README

This is the README file for the BioPerl central distribution.

o Getting Started

 Please see the the INSTALL or INSTALL.WIN documents for installation
 instructions.

o About BioPerl

 BioPerl is a package of public domain Perl tools for computational
 molecular biology.

 Our website, http://bioperl.org/, provides an online resource of
 modules, scripts, and web links for developers of Perl-based software
 for life science research.

o Contact info

 BioPerl mailing list: bioperl-l@bioperl.org

 Project website : http://bioperl.org/

 Bug reports : https://github.com/bioperl/bioperl-live/issues

     Please send us bugs, in particular about documentation which you
     think is unclear or problems in installation. We are also very
     interested in functions which don't work the way you think they
     do!

o The directory structure

 The BioPerl directory structure is organized as follows:

   - Bio/ - BioPerl modules

   - deobfuscator/ - Code for tracing OOP relationships

   - examples/ - Scripts demonstrating the many uses of BioPerl

   - ide/ - files for developing BioPerl using an IDE

   - maintenance/ - BioPerl housekeeping scripts

   - models/ - DIA drawing program generated OO UML for BioPerl classes
               (these are quite out-of-date)

   - scripts/ - Useful production-quality scripts with POD documentation

   - t/ - Perl built-in tests, tests are divided into subdirectories 
          based on the specific classes being tested

   - t/data/ - Data files used for the tests, provides good example data

   - travis_scripts/ - script to customize Travis


o Documentation

 For documentation on BioPerl see the HOWTO documents at 
 http://www.bioperl.org/wiki/HOWTOs.

 Useful documentation in the form of example code can also be found in
 the examples/ and scripts/ directories. The current collection
 includes scripts that run BLAST, index flat files, parse PDB
 structure files, make primers, retrieve ESTs based on tissue, align
 protein to nucleotide sequence, run GENSCAN on multiple sequences,
 and much more! See bioscripts.pod for a complete listing.

 Individual *.pm modules have their own embedded POD documentation as
 well. A complete set of hyperlinked POD, or module, documentation is
 available at http://www.bioperl.org/.

 Remember that 'perldoc' is your friend. You can use it to read any
 file containing POD formatted documentation without needing any type
 of translator (e.g. 'perldoc Bio::SeqIO').
 
 If you used the Build.PL installation, and depending on your
 platform, you may have documentation installed as man pages, which
 can be accessed in the usual way.

o Releases
  
 BioPerl releases are always available from the website at
 http://www.bioperl.org/DIST or in CPAN. The latest code can be found
 at https://github.com/bioperl.

 BioPerl formerly used a numbering scheme to indicate stable release
 series vs. development release series. A release number is a three
 digit number like 1.2.0. The first digit indicates the major release
 - the idea being that all the API calls in a major release are
 reasonably consistent. The second number is the release series. This
 is probably the most important number.
 
 From the 1.0 release until the 1.6 release, even numbers (1.0, 1.2
 etc) indicated stable releases. Stable releases were well tested and
 recommended for most uses. Odd numbers (1.1, 1.3 etc) were development
 releases which one would only use if one were interested in the
 latest and greatest features. The final number (e.g. 1.2.0, 1.2.1) is
 the bug fix release. The higher the number the more bug fixes has
 been incorporated. In theory you can upgrade from one bug fix release
 to the next with no changes to your own code (for production cases,
 obviously check things out carefully before you switch over).
 
 The 1.6 release will be the last release series to utilize the
 alternating 'stable'/'developer' convention. Starting immediately
 after the 1.6 branch, we will start splitting BioPerl into several
 smaller easier-to-manage distributions, including a developer
 distribution for cutting-edge (in development) code, untested
 modules, and alternative implementations.

o Caveats and warnings

 When you run the tests ("./Build test") some tests may issue warnings
 messages or even fail. Sometimes this is because we didn't have
 anyone to test the test system on the combination of your operating
 system, version of perl, and associated libraries and other modules.
 Because BioPerl depends on several outside libraries we may not be
 able to test every single combination so if there are warnings you
 may find that the package is still perfectly useful.
 
 If you install the bioperl-run system and run tests when you don't
 have the program installed you'll get messages like 'program XXX not
 found, skipping tests'. That's okay, BioPerl is doing what it is
 supposed to do. If you wanted to run the program you'd need to
 install it first.
 
 Not all scripts in the examples/ directory are correct and up-to-date.
 We need volunteers to help maintain these so if you find they do not
 submit a bug report to https://github.com/bioperl/bioperl-live/issues
 and consider helping out in their maintenance.

 If you are confused about what modules are appropriate when you try
 and solve a particular issue in bioinformatics we urge you to look at
 HOWTO documents first.

o A simple module summary

 Here is a quick summary of many of the useful modules and how the
 toolkit is laid out:

 All modules are in the Bio/ namespace,

 - Perl is for newbies and gives a functional interface to the main
   parts of the package

 - Seq is for Sequences (protein and DNA).
   o Bio::PrimarySeq is a plain sequence (sequence data + identifiers)
   o Bio::Seq is a PrimarySeq plus it has a Bio::Annotation::Collection
     and Bio::SeqFeatureI objects attached
     (via Bio::FeatureHolderI).
   o Bio::Seq::RichSeq is all of the above plus it has slots for
     extra information specific to GenBank/EMBL/SwissProt files.
   o Bio::Seq::LargeSeq is for sequences which are too big for
     fitting into memory.

 - SeqIO is for reading and writing Sequences, it is a front end
   module for separate driver modules supporting the different
   sequence formats

 - SeqFeature - start/stop/strand annotations of sequences
   o Bio::SeqFeature::Generic is basic catchall
   o Bio::SeqFeature::Similarity a similarity sequence feature
   o Bio::SeqFeature::FeaturePair a sequence feature which is pairwise
     such as query/hit pairs

 - SearchIO is for reading and writing pairwise alignment reports like
   BLAST or FASTA

 - Search is where the alignment objects are defined
   o Bio::Search::Result::GenericResult is the result object (a blast
     query is a Result object)
   o Bio::Search::Hit::GenericHit is the Hit object (a query will have
     0 -> many hits in a database)
   o Bio::Search::HSP::GenericHSP is the High-scoring Segment Pair
     object defining the alignment(s) of the query and hit.

 - SimpleAlign is for multiple sequence alignments

 - AlignIO is for reading and writing multiple sequence alignment
   formats

 - Assembly provides the start of an infrastructure for assemblies and
   Assembly::IO IO converters for them

 - DB is the namespace for all the database query objects
   o Bio::DB::GenBank/GenPept are two modules which query NCBI entrez
     for sequences
   o Bio::DB::SwissProt/EMBL query various EMBL and SwissProt
     repositories for a sequences
   o Bio::DB::GFF is Lincoln Stein's fast, lightweight feature and
     sequence database which is the backend to his GBrowse system (see
     www.gmod.org)
   o Bio::DB::Flat is a fast implementation of the OBDA flat-file
     indexing system (cross-language and cross-platform supported by
     O|B|F projects see http://obda.open-bio.org).
   o Bio::DB::BioFetch/DBFetch for OBDA, Web (HTTP) access to remote
     databases.
   o Bio::DB::InMemoryCache/FileCache (fast local caching of sequences
     from remote dbs to speed up your access).
   o Bio::DB::Registry interface to the OBDA specification for remote
     data sources
   o Bio::DB::Biblio for access to remote bibliographic databases.
   o Bio::DB::EUtilities is the initial set of modules used for
     generic queried using NCBI's eUtils.

 - Annotation collection of annotation objects (comments, DBlinks,
   References, and misc key/value pairs)

 - Coordinate is a system for mapping between different coordinate
   systems such as DNA to protein or between assemblies

 - Index is for locally indexed flatfiles with BerkeleyDB

 - Tools contains many miscellaneous parsers and function for
   different bioinformatics needs
   o Gene prediction parser (Genscan, MZEF, Grail, Genemark)
   o Annotation format (GFF)
   o Enumerate codon tables and valid sequences symbols (CodonTable,
     IUPAC)
   o Phylogenetic program parsing (PAML, Molphy, Phylip)

 - Map genetic and physical map representations

 - Structure - parse and represent protein structure data

 - TreeIO is for reading and writing Tree formats

 - Tree is the namespace for all the associated Tree objects
   o Bio::Tree::Tree is the basic tree object
   o Bio::Tree::Node are the nodes which make up the tree
   o Bio::Tree::Statistics is for computing statistics for a tree
   o Bio::Tree::TreeFunctionsI is where specific tree functions are
     implemented (like is_monophyletic and lca)

 - Bio::Biblio is where bibliographic data and database access objects
   are kept

 - Variation represent sequences with mutations and variations applied
   so one can compare and represent wild-type and mutation versions of
   a sequence.

 - Root, basic objects for the internals of BioPerl

o Upgrading from an older version
 
 If you have a previously installed version of BioPerl on your system
 some of these notes may help you.

 Some modules have been removed because they have been superceded by
 new development efforts. They are documented in the DEPRECATED file
 that is included in the release. In addition some methods, or the
 Application Programming Interface (API), have changed or been
 removed. You may find that scripts which worked with BioPerl 1.4 may
 give you warnings or may not work at all (although we have tried very
 hard to minimize this!). Send an email to the list and we'll be happy
 to give you pointers.