Core 0.5.1 0.6.0 delta

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