Core 0.6.1 0.6.2 delta

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These are detailed notes on changes made between bioperl-06-1 and release-06-2.

Bio::AlignIO
Initial install of AlignIO files
Bio::AlignIO::clustalw
Initial install of AlignIO files
Bio::AlignIO::fasta
Initial install of AlignIO files
Bio::AlignIO::mase
Initial install of AlignIO files
Bio::AlignIO::msf
Initial install of AlignIO files
Bio::AlignIO::pfam
Initial install of AlignIO files
Bio::AlignIO::prodom
Initial install of AlignIO files
Bio::AlignIO::selex
Initial install of AlignIO files
Bio::AlignIO::stockholm
Initial install of AlignIO files
Bio::Annotation
added CVS ID tag to top of module. cdagdigian
Added object type test to ->add_DBLink and fixed examples in synopsis
Added functions for removing
Some doc bugs (updating mailing address for bioperl)
Bio/Annotation.pm - update for 0.6.2 o corrected whitespace in SYNOPSIS (C) o corrected SYNOPSIS to talk about $link->database rather than $link->db (D) o corrected ->add_Reference documentation line (D) o added check to see if argument isa() Bio::Annotation::DBLink in add_DBLink (B)
Bio::Annotation::DBLink
Added examples and ->_initialize code
Bio::Annotation::Reference
Removed implementation of comment() -- is inherited. Added pubmed(). Changed database() to allow for changing the hard-coded default MEDLINE.
Corrected a left-over from copy-and-paste.
Fixed doc of rp(). Given the code, the value supplied is never parsed, regardless of its contents.
Fixed bug in _initialize(): args were not passed on.
Comitted apparently forgotten minor fixes.
Fixed propagation of arguments to delegation methods.
Bio::DB::GenBank
Added the option to set and change the retrieval format. So far, GenBank and Fasta are supported. See method request_format().
Forgot get_Seq_by_id().
Bio::DB::GenPept
Bug#242
Bug #243 and more error checking
Added capability to retrieve sequences in both Genbank and Fasta format. See request_format().
Bio::DB::RandomAccessI
Needed a space before =head
Bio::DB::UpdateableSeqI
Added updateable seq interface
Bio::DBLinkContainerI
added CVS ID tag and updated email-list address info. cdagdigian
Bio::Index::Abstract
added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.
Add throw on make index on write only
Merged stable branch fixes in
Fix to Bio::Root::RootI::_rearrange method which assigned empty strings to variables when called without arguments. Added allow_relative_paths() to Bio::Index::Abstract Added throwing an exception to Bio::Index::AbstractSeq::fetch if ID given is not in index.
Bio::Index::AbstractSeq
Changed abstractseq
Did kris fix to abstractseq.pm
V. minor tidy up
V. minor tidy up
Fixed AbstractSeq.pm so it doesn't throw an exception if the seq requested isn't in the index
added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.
Fixed get_all_primary_ids bug
Merged in changes from stable
Fix to Bio::Root::RootI::_rearrange method which assigned empty strings to variables when called without arguments. Added allow_relative_paths() to Bio::Index::Abstract Added throwing an exception to Bio::Index::AbstractSeq::fetch if ID given is not in index.
Excessive compulsive checking on object before adding primary_id
Documentation fix and insure $seq exists before calling $seq->primary_id()
Bio::Index::EMBL
added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.
Fixed abstract to throw on readonly write; fixed documentation bugs
Merged stable branch fixes in
Bio::Index::Fasta
added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.
Fixed abstract to throw on readonly write; fixed documentation bugs
Merged stable branch fixes in
Bio::Index::GenBank
added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.
Bio::Index::SwissPfam
added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.
Bio::Index::Swissprot
Added Swissprot index file
added CVS Id tags and updated bioperl mailing list info where necessary. cdagdigian.
Bio::LocatableSeq
Some doc bugs (updating mailing address for bioperl)
Fixed sort_alphabetically bug
Merged simpled align bug fixes across
Bio::PrimarySeq
Made some changes to improve efficiency when working with large sequences: - Deleted the line in seq() that needlessly made an extra copy of the sequence just before the method returned. - subseq() uses data members directly instead of the accessor method call (i.e., $self->{'seq'} instead of $self->seq()). This may upset the OO purists, but for simple accessors within the class that manages the data, I think it is fine.
Made some changes to improve efficiency when working with large sequences: - Deleted the line in seq() that needlessly made an extra copy of the sequence just before the method returned. - Added definition of length() (moved from PrimarySeqI.pm. This prevents another sequence from being created when PrimarySeqI::length() called seq(). - subseq(), length() use data members directly instead of the get accessor method call (i.e., $self->{'seq'} instead of $self->seq()). This may upset the OO purists, but for simple accessors within the class that manages the data, I think it is fine.
Fixed bug in SeqIO/(embl|genbank) which caused accession to become "unknown". Was due to Bio::PrimarySeq being made directly, which is not necessary.
Some doc bugs (updating mailing address for bioperl)
Move bug fixes of simplealign and rev_and_trans to main trunk
Bio::PrimarySeqI
Made some changes to improve efficiency when working with large sequences: - Made length() virtual so that it must be defined in concrete subclasses (PrimarySeq::length()) where it can call CORE::length() directly on its seq data member. This prevents another sequence from being created when PrimarySeqI::length() called seq().
Added code into the translate method to replace the first amino acid into M if it is not M and the codon is valid the initiator codon.
Fixed method translate to put M as the first amino acid when the first codon is a valid initiator codon
Added seq ID when warning for non initiator start codon (warns only when verbose is true)
Fixed molecular weight bug in SeqStats.pm where Mwts were calculated without taking into account H20
2nd attempt on fixing initator codons in translate
Some doc bugs (updating mailing address for bioperl)
Fixed subtle bug wrt to Ensembl. We need translate to give the completely computationally "unedited" translation. New option to translate function in PrimarySeqI to not edit. Probably should move this out into a Util area and make interfaces pure sometime....
Fixed seqpattern case bug
Small changes in revcom() and trunc() to retain the description in the returned sequence object.
Handle null $char vals
Fixed GCG_checksum to handle null $char values
Final fixes?
Bio::Range
ToString() now includes strand information.
ToString() now includes strand information.
Doc fix
Some doc bugs (updating mailing address for bioperl)
Bio::RangeI
- Modified intersection() and union() to preserve strand information if the strands of all ranges being compared are the same. Otherwise, strand in the result is 0. Previously, it was always returning 0 for strand. - Fixed calls to _testStrand() to include the range object being compared. Previously, some salls to _testStrand() only included the strand option scalar. - Fixed bug in _strong(): using = instead of ==
- Modified intersection() and union() to preserve strand information if the strands of all ranges being compared are the same. Otherwise, strand in the result is 0. Previously, it was always returning 0 for strand. - Fixed calls to _testStrand() to include the range object being compared. Previously, some salls to _testStrand() only included the strand option scalar. - Fixed bug in _strong(): using = instead of ==
Some doc bugs (updating mailing address for bioperl)
Bio::Root::Err
updated mailing list address info where necessary. cdagdigian.
Silly doc bug
Doc fix
Bio::Root::Global
updated mailing list address info where necessary. cdagdigian.
Bio::Root::IOManager
updated mailing list address info where necessary. cdagdigian.
Bio::Root::Object
updated mailing list address info where necessary. cdagdigian.
Moved _set_warning from Bio::Root::Object to Bio::Root::RootI, because RootI needs it
Moved _set_err_state from Bio::Root::Object to Bio::Root::RootI, because RootI needs it
Moved subs _set_warning and _set_err_state from Bio::Root::Object to Bio::Root::RootI
Bio::Root::RootI
updated mailing list address info where necessary. cdagdigian.
Moved _set_warning from Bio::Root::Object to Bio::Root::RootI, because RootI needs it
Moved _set_err_state from Bio::Root::Object to Bio::Root::RootI, because RootI needs it
Moved subs _set_warning and _set_err_state from Bio::Root::Object to Bio::Root::RootI
Verbosity undef caused some silly errors
Fix to Bio::Root::RootI::_rearrange method which assigned empty strings to variables when called without arguments. Added allow_relative_paths() to Bio::Index::Abstract Added throwing an exception to Bio::Index::AbstractSeq::fetch if ID given is not in index.
Bio::Root::Utilities
Fixed bug in create_filehandle(). Now checks that client is a ref.
updated mailing list address info where necessary. cdagdigian.
Added some move validation on client before running get_newline
Ref() instead of !
Bio::Root::Vector
updated mailing list address info where necessary. cdagdigian.
Bio::Root::Xref
updated mailing list address info where necessary. cdagdigian.
Bio::SearchDist
Some doc bugs (updating mailing address for bioperl)
Bio::Seq
Fixed add_SeqFeature in Bio::SeqFeature::Generic, and added tests to t/SeqFeature.t
Made some changes to improve efficiency when working with large sequences: - Add length() method to Seq.pm that delegates to its PrimarySeq. This is necessary now that PrimarySeqI::length() is virtual. - subseq() uses data members directly instead of the accessor method call (i.e., $self->{'primary_seq'} instead of $self->primary_seq()). This may upset the OO purists, but for simple accessors within the class that manages the data, I think it is fine.
Bio/Seq.pm: added a new method, feature_count(), which returns the number of SeqFeature objects contained in a sequence. Bio/SeqIO/embl.pm: changed next_seq() to handle EMBL files without feature table (FH/FT) or incomplete FT (FH without FT). changed write_seq() to only write FH lines if there are SeqFeatures to write out (uses feature_count() method)
Method accession now references method accession_number and data is no longer stored in $obj->{'accession'}.
Changed reference from $seq->accession to $seq->accession_number and made accession routine point to accession_number in Bio::Seq
Fixed add_SeqFeature -- now correctly adds a primary_seq
Fixed version bug
Fixed bug in SeqIO/(embl|genbank) which caused accession to become "unknown". Was due to Bio::PrimarySeq being made directly, which is not necessary.
Doc fix (update mailing list addres)
Removed sub_species(). Use $seq->species()->sub_species() for that.
Final fixes?
Bio::Seq::LargePrimarySeq
Added LargePrimarySeq in Bio::Seq; added test; removed annoying EMBL test case; tests pass
Added a check for existence of fh before trying to close
Bio::SeqAnalysisParserI
Interfaces for abstracting automated feature additions from analysis program output
Fixed a bug in parse() doc.
Bio::SeqFeature::FeaturePair
Added has_tag() and each_tag_value() as dummies (they are required by SeqFeatureI).
Removed methods implementing Bio::SeqFeatureI required methods without functionality. Changed to inherit off Bio::SeqFeature::Generic.
Removed methods implementing Bio::SeqFeatureI required methods without functionality. Changed to inherit off Bio::SeqFeature::Generic.
Fixed unquoted hash keys.
Corrected a bug in _initialize(): @args were not passed on.
Removed length() (inherited).
Bio::SeqFeature::GeneStructure
Initial revision.
Bug corrections. Added correct_phase() and the option to call it in cds().
Added the option to provide the id of the codon table to be used to cds().
Fixed bug #842.
Fixed documentation (NAME section).
Removed _tag_value (moved to SeqFeature::Generic).
Corrected a bug in cds().
Bio::SeqFeature::Generic
Fixed add_SeqFeature in Bio::SeqFeature::Generic, and added tests to t/SeqFeature.t
Corrected a bug in _initialize() preventing tag/value pairs passed to the constructor to be set properly.
Fixed frame() (allowed for 1,2,3 instead of 0,1,2). Added annotation().
Splitted out _expand_region() from add_sub_SeqFeature(). This may be usefule for derived classes as well.
BPlite now uses Bio::SeqFeature::SimilarityPair instead of FeaturePair
Made some fixes on the branch for checking start/end feature sets and other things
Fixed bug #848 (had already been fixed on the main trunk).
Fix to Bio::Root::RootI::_rearrange method which assigned empty strings to variables when called without arguments. Added allow_relative_paths() to Bio::Index::Abstract Added throwing an exception to Bio::Index::AbstractSeq::fetch if ID given is not in index.
Added _tag_value(). This seems to be useful for many derived modules.
Small modification to add_sub_SeqFeature() in order to suppress 'uninitialized value' warnings. (do we really need equality to EXPAND instead of just something evaluating to TRUE?)
Fixed strand() and frame() to catch attempts to set to undefined.
Bio::SeqFeature::Similarity
Initial revision.
Fixed bug #842.
Fixed documentation (NAME section). Added documentation.
Removed _tag_value (moved to SeqFeature::Generic).
Bio::SeqFeature::SimilarityPair
Initial revision.
Fixed documentation (NAME section).
Corrected a doc bug and a code bug.
Fixed the propagation of arguments to delegation methods.
Bio::SeqFeatureI
Corrected the documentation of has_tag() to correctly reflect naming and implementation as, e.g., implemented in SeqFeature::Generic.
Made example code 'actually' work (missing some commas)
Further corrected documentation. Added each_tag_value() as a consequence of the has_tag() fix.
Some doc bugs (updating mailing address for bioperl)
Fixed documentation. Added missing each_tag_value(). (Fixes propagated from the main trunk.)
Small change in gff_string to get rid of 'uninitialized value' warnings.
Bio::SeqFeatureProducerI
SeqFeatureProducerI and GFF implementor added for producing sequence features
MZEF SeqFeatureProducer added
Corrected doc bugs (and spelling of my name :-)
Interfaces for abstracting automated feature additions from analysis program output
Added SeqFeatureProducer interface
Fixed documentation (NAME section).
Bio::SeqI
Some doc bugs (updating mailing address for bioperl)
Bio::SeqIO
Added _concatenate_lines() needed to fix a bug in embl.pm. May be useful for other SeqIO modules, too.
Added _concatenate_lines() needed to fix a bug in embl.pm. May be useful for other SeqIO modules, too.
Bio::SeqIO::FTHelper
Updated mailing list address on maintrunk
Bio::SeqIO::GAMEHandler
Updated mailing list address on maintrunk
Bio::SeqIO::MultiFile
Updated mailing list address on maintrunk
Bio::SeqIO::ace
Updated mailing list address on maintrunk
Bio::SeqIO::bioxml
Updated mailing list address on maintrunk
Bio::SeqIO::embl
Bio/Seq.pm: added a new method, feature_count(), which returns the number of SeqFeature objects contained in a sequence. Bio/SeqIO/embl.pm: changed next_seq() to handle EMBL files without feature table (FH/FT) or incomplete FT (FH without FT). changed write_seq() to only write FH lines if there are SeqFeatures to write out (uses feature_count() method)
Changed reference from $seq->accession to $seq->accession_number to provide a cleaner inteface (and eliminate confusion as to where accession is actually stored)
Changed reference from $seq->accession to $seq->accession_number and made accession routine point to accession_number in Bio::Seq
Fixed molecular weight bug in SeqStats.pm where Mwts were calculated without taking into account H20
Fixed bug in SeqIO/(embl|genbank) which caused accession to become "unknown". Was due to Bio::PrimarySeq being made directly, which is not necessary.
Fixed DE lines not being added to "desc" field
Genbank and embl SeqIO description fixes
Some error checking
Fixed accession number reference
Propagated some fixes concerning accnr and prim.seq. setting in order to test for bug fix.
Fixed all issues reported in #239 (partly in a different way, some were already fixed).
Fixed all issues reported in #239 (partly in a different way, some were already fixed).
Propagated fixes from the main trunk in order to be able to test.
Removed superfluous label.
Updated mailing list address on maintrunk
Bio::SeqIO::fasta
Changed Bio::SeqIO::fasta::write_seq to check that the "desc" method can be called before calling it
Changed SeqIO::fasta to see if a seq can "desc" before it calls desc
Fixed bug #254.
Corrected next_seq() to be able to deal with even more consecutive greater chars in the description.
Fixed mailing list address
Updated mailing list address on maintrunk
Handle > in the description line of fasta files hilmar's fix propigated to branch from main trunk
Bio::SeqIO::gcg
Updated mailing list address on maintrunk
Bio::SeqIO::genbank
Changed reference from $seq->accession to $seq->accession_number to provide a cleaner inteface (and eliminate confusion as to where accession is actually stored)
Changed reference from $seq->accession to $seq->accession_number and made accession routine point to accession_number in Bio::Seq
Added handling for featureless files
Adj LOCUS pattern in case Date is not in GenBank file
Fixed bug #833. Partially revised and fixed read_GenBank_References, there were other bugs, too, which haven't been exposed yet.
Fixed the code to be able to deal with GenPept. Tried to tidy up some of the branching etc in next_seq().
Fixed bug in SeqIO/(embl|genbank) which caused accession to become "unknown". Was due to Bio::PrimarySeq being made directly, which is not necessary.
Fixed DE lines not being added to "desc" field
Genbank and embl SeqIO description fixes
Fixed bug #838: qualifiers not satisfying the /tag=value syntax are reported through warn(), not throw().
Bug 838 and accession_number to accession routine migration
Fix to Bio::Root::RootI::_rearrange method which assigned empty strings to variables when called without arguments. Added allow_relative_paths() to Bio::Index::Abstract Added throwing an exception to Bio::Index::AbstractSeq::fetch if ID given is not in index.
Removed _filehandle() -- is inherited.
Updated mailing list address on maintrunk
Bio::SeqIO::pir
Made some fixes on the branch for checking start/end feature sets and other things
Updated mailing list address on maintrunk
Bio::SeqIO::raw
Updated mailing list address on maintrunk
Bio::SeqIO::scf
Updated mailing list address on maintrunk
Bio::SeqIO::swiss
Changed reference from $seq->accession to $seq->accession_number to provide a cleaner inteface (and eliminate confusion as to where accession is actually stored)
Changed reference from $seq->accession to $seq->accession_number and made accession routine point to accession_number in Bio::Seq
Small bugfix
Another small fix
Improved writing functionality
Reference to $acc was not correct
Even more improved writing, thx to james gilbert and andrew su
Added swiss format to scripts
Fixed bug #839: display_id() used for default construction of the id-line.
Fixed mailing list doc.
Merged swiss-prot fix for bug 839
Added _$div back to swiss output
Removed again _$div from output ID line generation. Guys, you cannot have there $seq->display_id()."_".$div, it is simply wrong. display_id() is set to the *full* ID (primary_id()."_".$div) in next_seq(), and adding $div a second time cannot be correct. This also means that any sequence _read_ by swiss.pm should have the correct ID on output. If this is not the case for you please indicate an example record (hlapp@gmx.net). In addition, it makes seqs retrieved from GenPept being written with at least the correct ID, which is essential IMHO.
Revoked my bad edit on the branch (adding _div) - see Hilmar's message for good explaination
Some bugfixes and enhancements for writing (viruses!)
Corrected a comment.
RX line now using optional PubMed method from Annotation::Reference
Fixed bug consisting of explicit creation of PrimarySeq.
Applied primary_seq fix in next_seq().
Added warning to write_seq(). DO NOT propagate this to the main trunk.
Bio::SimpleAlign
Fixed bug #826 by applying the provided fix. Added file descriptor to another print statement (not sure whether this is correct).
Fixed bug #827 with the solution given there.
Fixed bugs #840 (fasta in simplealign) #845 (rev_and_trans.pl in examples)
Move bug fixes of simplealign and rev_and_trans to main trunk
Fixed sort_alphabetically bug
Merged simpled align bug fixes across
Final fixes?
Bio::Tools::Alignment::Clustalw
Initial commit of clustalw wrapper files
Bio::Tools::AnalysisResult
Initial revision.
Bio::Tools::BPlite
Added BPlite module and began porting...
First running version of BPlite port
Small enhancemants to BPlite module, added test script
Small fix in ->seqname
BPlite now uses Bio::SeqFeature::SimilarityPair instead of FeaturePair
Bio::Tools::BPlite::HSP
First running version of BPlite port
Small enhancemants to BPlite module, added test script
BPlite now uses Bio::SeqFeature::SimilarityPair instead of FeaturePair
Bio::Tools::BPlite::Sbjct
First running version of BPlite port
Small enhancemants to BPlite module, added test script
BPlite now uses Bio::SeqFeature::SimilarityPair instead of FeaturePair
Bio::Tools::Blast
Fixed false (in the sense that Perl complains) range in [\w-.] to [\w-\.].
Fixed failure on empty (single) reports. Fixed ambiguous [] range in regexp.
Fixed regexps in hit() to unambiguously identify the options.
Silly doc bug
Doc fix
Fixed bugs #834 and #835.
Synchronized with the head version (there were solely bug fixes).
Bio::Tools::CodonTable
Fixed speed problem in translate method as suggested by Kim Rutherford <kmr@sanger.ac.uk>
Method translate now is faster when there are no ambuigities in the codon. Fix suggested by Kim Rutherford <kmr@sanger.ac.uk>
Corrected a bug affecting terminator codons in ->revtranslate
Fixed bug in ->revtranslaed affecting stop codons
Documentation changes
Added a note in the documentaion that translation from codon table 11, "Bacterial" is identical to the standard tranlation.
Bio::Tools::ESTScan
Initial revision.
Fixed the remaining bug in next_prediction() for reverse strand strand predictions.
Bio::Tools::Genscan
Initial revision.
Corrected a small documentation legacy left over.
Changed storage of predicted sequences to storing Bio::PrimarySeq objects. Recorded Ns prepended to predicted CDS as frame.
Fixed a potential incompatibility with Perl 5.6.0.
Reorganized some of the initialization code. Adapted in order to implement the SeqAnalysisParserI interface.
Fixed a doc bug.
Fixed a potential bug in re-initialization (wasn't an issue before).
Adapted to inheriting and utilizing Bio::Tools::AnalysisResult.
Corrected storing of method and version as parsed from the result file.
Corrected a bug assigning the wrong predicted protein/CDS if there were predictions not giving rise to a sequence (e.g. promotor only).
Bio::Tools::HMMER::Domain
Changed to inherit off Bio::SeqFeature::FeaturePair directly.
Changed to inherit off Bio::SeqFeature::FeaturePair directly.
Bio::Tools::MZEF
Initial revision.
Adapted to inherit off Bio::Tools::AnalysisResult.
Bio::Tools::OddCodes
Added OddCodes
Bio::Tools::Prediction::Exon
Initial revision.
Fixed bug #842.
Fixed documentation (NAME section).
Removed _tag_value (moved to SeqFeature::Generic). Added predicted_cds() and predicted_protein().
Bio::Tools::Prediction::Gene
Initial revision.
Changed documentation of predicted_protein() and predicted_cds() to return/accept Bio::PrimarySeqI objects instead of strings -- however, it is not ensured currently.
Fixed doc bug.
Bio::Tools::SeqPattern
Fixed seqpattern case bug
Bio::Tools::SeqStats
Fixed molecular weight bug in SeqStats.pm where Mwts were calculated without taking into account H20
SeqStats.pm: minor documentation corrections
Bio::Tools::Sim4::Exon
Fixed sim4 code to compile
Revised code and documentation. Fixed _initialize(). Added est_hit() for clarity.
Remove Sim4 parser because it was never functional.
Added and corrected documentation. Changed to inherit off Bio::SeqFeature::SimilarityPair. Changed percentage_id() to alias to frac_identical() if supported.
Bio::Tools::Sim4::ExonSet
Added ExonSet object
Removed because no longer needed.
Bio::Tools::Sim4::Results
Major code revision. New functions for parsing (parse_next_alignment, and next_exonset). Adapted documentation. No longer depends on ExonSet. Tests ok so far.
Small codefix to remove a legacy left-over.
Remove Sim4 parser because it was never functional.
Modified to inherit off Bio::Tools::AnalysisResult and implement Bio::SeqAnalysisParserI. Improved code in parse_next_alignment by adding fall-backs.
Bio::Tools::pSW
Bug #823
Fixed bug #824 (Bio::Seq instead of Bio::LocatableSeq).
Final fixes?
Bio::UnivAln
Fixed bug #832.
Defined (@array) is deprecated
Fixed doc bug and defined(@array)
Not using ary function on seqs
Bio::Variation::AAChange
The first version of Bio::Variation classes and 185 tests.
Bio::Variation::AAReverseMutate
The first version of Bio::Variation classes and 185 tests.
Bio::Variation::Allele
The first version of Bio::Variation classes and 185 tests.
Bio::Variation::DNAMutation
The first version of Bio::Variation classes and 185 tests.
Bio::Variation::IO
The first version of Bio::Variation classes and 185 tests.
Bio::Variation::IO::flat
The first version of Bio::Variation classes and 185 tests.
Bio::Variation::IO::xml
The first version of Bio::Variation classes and 185 tests.
Bio::Variation::MutationI
The first version of Bio::Variation classes and 185 tests.
Added my mistake.
Bio::Variation::README
A general introductin to Bio::Variation classes.
Bio::Variation::RNAChange
The first version of Bio::Variation classes and 185 tests.
Bio::Variation::SeqDiff
The first version of Bio::Variation classes and 185 tests.
Bio::Variation::VariantI
The first version of Bio::Variation classes and 185 tests.
Makefile.PL
Final fixes?
examples/gsequence
Just renamed
examples/gsequence.pl
Added script to cvs
Just renamed
examples/rev_and_trans.pl
Fixed bugs #840 (fasta in simplealign) #845 (rev_and_trans.pl in examples)
Move bug fixes of simplealign and rev_and_trans to main trunk
examples/test-genscan.pl
Initial revision.
Adapted to API change in Bio::Tools::Prediction::Gene.
scripts/blast_fetch.pl
Added simple script to parse a blast file and download all the sequences automagically from genbank
More versitile blast parse + download seqs example script
scripts/bpfetch.pl
Added swiss format to scripts
scripts/bpindex.pl
Added swiss format to scripts
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