Core 0.5.1 0.6.0 delta

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These are detailed notes on changes made between release-0-05-1 and release-06.

Bio::AnnSeq
Added gene/exon/transcript/translations and testing stuff
Jgrg - Added Species.pm, a simple module for storing taxonomic information.
Added some fiddles to get AnnSeq etc to work correctly
Fixed some EMBL parsing/dumping issues. Get alot more fresh with the EMBL stuff Got Sim4 tools to work and tested.
Added more AnnSeq/SeqFeature stuff
Fixed embl dumping problems
Added things for Tim
Added comments to annseq/embl
Added accession, version, keywords, division and molecule reading from GenBank and writing to EMBL. Added molecule method to AnnSeq.pm to store molecule type
Added DATE, corrected problem with <n..n> location lines Full entry GenBank to EMBL conversion and viceversa
Finished revising conversion from GenBank to EMBL and viceversa. Added test to check GenBank.pm Included comments to both modules. First "Beta" version!
Fixed bugs from bug reports: added multi-date capability, organelle method in Species object, reading of tags without values
Fixed some issues (?) I hope...
Added swiss.pm, reader/writer for the Swissprot format Added some methods to other files to implement Swissprot, such as gene name, secondary accession number.
AC line read into an AC number and an array of secondary accession numbers Also, RP line read into Reference start and end if they are present, and into a new rp method otherwise
Fixed bad bug in fasta.pm
Started the big renaming
Bio::AnnSeqI
Added some fiddles to get AnnSeq etc to work correctly
Fixed alot of stuff for the embl dumping
Started the big renaming
Bio::AnnSeqIO
Added annseqio handler
The synopsis contained 2 errors. 1. while $var ($fh->next_annseq()) is syntactically wrong 2. write_annseq expects a sequence object as parameter
Fixed simple align stuff
Bio::Annotation
Added annotation stuff and updated the EMBL parsing stuff
Fixed bugs from bug reports: added multi-date capability, organelle method in Species object, reading of tags without values
Added swiss.pm, reader/writer for the Swissprot format Added some methods to other files to implement Swissprot, such as gene name, secondary accession number.
AUTOLOAD and Exporter cleanup
Bio::Annotation::Comment
Added annotation stuff and updated the EMBL parsing stuff
AUTOLOAD and Exporter cleanup
Final documentation additions and more tests on annotation package
Bio::Annotation::DBLink
Added annotation stuff and updated the EMBL parsing stuff
Added DR (DBXref) line parsing to Bio/AnnSeqIO/EMBL.pm
Final documentation additions and more tests on annotation package
Bio::Annotation::Reference
Added annotation stuff and updated the EMBL parsing stuff
Both modules can now read and write the bases to which each reference refers, i.e. RP line in EMBL, and (bases n to n) in reference header in GenBank
Fixed bugs from bug reports: added multi-date capability, organelle method in Species object, reading of tags without values
AC line read into an AC number and an array of secondary accession numbers Also, RP line read into Reference start and end if they are present, and into a new rp method otherwise
AUTOLOAD and Exporter cleanup
Final documentation additions and more tests on annotation package
Bio::DB::Ace
Renamed DB interface modules from DBI to I
AUTOLOAD and Exporter cleanup
Bio::DB::BioSeqI
Renamed interfaces
Bio::DB::GenBank
Fixed: Message summary for PR#75 From: bradford_powell@med.unc.edu Subject: GenBank.pm: passing an array to get_Stream_by_batch Date: Thu, 22 Jul 1999 15:21:11 -0400
Added new files
Fixed inheritance of 'new' function
Renamed DB interface modules from DBI to I
AUTOLOAD and Exporter cleanup
Bio::DB::GenPept
Fixed: Message summary for PR#75 From: bradford_powell@med.unc.edu Subject: GenBank.pm: passing an array to get_Stream_by_batch Date: Thu, 22 Jul 1999 15:21:11 -0400
Added new files
Fixed inheritance of 'new' function
Renamed DB interface modules from DBI to I
AUTOLOAD and Exporter cleanup
Bio::DB::RandomAccessDBI
Added new files
Renamed interfaces
Bio::DB::RandomAccessI
Renamed interfaces
Changed to depending on RootI rather than Object
AUTOLOAD and Exporter cleanup
Bio::DB::SeqDBI
Added new files
Added more DB support
Renamed interfaces
Bio::DB::SeqI
Renamed interfaces
Bio::Index::Abstract
Changed add_record so that if a reference to an array is given as the id, then an entry is added to the index under each member of the array.
Did primaryseq making etc
AUTOLOAD and Exporter cleanup
Improvements to Index system, and eliminated warnings from CodonTable
Lots of minor fixes, coordinated with jitterbug
Fixed error in Bio::Index::Abstract on systems without DB_File
Bio::Index::AbstractSeq
./AbstractSeq.pm - move/rename FROM MultiFileSeq.pm
Completed renaming of MultiFileSeq -> AbstractSeq
Bio::Index::EMBL
Index by all accession numbers in the entry rather than the first only
Fixed index bugs, and fixed makefile
Done merge
Added new files
Added more DB support
Improvements to Index system, and eliminated warnings from CodonTable
Completed renaming of MultiFileSeq -> AbstractSeq
Bio::Index::Fasta
Fixed index bugs, and fixed makefile
Done merge
Added more DB support
Improvements to Index system, and eliminated warnings from CodonTable
Completed renaming of MultiFileSeq -> AbstractSeq
Bio::Index::MultiFileSeq
Added more DB support
Renamed DB interface modules from DBI to I
AUTOLOAD and Exporter cleanup
Improvements to Index system, and eliminated warnings from CodonTable
MultiFileSeq.pm - move/rename TO ./AbstractSeq.pm
Bio::Index::SwissPfam
Fixed index bugs, and fixed makefile
Done merge
AUTOLOAD and Exporter cleanup
Improvements to Index system, and eliminated warnings from CodonTable
Bio::LocatableSeq
Fixed simple align stuff
Final documentation additions and more tests on annotation package
Bio::NewSeq
Added NewSeq stuff
Reorganization of Bio::SeqIO modules
Fixed some issues (?) I hope...
Fixed bugs in Bio::SeqIO::embl::next_seq() and Bio::Seq doc.
Did primaryseq making etc
Bio::Parse
Done merge
Removed some cruft
Bio::PrimarySeq
Did primaryseq making etc
Removed some cruft
Started the big renaming
Got the tests to pass
Added new files
Alowing stop codons in PrimarySeq.
Improvements to Index system, and eliminated warnings from CodonTable
Made more jitterbug fixes
Fixed bad reference to seq not self object
Bio::PrimarySeqI
Did primaryseq making etc
Started the big renaming
Got the tests to pass
Added out_fasta
Bug fix
Added frame issues to PrimarySeqI translate
AUTOLOAD and Exporter cleanup
Added IUPAC ambiquity into CodonTable.pm. Old translate method in PrimarySeqI.pm is now called translate_old. The new one using CodonTable.pm is in place. CodonTable tests updated.
Improvements to Index system, and eliminated warnings from CodonTable
Nl character before =cut was missing and code was getting into documentation.
Made more jitterbug fixes
Add restriction enzyme stuff, fixed primary seq stuff
Fixed alot of the final bugs
Bio::RangeI
Fixed some issues with features etc
Reorganization of Bio::SeqIO modules
Bio::Root::Err
AUTOLOAD and Exporter cleanup
Bio::Root::Global
Done merge
AUTOLOAD and Exporter cleanup
Bio::Root::IOManager
Fixed bug in file() so it works with FileHandles and Glob refs too.
- Resetting $/ before calling function references invoked during read().
- Fixed bug reported in PR#85. Bio::Root::Utilities::get_newline() returns "\n" by default. - IOManager::read doesn't call alarm() if it isn't available (fixes bug #PR98). - Root::Object::_set_io() does not pass @_ to the IOManager constructor call (incorporates suggestion from Scot Harker, jitterbut PR#192).
Merging in changes from the stable-0-05-new branch from the after-05-06-merge tag.
Bio::Root::Object
Done merge
Refactored RootI to get exception throwing cleanly out Fixed minor issues in multifile.pm Minor fix to IUPAC added exception test tidied up SeqStats.pm
Made Object/RootI split
AUTOLOAD and Exporter cleanup
- Fixed bug reported in PR#85. Bio::Root::Utilities::get_newline() returns "\n" by default. - IOManager::read doesn't call alarm() if it isn't available (fixes bug #PR98). - Root::Object::_set_io() does not pass @_ to the IOManager constructor call (incorporates suggestion from Scot Harker, jitterbut PR#192).
Merging in changes from the stable-0-05-new branch from the after-05-06-merge tag.
Bio::Root::RootI
Refactored RootI to get exception throwing cleanly out Fixed minor issues in multifile.pm Minor fix to IUPAC added exception test tidied up SeqStats.pm
Made Object/RootI split
AUTOLOAD and Exporter cleanup
Bio::Root::Utilities
Fixed some bugs in create_filehandle() and get_newline() that allow them to play better with STDIN and FileHandle objects. Note that the -file argument to create_filehandle should be either a FileHandle ref or \*STDIN. Any Glob that is passed in is now assumed to be STDIN.
Okay, I fixed create_filehandle() so it doesn't always assume a Glob ref is STDIN.
AUTOLOAD and Exporter cleanup
- Fixed bug reported in PR#85. Bio::Root::Utilities::get_newline() returns "\n" by default. - IOManager::read doesn't call alarm() if it isn't available (fixes bug #PR98). - Root::Object::_set_io() does not pass @_ to the IOManager constructor call (incorporates suggestion from Scot Harker, jitterbut PR#192).
Merging in changes from the stable-0-05-new branch from the after-05-06-merge tag.
Bio::Search::Hit::Fasta
AUTOLOAD and Exporter cleanup
Bio::Search::Hit::HitI
AUTOLOAD and Exporter cleanup
Bio::Search::Processor
Small tidyups
AUTOLOAD and Exporter cleanup
Bio::Search::Result::Fasta
AUTOLOAD and Exporter cleanup
Bio::Search::Result::ResultI
AUTOLOAD and Exporter cleanup
Bio::SearchDist
Fixed Bio::Ext::Align switches
Done merge
AUTOLOAD and Exporter cleanup
Bio::Seq
Added sequence error trapping... added more embl dumping hooks
Fixed up bugs 70, 82 dealing with translate() function
Fixed alot of stuff for the embl dumping
Done merge
Changed Seq.pm to accept Ns in the translation functions when there is complete ambiguity in the third base (i.e. XXN coding for one amino acid) Eliminated a print STDERR command in GenBank.pm
Fixed bugs in Bio::SeqIO::embl::next_seq() and Bio::Seq doc.
Started the big renaming
Got the tests to pass
AUTOLOAD and Exporter cleanup
Improvements to Index system, and eliminated warnings from CodonTable
Bio::SeqFeature::Exon
Added gene/exon/transcript/translations and testing stuff
Added more stuff to genes/transcripts/exons etc
Removed some cruft
Bio::SeqFeature::FeaturePair
Added FeaturePair.pm as a replacement for Homol.pm
Added support to FeaturePair
Checked for defined $arg in sub feature2
AUTOLOAD and Exporter cleanup
Bio::SeqFeature::Gene
Added gene/exon/transcript/translations and testing stuff
Added more stuff to genes/transcripts/exons etc
More stuff added to gene
Removed some cruft
Bio::SeqFeature::Generic
Added annotation stuff and updated the EMBL parsing stuff
Added gene/exon/transcript/translations and testing stuff
Added some fiddles to get AnnSeq etc to work correctly
Fixed some EMBL parsing/dumping issues. Get alot more fresh with the EMBL stuff Got Sim4 tools to work and tested.
Added more AnnSeq/SeqFeature stuff
Fixed alot of stuff for the embl dumping
Fixed some issues with features etc
Added some fiddles to Generic and GenBank dumping
Added more feature stuff
Fixed simple align stuff
AUTOLOAD and Exporter cleanup
Fixed various bugs in EMBL parsing and writing. Added support for features which run off the sequence (< and > locations) and zero-width features. Fixed species support in embl.pm
Bio::SeqFeature::Homol
Added homol file
Added more HMMER stuff. Fixed homol seq objects. Done other stuff
Removed some cruft
Bio::SeqFeature::Transcript
Added gene/exon/transcript/translations and testing stuff
Added more stuff to genes/transcripts/exons etc
Removed some cruft
Bio::SeqFeature::Translation
Added gene/exon/transcript/translations and testing stuff
Added more stuff to genes/transcripts/exons etc
Removed some cruft
Bio::SeqFeatureI
Added some fiddles to get AnnSeq etc to work correctly
Added more AnnSeq/SeqFeature stuff
Fixed alot of stuff for the embl dumping
AUTOLOAD and Exporter cleanup
Final documentation additions and more tests on annotation package
Bio::SeqI
Added SeqI
Added SeqI docs. Added EMBL no dna printing and sorting post-hoc
SeqI additions
Added NewSeq stuff
Added more HMMER stuff. Fixed homol seq objects. Done other stuff
Did primaryseq making etc
Started the big renaming
AUTOLOAD and Exporter cleanup
Minor fixes in embl parsing
Bio::SeqIO
Documentation fixup's (lots).
Reorganization of Bio::SeqIO modules
Improvements to EMBL Reference dumping
Added new files
- Added sub moltype() for setting the moltype on produced Seq objects. - Fixed and added comments.
Added more DB support
Lots of minor fixes, coordinated with jitterbug
Fixed seqio self bug
Added some small jitterbug fixes
Fixed various bugs in EMBL parsing and writing. Added support for features which run off the sequence (< and > locations) and zero-width features. Fixed species support in embl.pm
Bio::SeqIO::EMBL
Reorganization of Bio::SeqIO modules
Bio::SeqIO::FTHelper
Added seqio files
Added new files
AUTOLOAD and Exporter cleanup
Fixed various bugs in EMBL parsing and writing. Added support for features which run off the sequence (< and > locations) and zero-width features. Fixed species support in embl.pm
Bio::SeqIO::Fasta
Reorganization of Bio::SeqIO modules
Bio::SeqIO::GCG
Reorganization of Bio::SeqIO modules
Bio::SeqIO::GenBank
Simple module for extraction of sequence/ id/ description/ type from GenBank formatted sequences. nextseq still gobbles up all the sequences it can find in a multiple entry GenBank file. This is definitely alpha at the moment.
Cleaned up test suite
Reorganization of Bio::SeqIO modules
Bio::SeqIO::Handler
Reorganization of Bio::SeqIO modules
Bio::SeqIO::MultiFile
Added new files
Refactored RootI to get exception throwing cleanly out Fixed minor issues in multifile.pm Minor fix to IUPAC added exception test tidied up SeqStats.pm
AUTOLOAD and Exporter cleanup
Bio::SeqIO::PIR
Reorganization of Bio::SeqIO modules
Bio::SeqIO::Raw
Reorganization of Bio::SeqIO modules
Bio::SeqIO::SCF
Reorganization of Bio::SeqIO modules
Bio::SeqIO::embl
Reorganization of Bio::SeqIO modules
Fixed bugs in Bio::SeqIO::embl::next_seq() and Bio::Seq doc.
Fixed simple align stuff
AUTOLOAD and Exporter cleanup
Made it so IO is abstracted to the _print and _readline functions so that streams can be tie-ed rather than just files handles
Fixed various bugs in EMBL parsing and writing. Added support for features which run off the sequence (< and > locations) and zero-width features. Fixed species support in embl.pm
Minor fixes in embl parsing
Bio::SeqIO::fasta
Reorganization of Bio::SeqIO modules
Fixed bad bug in fasta.pm
Added more DB support
Improvements to Index system, and eliminated warnings from CodonTable
SeqIO/fasta.pm no longer upcases sequences on the way in and out
Lots of minor fixes, coordinated with jitterbug
Bio::SeqIO::gcg
Reorganization of Bio::SeqIO modules
Got the tests to pass
Bio::SeqIO::genbank
Reorganization of Bio::SeqIO modules
Got the tests to pass
Fixed simple align stuff
- Removed reference to annseq in docs. - Supressing warnings about uninitialized fields in write_seq.
AUTOLOAD and Exporter cleanup
Made it so IO is abstracted to the _print and _readline functions so that streams can be tie-ed rather than just files handles
Bio::SeqIO::pir
Reorganization of Bio::SeqIO modules
- write_seq() was calling Seq::names(). Removed this call since names are no longer stored in the Seq. - Fixed redeclaration of my $seq in next_seq().
Bio::SeqIO::raw
Reorganization of Bio::SeqIO modules
Made more jitterbug fixes
Bio::SeqIO::scf
Reorganization of Bio::SeqIO modules
- Removed new() so it will use the inherited new() from SeqIO. (Also, there was a bug in the unshift call in the old new()).
Bio::SeqIO::swiss
Added seqio files
- Removed import statement for StreamI. - cleaned up some checks for undefinedness in write_seq(). Also supressing warnings for undefined fields in write_seq(). - Useless use of hash element in void context in _read_FTHelper_swissprot(): $out->field->{$key}; # was this $out->field($key); # I changed to this (what's the purpose?)
AUTOLOAD and Exporter cleanup
Fixed swissprot parsing
Made it so IO is abstracted to the _print and _readline functions so that streams can be tie-ed rather than just files handles
Lots of minor fixes, coordinated with jitterbug
Bio::SeqStats
Added multi_1 test and SeqStats
Refactored RootI to get exception throwing cleanly out Fixed minor issues in multifile.pm Minor fix to IUPAC added exception test tidied up SeqStats.pm
Moved SeqStats, added SeqWords
Bio::SimpleAlign
Removed Pfam specefic methods (placed in a new Pfam alignment object)
Done merge
Fixed simple align stuff
AUTOLOAD and Exporter cleanup
Bio::Species
Jgrg - Added Species.pm, a simple module for storing taxonomic information.
Reorganization of Bio::SeqIO modules
Fixed bugs from bug reports: added multi-date capability, organelle method in Species object, reading of tags without values
Added species issues
Fixed various bugs in EMBL parsing and writing. Added support for features which run off the sequence (< and > locations) and zero-width features. Fixed species support in embl.pm
Bio::Tools::AlignFactory
Added bio::ext support
Fixed Bio::Ext::Align switches
Done merge
AUTOLOAD and Exporter cleanup
Merging in changes from the stable-0-05-new branch.
Bio::Tools::Blast
Done merge
AUTOLOAD and Exporter cleanup
Added bugfixes and features as described in the CHANGES file listed for v0.09
Merging in changes from the stable-0-05-new branch.
Bio::Tools::CodonTable
Added IUPAC ambiquity into CodonTable.pm. Old translate method in PrimarySeqI.pm is now called translate_old. The new one using CodonTable.pm is in place. CodonTable tests updated.
Improvements to Index system, and eliminated warnings from CodonTable
Bio::Tools::Fasta
Started the big renaming
Adding this module back but with a deprecation warning to use the SeqIO system instead.
AUTOLOAD and Exporter cleanup
Bio::Tools::HMMER::Domain
Committed HMMER results files
Added more HMMER stuff. Fixed homol seq objects. Done other stuff
Added HMMER results etc
Modified Bio::Tools:HMMER modules to use the new Bio::SeqFeature::FeaturePair model instead of the old Bio::SeqFeature::Homol
Merging in changes from the stable-0-05-new branch.
Bio::Tools::HMMER::Results
Committed HMMER results files
Added HMMER results etc
Modified Bio::Tools:HMMER modules to use the new Bio::SeqFeature::FeaturePair model instead of the old Bio::SeqFeature::Homol
AUTOLOAD and Exporter cleanup
Lots of minor fixes, coordinated with jitterbug
Bio::Tools::HMMER::Set
Committed HMMER results files
Added HMMER results etc
Modified Bio::Tools:HMMER modules to use the new Bio::SeqFeature::FeaturePair model instead of the old Bio::SeqFeature::Homol
Added more DB support
AUTOLOAD and Exporter cleanup
Merging in changes from the stable-0-05-new branch.
Bio::Tools::IUPAC
Got the tests to pass
Refactored RootI to get exception throwing cleanly out Fixed minor issues in multifile.pm Minor fix to IUPAC added exception test tidied up SeqStats.pm
AUTOLOAD and Exporter cleanup
Added IUPAC ambiquity into CodonTable.pm. Old translate method in PrimarySeqI.pm is now called translate_old. The new one using CodonTable.pm is in place. CodonTable tests updated.
Bio::Tools::RestrictionEnzyme
Got the tests to pass
AUTOLOAD and Exporter cleanup
Add restriction enzyme stuff, fixed primary seq stuff
Bio::Tools::SeqAnal
AUTOLOAD and Exporter cleanup
Bio::Tools::SeqPattern
Done merge
Minor changes to SeqPattern
Fixed alot of the final bugs
Bio::Tools::SeqStats
Moved SeqStats, added SeqWords
Bio::Tools::SeqWords
Moved SeqStats, added SeqWords
Fixed SeqWords. Backed out bioxml addition
Bio::Tools::Sigcleave
Got the tests to pass
Bio::Tools::Sim4::Exon
Added sim4 stuff
Fixed some EMBL parsing/dumping issues. Get alot more fresh with the EMBL stuff Got Sim4 tools to work and tested.
AUTOLOAD and Exporter cleanup
Merging in changes from the stable-0-05-new branch.
Bio::Tools::Sim4::ExonSet
Added sim4 stuff
Fixed some EMBL parsing/dumping issues. Get alot more fresh with the EMBL stuff Got Sim4 tools to work and tested.
Merging in changes from the stable-0-05-new branch.
Bio::Tools::Sim4::Results
Added sim4 stuff
Fixed some EMBL parsing/dumping issues. Get alot more fresh with the EMBL stuff Got Sim4 tools to work and tested.
Added more AnnSeq/SeqFeature stuff
AUTOLOAD and Exporter cleanup
Merging in changes from the stable-0-05-new branch.
Bio::Tools::WWW
AUTOLOAD and Exporter cleanup
Bio::Tools::pSW
Added bio::ext support
Fixed Bio::Ext::Align switches
Done merge
AUTOLOAD and Exporter cleanup
Bio::UnivAln
Done merge
AUTOLOAD and Exporter cleanup
Makefile.PL
Added NewSeq stuff
Done merge
Added final fixes
Fixed alot of the final bugs
fixed the syntax of the %packeges hash as it had a misplaced comma ','
added cvs id tag
biodesign.pod
Added NewSeq stuff
Added design docs.
Reorganization of Bio::SeqIO modules
Final documentation additions and more tests on annotation package
bioperl.idl
Added bioperl.idl
Fixed simple align stuff
bioperl.pod
Added NewSeq stuff
Added new files
Added final fixes
biostart.pod
Added new files
Added final fixes
examples/restriction.pl
Done merge
examples/seq_pattern.pl
Done merge
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