methods in the constructor, '$self->' missing
Bio::Variation::AAReverseMutate
Added $id$ lines, checked that modules end in 1;
Bio::Variation::Allele
Added $id$ lines, checked that modules end in 1;
Inheritance from RootI
Bio::Variation::DNAMutation
Added $id$ lines, checked that modules end in 1;
Outdated methods in the constructor, '$self->' missing
Bio::Variation::IO
Removed RootI dependance
Added $id$ lines, checked that modules end in 1;
Moved PRINT method from Bio::SeqIO to supress a warning
Removed old, non-functional code from the constructor. Joys of copy and paste (in this case from Bio::SeqIO)!
Bio::Variation::IO::flat
Removed RootI dependance
Reverted to 1.2 code that was unintentionally overwritten
Added $id$ lines, checked that modules end in 1;
Negative genomic locations were off by 1.
Deleted (unused) code for adding HTML hypertext links into the output. It did not really belong here.
Bio::Variation::IO::xml
Removed RootI dependance
Changed IO::String creation to OO style. Appears to be required.
Added $id$ lines, checked that modules end in 1;
Bio::Variation::RNAChange
Added $id$ lines, checked that modules end in 1;
Fixed outdated method calls
Bio::Variation::SeqDiff
Added $id$ lines, checked that modules end in 1;
Added quotes around hash keyword to prevent a warning
Added two new methods: 1. rna_offset to hold the offset from the start of the mRNA to the coding start 2. $rna_id to hold the UID for the transcript used
Added ->seqobj which returns the original or mutated dna, rna or protein sequence as a PrimarySeq object. Bio::Variation objects now link better with the rest of the bioperl. Migrated tests to Test and added a few for the seqobj method.
Fixed incompatibility with earlier perl5 versions: $self->$value which works with latest perl has to be written: $self->{$value}
Fixed the example in synopsis section of docs.
Bio::Variation::VariantI
Added $id$ lines, checked that modules end in 1;
Removed DOS LF
Makefile.PL
Added XML::* and IO::* dependencies.
Added missing commas
Silly capitalization mistake
Added File::Temp dependancy
Added dependcy check for XML::Node which is needed by Bio::Variation::IO::xml.pm
Added HTML::Parser dependancy
Updated MANIFEST file to reflect all the new files in the 07 distribution. Tweaked the warning message in Makefile.PL and updated VERSION to 0.07. Added OpenBSd entry to PLATFORMS. cdagdigian.
When doing 'make dist' noticed that version was incorecctly set to "0.07.0". I changed this to "0.7" - cdagdigian
bioperl.lisp
Replaced bioperl-guts-l@bioperl.org by bioperl-l@bioperl.org
bioperl.pod
Replaced: bioperl-guts-l@bioperl.org and vsns-bcd-perl-guts@lists.uni-bielefeld.de by bioperl-l@bioperl.org (File seems to be out of date anyway: sending mail to bioperl-bugs)
Took trivial doc changes I made in branch-07 and committed them to head. cdagdigian
bptutorial.pl
Initial commit of bptutorial.pl introductory tutorial & tutorial script.
Removed /013 characaters (^M) and wraped text in paragraphs
The examples can be run now. 'require Bio::Tools::pSW' failing is handled gracefully. ... really minor formatting changes were done in the text part.
Translate & liveseq revisions to bptutorial
SeqPattern.pm fixes and revisions
Updated bptutorial and other documentation
Added appendix listing available methods to bptutorial.pl
Fixed bug #886.
Adopted changes to BPbl2seq calling
examples/change_gene.pl
Restructured Mutator.pm. Added Mutation.pm to hold mutation information. Tests for both. Example script.
Changed EMBL-feature loading code to use the new SplitLocation
examples/clustalw.pl
Added clustal.pl; also minor bug fixes
Fixed bug in Clustalw.pm sub exists_clustal
Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl
Migrated alignment code to new dir structure in Bio::Tools
examples/getGenBank.pl
How to retrieve GenBank entries over the Web
examples/hitdisplay.pl
Hitdisplay.pl is a demo of the HitDisplay.pm module in Bio::Tk
Fix: Changed @data into correct variable @hits. Script works now.
examples/standaloneblast.pl
Added example script standaloneblast.pl. Also some mods to StandAloneBlast.pm and BPpsilite.pm
Added parsing of phiBLAST reports to BPlite and BPpsilite. Modified consensus methods in SimpleAlign to enable thresholds. Added threshold varying example to standaloneblast.pl
Migrated alignment code to new dir structure in Bio::Tools
scripts/bpindex.pl
Correct location behavior to return min_start == max_start when start is defined SplitLocation->start will return the value of the 1st (sorted) contained location Location.t was updated to test for this as well
scripts/subsequence.cgi
Extract a short subsequence of DNA from a large GenBank entry
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