Core 0.7.0 0.7.1 delta

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These are detailed notes on changes made between release-0-7-0 and release-0-7-1.

Bio::AlignIO
Made code in SYNOPSIS cut and runnable
Made code in SYNOPSIS cut and runnable
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
Added initial versions for PHYLIP and NEXUS AlignIO modules, and test data files for each
Bio::AlignIO::bl2seq
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
Bio::AlignIO::clustalw
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Bio::AlignIO::fasta
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Bio::AlignIO::mase
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Was including gap characters into end() of the LocatebleSeq.
Was including gap characters into end() of the LocatebleSeq.
Bio::AlignIO::meme
An AlignIO module that reads the "alignment" sections of MEME output files (must be version 3.0 or greater.)
Bio::AlignIO::msf
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Next_aln() got into endless loop added empty lines to output for readability
Next_aln() got into endless loop added empty lines to output for readability aligned sequence names to left in the output according to custom
Output was printing type P, now it prints N if the first sequence is nucleotides
Bio::AlignIO::nexus
Added initial versions for PHYLIP and NEXUS AlignIO modules, and test data files for each
Bio::AlignIO::pfam
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Bio::AlignIO::phylip
Added initial versions for PHYLIP and NEXUS AlignIO modules, and test data files for each
Bio::AlignIO::prodom
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Bio::AlignIO::selex
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Bio::AlignIO::stockholm
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Fix a bug in reading in multiline sequences
Fix a bug in reading in multiline sequences
Bio::Annotation
Made code in SYNOPSIS cut and runnable
Made code in SYNOPSIS cut and runnable
Bio::Annotation::DBLink
Bug #912 fixed -- added documentation
Bio::DB::EMBL
Initial commmit, retrieve EMBL entries over the Web
Moved from emblfetch to more general dbfetch script
Bio::DB::Fasta
Added Bio::DB::Fasta which provides fast indexed access to a directory of Fasta files
Removing perl >= 5.6.0 directives Lincoln was using
Updated to inherit from Bio::DB::SeqI and use RootI throw instead of croakadded method documentation to some methods
Fixed divide by zero errors when indexing empty fasta files
$_ is always null does not need to be part of the calculation
Bio::DB::GDB
Tests pass even when IO::String is not installed
Bio::DB::GenBank
Added documentation about what to do for NT contigs.
Merging changes/fixes from branch-07.
Minor doc fix
Doc formatting
Bio::DB::GenPept
Doc fix
Doc fix
Bio::DB::NCBIHelper
Added documentation about the URLs used.
Merging changes/fixes from branch-07.
Bio::DB::RandomAccessI
Doc formatting
Bio::DB::SeqI
Mailing list update
Mailing list update - purge references to bielefeld list
Bio::DB::SwissProt
Bio::DB::SwissProt updates to point to batch retrieval script and more correctly call these scripts. Batch mode now supported and tested DB.t
Bio::DB::SwissProt updates migrated to branch after testing on main trunk
Added other method documentation
Added Heikki's ebi dbfetch URL for retrieving swissprot entries from a remote web db
Added Heikki's ebi dbfetch URL for retrieving swissprot entries added doc needed for 0.7.1 release
Bio::DB::Universal
Added universal db - as suggested by lincoln
Bio::DB::WebDBSeqI
Bio::DB::SwissProt updates to point to batch retrieval script and more correctly call these scripts. Batch mode now supported and tested DB.t
Bio::DB::SwissProt updates migrated to branch after testing on main trunk
Fixed bug #958
Fixed bug #958
Bio::Index::EMBL
Doc fixes
Doc fixes
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Index::Fasta
Doc fixes
Doc fixes
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Index::GenBank
Doc fixes
Doc fixes
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Index::SwissPfam
Doc fixes
Doc fixes
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Index::Swissprot
Doc fixes
Doc fixes
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::LiveSeq::AARange
Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.
Copying over LiveSeq-wide warning system from main trunk
Merged forgotten carp() -> $self->warn() migration.
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::Chain
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::LiveSeq::ChainI
Moving from carp to LiveSeq-wide warn
Moving from carp to LiveSeq-wide warn
Update mailing list even on those modules that are deprecated
Mailing list update - purge references to bielefeld list
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::DNA
Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.
Copying over LiveSeq-wide warning system from main trunk
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::Exon
Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.
Copying over LiveSeq-wide warning system from main trunk
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::Gene
Doc change and adding global (= gene wide) method verbose to Gene
Doc changes from 07 branch
Doc change and adding global (= gene wide) method verbose to Gene
Moving from carp to LiveSeq-wide warn
Moving from carp to LiveSeq-wide warn
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::IO::BioPerl
Added support for Bio::DB::EMBL's "get_Seq_by_id" so that an EMBL entry can be fetched through the web instead than read from a file.
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::IO::Loader
Added support for Bio::DB::EMBL's "get_Seq_by_id" so that an EMBL entry can be fetched through the web instead than read from a file.
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::IO::SRS
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::LiveSeq::Intron
Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.
Copying over LiveSeq-wide warning system from main trunk
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::Mutator
Fixed value of AAChange::end for inframe indels on codon pos 1
Fixed value of AAChange::end for inframe indels on codon pos 1
Added third coordinate system: 'gene'. Changes in methods numbering and change_gene.
Added third coordinate system: 'gene'. Changes in methods numbering and change_gene.
Numerous fixes for complex mutations, exon and intron numbers are now reported, distance from intron/exon boundary is shown...
Numerous fixes for complex mutations, exon and intron numbers are now reported, distance from intron/exon boundary is shown...
Fixed genomic gene based coordinate system
Fixed genomic gene based coordinate system
Moving from carp to LiveSeq-wide warn
Moving from carp to LiveSeq-wide warn
Fixed polypeptide mutated allele for frameshifs
Fixed polypeptide mutated allele for frameshifs
New method change_gene_with_alignment()
Escape '+', validate pos and len
Bio::LiveSeq::Mutation was not 'use'd
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::LiveSeq::Prim_Transcript
Removed unused 'use Carp'
Removed unused 'use Carp'
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::Range
Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.
Copying over LiveSeq-wide warning system from main trunk
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::Repeat_Region
Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.
Copying over LiveSeq-wide warning system from main trunk
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::Repeat_Unit
Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.
Copying over LiveSeq-wide warning system from main trunk
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::SeqI
Commented out a repeated printed warning
Commented out a repeatedly printed warning
Started the process of changing all "carp" warnings into $self->warn and $self->throw, with customizable verbosity level, inherited from SeqIO.
Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.
Doc change and adding global (= gene wide) method verbose to Gene
Doc changes from 07 branch
Doc change and adding global (= gene wide) method verbose to Gene
Moving from carp to LiveSeq-wide warn
Moving from carp to LiveSeq-wide warn
Update mailing list even on those modules that are deprecated
Mailing list update - purge references to bielefeld list
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::Transcript
Commented out a verbose warning
Started the process of changing all "carp" warnings into $self->warn and $self->throw, with customizable verbosity level, inherited from SeqIO.
Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.
Copying over LiveSeq-wide warning system from main trunk
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LiveSeq::Translation
Commented out verbose warning
Replaced carp and croak with ->warn and ->throw. Now the verbosity level should filter out some ignorable warnings, if set to "0". The default is "1": all warnings, no stack trace dump.
Copying over LiveSeq-wide warning system from main trunk
Removed redundant inheritance from Bio::LiveSeq::SeqI
Removed redundant inheritance from Bio::LiveSeq::SeqI
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Refixed $VERSION
Bio::LocatableSeq
Changed inheritance to Bio::PrimarySeq.
Changed inheritance to PrimarySeq.
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Added a test for sequence length into end(). If start() and $seq() are defined it calculates the expected end value and overrides the given value if necessary and prints a warning. (lots of them from current test data! ) This a work in progress! Also included are two new experimental methods no_gaps() for counting the number of internal gaps in the alignment column_from_residue_number() which is migrated here from SimpleAlign
Better error message when end() is tried to set into a value not supported by sequence
Bio::Location::Fuzzy
Applying Steve L.'s patch to silence perl on some systems.
Made code in SYNOPSIS cut and runnable
Made code in SYNOPSIS cut and runnable
Bio::Location::Simple
Seq_id initializable in new args
Seqid initialization in new
Made code in SYNOPSIS cut and runnable
Made code in SYNOPSIS cut and runnable
Added is_remote method to Simple Locations, which makes life easier for bioperl-db system. Also, changed sub_Location method for Split Locations, now only ordered if the order paramter is defined, to get EMBL dumping to print them in the same way they were parsed in
Merged heikki's location fixes to branch
Bug #970
Fixed bug #970
Update mailing list even on those modules that are deprecated
Bio::Location::Split
Better parse/writing of locations listed on different sequences. I think that location parsing is still a bit inflexible and we probably can't really parse nested sub_locations (splits of splits) which would violate the dogfoodability of bioperl, perhaps we have to go to a different parsing scheme for the next version
Made code in SYNOPSIS cut and runnable
Made code in SYNOPSIS cut and runnable
Added is_remote method to Simple Locations, which makes life easier for bioperl-db system. Also, changed sub_Location method for Split Locations, now only ordered if the order paramter is defined, to get EMBL dumping to print them in the same way they were parsed in
Handle undefined order parameter as a '0'
Merged heikki's location fixes to branch
Bio::PrimarySeq
Seq method failed when resetting its value to because _guess_type method throws an exception.
Seq method failed when resetting its value to because _guess_type method throws an exception.
Added validate_seq() and made seq() call it for validation.
Added validate_seq(). (Merge from main trunk.)
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Validate_seq() accepts '?' characters into sequence
Bio::PrimarySeqI
Added validate_seq().
Removed validate_seq().
Translate() rewrite, ~4x faster. Suggested by Amir Karger
Bio::Root::Err
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Root::IO
Bug #903 fixed
Attempt at migrating rmtree in to IO.pm -- need to be sure that this will work in case of static obj call
Proper calling of package method
Fixed Issue #0503
Prevent a recursion loop from happening in older perl
Use syntax for perl 5.004 class method calling and dirs are removed
Handle dos linefeeds
Doc fix, unnecessary argument removed
Bio::Root::IOManager
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Root::Object
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Root::RootI
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Root::Utilities
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Root::Vector
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Root::Xref
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Search::Hit::HitI
Update mailing list even on those modules that are deprecated
Bio::Seq
Added implementation of validate_seq().
Added flush_SeqFeatures().
Mailing list update - purge references to bielefeld list
Mailing list update, doc formatting
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Set $VERSION to 0.9
Refixed $VERSION
Bio::Seq::LargePrimarySeq
Make sure initialize_io is called to insure tempfile cleanup
Bio::Seq::RichSeq
Underscoralize hash keys
Leading underscores for data keys in $self hash
Bio::SeqFeature::Exon
Added feature types Exon, Intron, UTR5, UTR3, Promoter, and PolyA. These all inherit from SeqFeature::Generic, but report themselves as the appropriate type when queried with an isa. They are absolutely bare bones at the moment, but there is lots of space for fleshing them out with additional methods and properties.
This is on Marks orders to fix a cvs problem
Rewrote my Exon object to be compatible with Hilmars GeneStrucuture objects, but without the restrictions on the generic feature tags. Initial tests have been successful, but I havent used GeneStructure objects enough to know how to test it rigorously. Some of the code is copied directly from Hilmars Exon object. Hilmar, can you do this testing when you get back?
Bio::SeqFeature::Gene::GeneStructure
Fixed a bug reported by Mark W.
Fixed a bug reported by Mark W.
Bio::SeqFeature::Gene::Transcript
Fixed bug reported by Mark W.
Fixed a bug reported by Mark W.
Bio::SeqFeature::Generic
Bug #947 fixed
Bug #970
Fixed bug #970
Fixed bug #947 on 0.7 branch
Changed Bio::SeqFeature::Generic so that it does not require new() to init data structures in the new object
Bio::SeqFeature::Intron
Added feature types Exon, Intron, UTR5, UTR3, Promoter, and PolyA. These all inherit from SeqFeature::Generic, but report themselves as the appropriate type when queried with an isa. They are absolutely bare bones at the moment, but there is lots of space for fleshing them out with additional methods and properties.
Features now initialized with a SUPER::new call, and removed Exon.pm because Hilmar as a much better one.
Bio::SeqFeature::PolyA
Added feature types Exon, Intron, UTR5, UTR3, Promoter, and PolyA. These all inherit from SeqFeature::Generic, but report themselves as the appropriate type when queried with an isa. They are absolutely bare bones at the moment, but there is lots of space for fleshing them out with additional methods and properties.
Features now initialized with a SUPER::new call, and removed Exon.pm because Hilmar as a much better one.
Bio::SeqFeature::Promoter
Added feature types Exon, Intron, UTR5, UTR3, Promoter, and PolyA. These all inherit from SeqFeature::Generic, but report themselves as the appropriate type when queried with an isa. They are absolutely bare bones at the moment, but there is lots of space for fleshing them out with additional methods and properties.
Features now initialized with a SUPER::new call, and removed Exon.pm because Hilmar as a much better one.
Bio::SeqFeature::UTR3
Added feature types Exon, Intron, UTR5, UTR3, Promoter, and PolyA. These all inherit from SeqFeature::Generic, but report themselves as the appropriate type when queried with an isa. They are absolutely bare bones at the moment, but there is lots of space for fleshing them out with additional methods and properties.
Features now initialized with a SUPER::new call, and removed Exon.pm because Hilmar as a much better one.
Bio::SeqFeature::UTR5
Added feature types Exon, Intron, UTR5, UTR3, Promoter, and PolyA. These all inherit from SeqFeature::Generic, but report themselves as the appropriate type when queried with an isa. They are absolutely bare bones at the moment, but there is lots of space for fleshing them out with additional methods and properties.
Features now initialized with a SUPER::new call, and removed Exon.pm because Hilmar as a much better one.
Bio::SeqIO
Doc update: example on how to do SeqIO into a string
Doc update: example on how to do SeqIO into a string
Bio::SeqIO::FTHelper
Better parse/writing of locations listed on different sequences. I think that location parsing is still a bit inflexible and we probably can't really parse nested sub_locations (splits of splits) which would violate the dogfoodability of bioperl, perhaps we have to go to a different parsing scheme for the next version
Commented out debugging line printing "dogfood location is..." :-)
Bug #930 parsing complement(join(...)) FT lines
Bug #930 protecting case when seqfeature is undef-ed (not really a safe way to do things...) when line is unparseable
Fixed bug #952
Removed debugging print statement
Added is_remote method to Simple Locations, which makes life easier for bioperl-db system. Also, changed sub_Location method for Split Locations, now only ordered if the order paramter is defined, to get EMBL dumping to print them in the same way they were parsed in
Merged FTHelper fixes for remote locations to branch
Protect against non SeqFeature::Generic features when writing a sequence out score and frame are not part of SeqFeatureI
Protect against non SeqFeature::Generic features when writing a sequence out score and frame are not part of SeqFeatureI
Fix for bug #965
Bug #965 test and fix
Commented out subseqfeature locations FT string printing, Jason to check
Removed STDERR
Minor missing things for the release
Bio::SeqIO::embl
Added guessing of seq->molecule based on seq->primary_seq->moltype and viceversa assigning of seq->primary_seq->moltype based on seq->molecule, purely for EMBL dumping purposes
Silly me... XXX is an EMBl thing, not a bioperl acceptmoltype
More strict embl writing
More strict embl writing,support for PUBMED
PubMed support, accesion versioon printing correctly
Bio::SeqIO::fasta
Added Alignment output for psiblast searches
Use display_id() for printing identifier
Use display_id() for printing identifier
Index.t changes
Bio::SeqIO::game
Bug #912 fixed -- added documentation
Bio::SeqIO::game::featureHandler
Bug #912 fixed -- added documentation
Bio::SeqIO::game::idHandler
Bug #912 fixed -- added documentation
Added RootI inheritance
Bio::SeqIO::game::seqHandler
Bug #912 fixed -- added documentation
Bio::SeqIO::genbank
Applied fixes submitted by Malcolm Cook <Malcolm.Cook@ppgx.com>.
Merged fixes suggested by Malcolm Cook.
Bug #956
Bug #956
Bug #950, stricter genbank formatting support for MEDLINE/PUBMED parsing & writing
Bug #950, strict writing of genbank format added support for MEDLINE and PUBMED parsing/writing as part of references
Die calls converted to throw calls
Bio::SeqIO::pir
Remove pir from 0.7 branch since it does not work
Bio::SeqIO::scf
Replaced STDIN by $fh in new() (bug report #920).
Bio::SeqIO::swiss
Fixes from emmanuel for more detailed swissprot format
Fixes from emmanuel for more detailed swissprot format - main trunk
Corrected _crc64 method which was wrong!!!
Corrected _crc64 method
Bug #946 - fixed regex per bug when parsing TrEMBL swissprot. This occurs becuase TrEMBL lists the id on the ID line as just an accession while SwissProt has ID_DIVISION
Migrated fix for bug #946 to branch
Doc fix
Better protecting of ! Bio::Seq::RichSeqI sequences being printed Handle all gene names through each_gene_name rather than deprecated gene_name
Better protecting of non Bio::Seq::RichSeqI sequences being printed Handle all gene names through each_gene_name rather than deprecated gene_name and join with the proper 'OR ' syntax
JitterIssue #2001
JitterIssue #2001
Bio::SimpleAlign
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
New method: slice()
Column_from_residue_number() uses now identically named method in LocatableSeq get_seq_by_pos() Gets one sequence based on its position in the alignment select() creates a new alignment from a continuous range of sequences dot() remaps residue columns to "dot" notation. output only!
Fixed a bug percentage_identity()
Minor formatting and underscoring of private data variables
Underscoralize private data variables because I'm a picky mofo
Reorganized methods into logical categories
Attribute setting methods missing_char(), unknown_char(), match_char(), gap_char() work now.
Removed unknown_char(). I do not know where I got that from. missing_char() does the same thing
Bio::Tools::BPbl2seq
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
Bio::Tools::BPlite
Doc fixes
Doc fixes
The solution yesterday was a bit too simplistic and failed if you started skimming over reports without ever parsing them by iteratively using the ->_parseHeader call. This is now fixed. In addition, it was necessary to distinguish between an empty Blast result, and the end of the input stream. _parseHeader now returns 0 for an empty Blast result, and -1 for an EOF. The return of 0 is usually not necessary to catch because the call to ->nextSbjct will also return 0 under these circumstances. I also made some changes to the documentation to correct some documented calls to a routine ->sbjct, which is actually ->subject. See the revised Synopsis for an example of usage. Please let me know if my changes are buggering anyone up...
Documentation fixes.
Documentation fixes.
Merged from main trunk the capability to parse multiple reports.
Applied Steve L.'s fix for bug #935.
Merged Steve L.'s fixes from branch (bug #935).
Added Alignment output for psiblast searches
Bio::Tools::BPlite::HSP
JB 949 - Creates too many warnings for blastx report. Future enhancement to BPLite::_parseHeader needed to set report type so that subject strand is used with tblastn and query strand with blastx
JB 949 - Creates too many warnings for blastx report. Future enhancement to BPLite::_parseHeader needed to set report type so that subject strand is used with tblastn and query strand with blastx
Fix small scientific values and validate P as numberic (Blast chooses to be different when reporting small values.)
Fix small scientific values and validate P as numberic (Blast chooses to be different when reporting small values.)
Oops method name was supposed to be percent not P
More stringent P checking, method name corrected, again - we lost percent in previous fixes
Bio::Tools::BPlite::Iteration
Added Alignment output for psiblast searches
Bio::Tools::BPlite::Sbjct
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
Bio::Tools::BPpsilite
Remove old doc cruft
Added Alignment output for psiblast searches
Bio::Tools::Blast
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Tools::CodonTable
Translate() rewrite, ~4x faster. Suggested by Amir Karger
Bio::Tools::Fasta
Corrected old mailing lists.
Merging over fixes from branch-07.
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Tools::GFF
Modified the GFF2 parser such that semicolons in the free-text value field of a tag/value pair will not break the parse. It is an ugly hack, and if I ever find time to make it better I promise to go back in and fix it... but it works for now anyway.
Fixed an error reported by Ann Loraine where the GFF attributes parser choked on having a quoted pound sign. It now recognizes quoted pound signs as NOT being the start of the comments field. The first un-quoted pound sign IS considered the start of the comments field. Sorry 'bout that all you who were affected by this.
Silenced perl by properly initializing the infamous loop variable $a. ;)
Merged over some fixes by Mark W. from the main trunk.
Bio::Tools::Genemark
Genemark.hmm eu- and prokaryot (2.2-1.3) parser, a adaptation of Genscan.pm
Small bugfixes + parse out date&matrixfile
Fixed wrong index to determine type of exon.
Updated: recognizes next gene based on gene-number instead of an empty line between two genes
Extacts cds from original sequence now since genemark does not give a predicted cds (my version does not in every case)
Added possibilty to get cds based on original sequence + small bugfixes
Get seqname from seqfile at least for now, Mark F and Jason to hash over details later, this lets test pass in t/Genepred.t
Bio::Tools::Genscan
Added parsing of the matrix name in analysis_subject()
Bio::Tools::Grail
Added Grail skeleton code
Bio::Tools::HMMER::Results
Added updated HMMER files; passes tests
Moved HMMER to main trunk. Fixed 76 --> 77 tests in BPlite
Bio::Tools::Prediction::Exon
Primary tag setting for predicted exon
Undo my bad changes
Bio::Tools::Prediction::Gene
Update mailing list even on those modules that are deprecated
Bio::Tools::RestrictionEnzyme
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Tools::Run::RemoteBlast
Pure perl (via HTTP) Remote blast submission and retrieval -- see test script for example usage
Quieter tests when verbose == 0, use tempfile for HTML -> text cleanup
Fixed tempfile filehandle handling in retrieve_blast().
Updated to use ncbi Blast.cgi script rather than blast.cgi Text formatting done by cgi rather than HTML tag stripping in module code
Status set to invalid on a failed retrieval
Bio::Tools::Run::StandAloneBlast
Io was not initialized, meaning tempfiles were not cleaned up - better argument matching
Intitialize io -- facilitate tempfile cleanup
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
Bio::Tools::SeqAnal
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Tools::SeqPattern
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Tools::SeqStats
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
Bio::Tools::Sigcleave
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Tools::WWW
Corrected mailing lists.
Merging over fixes from branch-07.
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Tools::pSW
Corrected MailList.*s*html link.
Merging over fixes from branch-07.
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
Bio::UnivAln
Major update to Bio::SimpleAlign. New, bioperl-like method names, doc fixes, tests. Changes are backward compatible except that Bio::AlignIO is now the ONLY way to read and write SimpleAligns.
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Variation::AAChange
Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation
Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Variation::AAReverseMutate
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Variation::Allele
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Variation::DNAMutation
Separator was missing from systematic name when mutation was 'complex' Fixed sysname method.
Separator was missing from systematic name when mutation was 'complex' Fixed sysname method.
Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation
Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Variation::IO
Removed redundant 'use Symbol'
Removed redundant 'use Symbol'
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Variation::IO::flat
Fixed Variation::IO::flat insertion locations from "55^55" into "54^55"
Fixed Variation::IO::flat insertion locations from "55^55" into "54^55"
Distance from region edge handled now
Distance from region edge handled now
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Variation::IO::xml
Distance from region edge handled now
Distance from region edge handled now
The xml output now separates each label inside individual element tags rather than pooling all into one.
The xml output now separates labels inot individual tags rather than pooling them into one.
Swapped the order of two elements for consistent output. \nBackward compatibel change
Swapped the order of two elements for consistent output. \nBackward compatibel change
XML::Writer was complaining about empty attribute values. Lesson: always run tests with -w!
XML::Writer was complaining about empty attribute values. Lesson: always run tests with -w!
Moved from XML::Node to XML::Twig in XML parsing
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Variation::RNAChange
Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation
Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Variation::SeqDiff
Fixed method alignment for nontranslated locations
Fixed method alignment for nontranslated locations
Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation
Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Bio::Variation::VariantI
Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation
Distance from region edge handled now, \nSeqDiff alignment recognizes end of translation
$VERSION is $version in all other files exept Bio/Seq.pm (and t/Test.pm)
Makefile.PL
Moved from XML::Node to XML::Twig in XML parsing
Updated MANIFEST and MANIFEST.skip to reflect new files in this distro. Also updated Makefile.PL to change the distro version number to 0.7.1pre --Chris Dagdigian
Update version to 0.7.1 for release
bioperl.lisp
Updated to new Bio::Root::RootI system
Dos2unix and better formatting for us emacs users
bptutorial.pl
Moved from XML::Node to XML::Twig in XML parsing
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
examples/clustalw.pl
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
examples/hitdisplay.pl
Bug #915 verifies that Bio::Tk::HitDisplay is actually installed before running script
Bug #915 verifiesthat Bio::Tk::HitDisplay is actually installed before running script
examples/psw.pl
Updated psw.pl to work with AlignIO.pm
Merged Peter S.'s fixes on the main trunk.
examples/remote_blast.pl
Example of how to use Bio::Tool::Run::RemoteBlast
Doc fix
examples/simplealign.pl
Updated simplealign.pl to work with AlignIO.pm
Merged Peter S.'s changes on the main trunk.
examples/standaloneblast.pl
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
examples/test-genscan.pl
Bug #917
Bug #917
Bug #917 - s/poly_A_sites/poly_A_site/
models/bio_liveseq_variation.dia
Bio::LiveSeq and Bio::Variation diagrams with methods
models/bioperl.dia
Initial commit of bioperl UML -- we can tag it to specify version
Added Bio::Variation UML
Added package for Bio::LiveSeq
scripts/DB/dbfetch
Initial version
Fixed polypeptide mutated allele for frameshifs
scripts/bpfetch.pl
Mailing list doc update
Added support for DB::EMBL and fixed mailing list doc info
scripts/bpindex.pl
Mailing list doc update
Added support for DB::EMBL and fixed mailing list doc info
scripts/gb_to_gff.pl
Turn a genbank file into a gff file suitable for gff2ps
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