bioperl 0.6.1
- Released by
- BIRNEY
- Version
- Release Date
- 2000-05-19
- Kwalitee
- 121.88
- Core Kwalitee
- 78.12
- LINKS
bioperl 0.6.1 Deleted
Kwalitee Issues
- has_meta_yml
-
Add a META.yml to the distribution. Your buildtool should be able to autogenerate it.
- no_files_to_be_skipped
-
Fix MANIFEST.SKIP or use an authoring tool which respects MANIFEST.SKIP. Note that each entry in MANIFEST.SKIP is a regular expression. You may need to add appropriate meta characters not to ignore necessary stuff.
Error: MANIFEST.SKIP,bioperl.lisp
- manifest_matches_dist
-
Run a proper command ("make manifest" or "./Build manifest", maybe with a force option), or use a distribution builder to generate the MANIFEST. Or update MANIFEST manually.
Error:
- MANIFEST (203) does not match dist (206):
- Missing in MANIFEST: MANIFEST.SKIP, bioperl.lisp, t/Species.t
- use_strict
-
Add 'use strict' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules are strictly written.
Error: Bio::Root::Xref
- prereq_matches_use
-
List all used modules in META.yml requires
Error:
- IO::Scalar
- main_module_version_matches_dist_version
-
Make sure that the main module name and version are the same of the distribution.
- no_pod_errors
-
Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.
Error: bioperl-0.6.1/Bio/Root/Err.pm -- Around line 987: Unterminated B<...> sequence bioperl-0.6.1/Bio/Root/Object.pm -- Around line 336: Can't have a 0 in =over 0 bioperl-0.6.1/Bio/Tools/Blast/HSP.pm -- Around line 83: Can't have a 0 in =over 0 bioperl-0.6.1/Bio/Tools/Blast/Run/Webblast.pm -- Around line 344: Can't have a 0 in =over 0 bioperl-0.6.1/Bio/Tools/Blast.pm -- Around line 339: Unterminated B<...> sequence
- has_meta_json
-
Add a META.json to the distribution. Your buildtool should be able to autogenerate it.
- proper_libs
-
Move your *.pm files in a directory named 'lib'. The directory structure should look like 'lib/Your/Module.pm' for a module named 'Your::Module'. If you need to provide additional files, e.g. for testing, that should not be considered for Kwalitee, then you should look at the 'provides' map in META.yml to limit the files scanned; or use the 'no_index' map to exclude parts of the distribution.
Error: Bio/Annotation.pm, Bio/Annotation/Comment.pm, Bio/Annotation/DBLink.pm, Bio/Annotation/Reference.pm, Bio/DB/Ace.pm, Bio/DB/GenBank.pm, Bio/DB/GenPept.pm, Bio/DB/RandomAccessI.pm, Bio/DB/SeqI.pm, Bio/Index/Abstract.pm, Bio/Index/AbstractSeq.pm, Bio/Index/EMBL.pm, Bio/Index/Fasta.pm, Bio/Index/SwissPfam.pm, Bio/LocatableSeq.pm, Bio/PrimarySeq.pm, Bio/PrimarySeqI.pm, Bio/Range.pm, Bio/RangeI.pm, Bio/Root/Err.pm, Bio/Root/Global.pm, Bio/Root/IOManager.pm, Bio/Root/Object.pm, Bio/Root/RootI.pm, Bio/Root/Utilities.pm, Bio/Root/Vector.pm, Bio/Root/Xref.pm, Bio/Search/Hit/Fasta.pm, Bio/Search/Hit/HitI.pm, Bio/Search/Processor.pm, Bio/Search/Processor/Fasta.pm, Bio/Search/Processor/ProcessorI.pm, Bio/Search/Result/Fasta.pm, Bio/Search/Result/ResultI.pm, Bio/SearchDist.pm, Bio/Seq.pm, Bio/SeqFeature/FeaturePair.pm, Bio/SeqFeature/Generic.pm, Bio/SeqFeatureI.pm, Bio/SeqI.pm, Bio/SeqIO.pm, Bio/SeqIO/FTHelper.pm, Bio/SeqIO/MultiFile.pm, Bio/SeqIO/embl.pm, Bio/SeqIO/fasta.pm, Bio/SeqIO/gcg.pm, Bio/SeqIO/genbank.pm, Bio/SeqIO/pir.pm, Bio/SeqIO/raw.pm, Bio/SeqIO/scf.pm, Bio/SeqIO/swiss.pm, Bio/SimpleAlign.pm, Bio/Species.pm, Bio/Tools/AlignFactory.pm, Bio/Tools/Blast.pm, Bio/Tools/Blast/HSP.pm, Bio/Tools/Blast/HTML.pm, Bio/Tools/Blast/Run/LocalBlast.pm, Bio/Tools/Blast/Run/Webblast.pm, Bio/Tools/Blast/Sbjct.pm, Bio/Tools/CodonTable.pm, Bio/Tools/Fasta.pm, Bio/Tools/HMMER/Domain.pm, Bio/Tools/HMMER/Results.pm, Bio/Tools/HMMER/Set.pm, Bio/Tools/IUPAC.pm, Bio/Tools/RestrictionEnzyme.pm, Bio/Tools/SeqAnal.pm, Bio/Tools/SeqPattern.pm, Bio/Tools/SeqStats.pm, Bio/Tools/SeqWords.pm, Bio/Tools/Sigcleave.pm, Bio/Tools/Sim4/Exon.pm, Bio/Tools/Sim4/Results.pm, Bio/Tools/WWW.pm, Bio/Tools/pSW.pm, Bio/UnivAln.pm
- meta_yml_has_license
-
Define the license if you are using in Build.PL. If you are using MakeMaker (Makefile.PL) you should upgrade to ExtUtils::MakeMaker version 6.31.
- use_warnings
-
Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.
Error: Bio::Annotation, Bio::Annotation::Comment, Bio::Annotation::DBLink, Bio::Annotation::Reference, Bio::DB::Ace, Bio::DB::GenBank, Bio::DB::GenPept, Bio::DB::RandomAccessI, Bio::DB::SeqI, Bio::Index::Abstract, Bio::Index::AbstractSeq, Bio::Index::EMBL, Bio::Index::Fasta, Bio::Index::SwissPfam, Bio::LocatableSeq, Bio::PrimarySeq, Bio::PrimarySeqI, Bio::Range, Bio::RangeI, Bio::Root::Err, Bio::Root::Global, Bio::Root::IOManager, Bio::Root::Object, Bio::Root::RootI, Bio::Root::Utilities, Bio::Root::Vector, Bio::Root::Xref, Bio::Search::Hit::Fasta, Bio::Search::Hit::HitI, Bio::Search::Processor, Bio::Search::Processor::Fasta, Bio::Search::Processor::ProcessorI, Bio::Search::Result::Fasta, Bio::Search::Result::ResultI, Bio::SearchDist, Bio::Seq, Bio::SeqFeature::FeaturePair, Bio::SeqFeature::Generic, Bio::SeqFeatureI, Bio::SeqI, Bio::SeqIO, Bio::SeqIO::FTHelper, Bio::SeqIO::MultiFile, Bio::SeqIO::embl, Bio::SeqIO::fasta, Bio::SeqIO::gcg, Bio::SeqIO::genbank, Bio::SeqIO::pir, Bio::SeqIO::raw, Bio::SeqIO::scf, Bio::SeqIO::swiss, Bio::SimpleAlign, Bio::Species, Bio::Tools::AlignFactory, Bio::Tools::Blast, Bio::Tools::Blast::HSP, Bio::Tools::Blast::HTML, Bio::Tools::Blast::Run::LocalBlast, Bio::Tools::Blast::Run::Webblast, Bio::Tools::Blast::Sbjct, Bio::Tools::CodonTable, Bio::Tools::Fasta, Bio::Tools::HMMER::Domain, Bio::Tools::HMMER::Results, Bio::Tools::HMMER::Set, Bio::Tools::IUPAC, Bio::Tools::RestrictionEnzyme, Bio::Tools::SeqAnal, Bio::Tools::SeqPattern, Bio::Tools::SeqStats, Bio::Tools::SeqWords, Bio::Tools::Sigcleave, Bio::Tools::Sim4::Exon, Bio::Tools::Sim4::Results, Bio::Tools::WWW, Bio::Tools::pSW, Bio::UnivAln
- consistent_version
-
Split the distribution, or fix the version numbers to make them consistent (use the highest version number to avoid version downgrade).
Error: 0.01,0.011,0.014,0.04,0.041,0.043,0.05,0.076,0.09,0.091,0.1,0.2,1.01,1.24
- has_separate_license_file
-
This is not a critical issue. Currently mainly informative for the CPANTS authors. It might be removed later.
- has_security_doc
-
Add SECURITY(.pod|md). See Software::Security::Policy.
- security_doc_contains_contact
-
Add SECURITY(.pod|md) and add a contact address. See Software::Security::Policy.
- has_contributing_doc
-
Add CONTRIBUTING(.pod|md). See https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors.
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::Annotation | A generic object for annotations | metacpan | |
| Bio::Annotation::Comment | A Comment on an Annotation | metacpan | |
| Bio::Annotation::DBLink | Database Link | metacpan | |
| Bio::Annotation::Reference | Literature Reference Block | metacpan | |
| Bio::DB::Ace | Database object interface to ACeDB servers | metacpan | |
| Bio::DB::GenBank | Database object interface to GenBank | metacpan | |
| Bio::DB::GenPept | Database object interface to GenPept | metacpan | |
| Bio::DB::RandomAccessI | Abstract interface for a sequence database | metacpan | |
| Bio::DB::SeqI | Abstract Interface for Sequence databases | metacpan | |
| Bio::Index::Abstract | Abstract interface for indexing a flat file | metacpan | |
| Bio::Index::AbstractSeq | Base class for AbstractSeq's | metacpan | |
| Bio::Index::EMBL | Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format). | 0.1 | metacpan |
| Bio::Index::Fasta | Interface for indexing (multiple) fasta files | 0.2 | metacpan |
| Bio::Index::SwissPfam | Interface for indexing swisspfam files | 0.1 | metacpan |
| Bio::LocatableSeq | A Sequence object with start/end points on it | metacpan | |
| Bio::PrimarySeq | Bioperl lightweight Sequence Object | metacpan | |
| Bio::PrimarySeqI | Interface definition for a Bio::PrimarySeq | metacpan | |
| Bio::Range | Pure perl RangeI implementation | metacpan | |
| Bio::RangeI | Range interface | metacpan | |
| Bio::Root::Err | 0.041 | metacpan | |
| Bio::Root::Global | Global variables and utility functions | metacpan | |
| Bio::Root::IOManager | Input and output manager for Perl5 objects. | 0.043 | metacpan |
| Bio::Root::Object | A core Perl 5 object. | 0.041 | metacpan |
| Bio::Root::RootI | Abstract interface to root object code | metacpan | |
| Bio::Root::Utilities | General-purpose utility module | 0.05 | metacpan |
| Bio::Root::Vector | Interface for managing linked lists of Perl5 objects. | 0.04 | metacpan |
| Bio::Root::Xref | A generic cross-reference object. | 0.01 | metacpan |
| Bio::Search::Hit::Fasta | Hit object specific for Fasta-generated hits | metacpan | |
| Bio::Search::Hit::HitI | Abstract interface for Hit objects | metacpan | |
| Bio::Search::Processor | DESCRIPTION of Object | metacpan | |
| Bio::Search::Processor::Fasta | Processor of Fasta-generated data streams | metacpan | |
| Bio::Search::Processor::ProcessorI | Abstract Interface for Processor Objects | metacpan | |
| Bio::Search::Result::Fasta | Result object for FASTA-generated data sources | metacpan | |
| Bio::Search::Result::ResultI | metacpan | ||
| Bio::SearchDist | A perl wrapper around Sean Eddy's histogram object | metacpan | |
| Bio::Seq | Sequence object, with features | metacpan | |
| Bio::SeqFeature::FeaturePair | hold pair feature information e.g. blast hits | metacpan | |
| Bio::SeqFeature::Generic | Generic SeqFeature | metacpan | |
| Bio::SeqFeatureI | Abstract interface of a Sequence Feature | metacpan | |
| Bio::SeqI | Abstract Interface of Sequence (with features) | metacpan | |
| Bio::SeqIO | Handler for SeqIO Formats | metacpan | |
| Bio::SeqIO::FTHelper | Helper class for Embl/Genbank feature tables | metacpan | |
| Bio::SeqIO::MultiFile | Treating a set of files as a single input stream | metacpan | |
| Bio::SeqIO::embl | EMBL sequence input/output stream | metacpan | |
| Bio::SeqIO::fasta | fasta sequence input/output stream | metacpan | |
| Bio::SeqIO::gcg | GCG sequence input/output stream | metacpan | |
| Bio::SeqIO::genbank | metacpan | ||
| Bio::SeqIO::pir | PIR sequence input/output stream | metacpan | |
| Bio::SeqIO::raw | raw sequence file input/output stream | metacpan | |
| Bio::SeqIO::scf | SCF sequence input/output stream | metacpan | |
| Bio::SeqIO::swiss | metacpan | ||
| Bio::SimpleAlign | metacpan | ||
| Bio::Species | Generic species object | metacpan | |
| Bio::Tools::AlignFactory | Base object for alignment factories | metacpan | |
| Bio::Tools::Blast | 0.09 | metacpan | |
| Bio::Tools::Blast::HSP | 0.09 | metacpan | |
| Bio::Tools::Blast::HTML | 0.076 | metacpan | |
| Bio::Tools::Blast::Run::LocalBlast | 0.01 | metacpan | |
| Bio::Tools::Blast::Run::Webblast | 1.24 | metacpan | |
| Bio::Tools::Blast::Sbjct | 0.091 | metacpan | |
| Bio::Tools::CodonTable | Bioperl codon table object | metacpan | |
| Bio::Tools::Fasta | 0.014 | metacpan | |
| Bio::Tools::HMMER::Domain | One particular domain hit from HMMER | metacpan | |
| Bio::Tools::HMMER::Results | Object representing HMMER output results | metacpan | |
| Bio::Tools::HMMER::Set | Set of identical domains from HMMER matches | metacpan | |
| Bio::Tools::IUPAC | metacpan | ||
| Bio::Tools::RestrictionEnzyme | 0.04 | metacpan | |
| Bio::Tools::SeqAnal | 0.011 | metacpan | |
| Bio::Tools::SeqPattern | 0.011 | metacpan | |
| Bio::Tools::SeqStats | Object holding statistics for one particular sequence | metacpan | |
| Bio::Tools::SeqWords | Object holding n-mer statistics for one sequence | metacpan | |
| Bio::Tools::Sigcleave | 0.01 | metacpan | |
| Bio::Tools::Sim4::Exon | A single | metacpan | |
| Bio::Tools::Sim4::Results | Results of one Sim4 run | metacpan | |
| Bio::Tools::WWW | 0.014 | metacpan | |
| Bio::Tools::pSW | DESCRIPTION of Object | metacpan | |
| Bio::UnivAln | Bioperl alignment object | 1.01 | metacpan |