Like it or not, but the SeqIO swissprot format has name 'swiss', not

[bioperl-live.git] / README

This is the README file for the Bioperl central distribution.

# $Id$

o Getting Started
 
 Thanks for downloading this distribution!

 For tutorials see Bioperl's bptutorial.pl (in this directory) or 
 howto documents in docs/howto or the online Bioperl tutorial
 at http://www.pasteur.fr/recherche/unites/sis/formation/bioperl. For
 information on databases and Bioperl see biodatabases.pod. To look at
 example code browse the scripts/ directories, and look at
 bioscripts.pod for a descriptions of all these scripts. The bioperl.pod file
 also gives a overview of the history and purpose of Bioperl. The FAQ
 may also be useful if you have a particular question.

 For people starting out with Perl and Bioperl, look at the Bio::Perl
 module (go perldoc Bio::Perl from the directory you are reading this file
 in). This module is designed to flatten the learning curve for newcomers.

 For a discussion of issues in design and development please see
 biodesign.pod, recommended for those who want to contribute code. And for
 a list of OS's and versions that are known to support Bioperl see the
 PLATFORMS file.
 
 For info on Bioperl read on!

o About Bioperl

 Bioperl is an association of developers of public domain Perl tools
 for computational molecular biology.

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

o Contact info

 Bioperl developers: bioperl-l@bioperl.org

 There's quite a variety of tools available in Bioperl, and more are
 added all the time. If the tool you're looking for isn't described in
 the documentation please write us, it could be undocumented or in process.

 Project website   : http://bioperl.org
 Project FTP server: bioperl.org (anonymous FTP ok)

 Bug reports       : http://bugzilla.bioperl.org/
                     bioperl-bugs@bioperl.org

 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!

 Please see the AUTHORS file for the complete list of bioperl
 developers and contributors.

 Please see the INSTALL document for installation instructions.

o About the directory structure

 The bioperl directory structure is organised as follows:

 Bio/      - Bioperl modules  
 models/   - DIA drawing program generated OO UML for bioperl classes
 t/        - Perl built-in tests
 t/data/   - Data files used for the tests - provides good data
             examples for those new to bioinformatics data.          
 scripts/  - Resuable scripts that use bioperl, some organisation in 
             attempted here (i.e. das contains das related scripts) 
 scripts/contributed - User submissions of useful scripts not necessarily 
                       integrated into bioperl.  Please see the README
                       in this directory.
 doc/ - "How To" files and the FAQ as XML

o Documentation

 The "meta" documentation can be found in the bioperl.pod file.
 This should be the starting point for you to read about what
 bioperl is, how to use it and who wrote it.

 The bptutorial.pl file is a POD formatted tutorial document 
 that contains useful information for new and existing Bioperl users.
 This file also contains a number of useful scripts that the 
 student of Bioperl may want to examine.

 Use your favorite pod2* translator turn it into the format of
 choice or view it directly via perldoc.

 For example, go 

   perldoc bioperl 
 
 or in this directory go
 
   pod2text bioperl.pod | more
 
   pod2text bptutorial.pl | more 

 pod2html, which comes with Perl, can be used to create web-browser
 navigable documentation files.

 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.  The most up-to-date 

 Remember 'perldoc' is your friend. You can use this to read any
 file containing POD formatted documentation without needing any type
 of translator.

 There is also an online course written at the Pasteur Institute. See:
 http://www.pasteur.fr/recherche/unites/sis/formation/bioperl.

 Useful documentation in the form of example code can also be found
 in the scripts/ directory. 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.

o Releases
  
 Bioperl releases are always available from the website
 http://www.bioperl.org or by FTP from ftp://bioperl.org.  (Note that
 we've had trouble with our new network setup which is not allowing
 FTP to support passive mode properly: use http://www.bioperl.org/DIST
 to get a listing of the distribution directory).  Each release is
 tested with the test suite and cross-tested on a number of different
 platforms.  See the PLATFORMS file for more information on a specific
 platform.  All efforts are made to release a bug-free package,
 however any known bugs in a release will be documented in the BUGS
 file.  See the Changes file for a listing of what features have been
 added or what APIs have changed between releases.

 Like many internet projects, Bioperl now has a consistent 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. Even
 numbers here (1.0, 1.2 etc) indicate stable releases. Stable releases
 are well tested and recommended for most uses. Odd numbers (1.1, 1.3
 etc) are development releases which one should only use if you are
 interested in the latest and greatest features. The final number (eg,
 1.2.0, 1.2.1 etc) is the bug fix release. The higher the number the
 more bug fixes has been incorportated. 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).

o Caveats, warnings, etc

 When you run the tests (make test) often some tests will issue
 warnings messages or even fail.  Sometimes this is because we didn't
 have anyone test the test system on the combintaion or 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 (mind you, now you've tested
 another possible situation and we encourage you to contribute back to
 the development process by emailing the list or submitted a bug), so
 if there are warnings you will find that in fact many things are not
 a big deal.  See the PLATFORMS file for reports of specific issues.
 
 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 this program you'd need to
 install it first.
 
 Not all scripts in the scripts directory are correct and up-to-date.
 We need volunteers to help maintain these so if you find they do not
 work, submit a bug report http://bugzilla.bioperl.org and/or consider
 helping out in their maintence.  Don't be disuaded by a script not
 working, often the SYNOPSIS of the module is the best place to start
 when trying to learn how to use them.  

 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
 the bptutorial 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 a Bio::SeqFeatureI objects attatched.
    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::XEMBL SOAP access to sequence databases
   o Bio::DB::Biblio for access to remote bibliographic databases.
 - 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 misc parsers and function for different
   bioinformatics needs
   o Gene prediction parser (Genscan, MZEF, Grail, Genemark)
   o Annotation format (GFF)
   o simulate RE cutting with RestrictionEnzyme
   o Enumerate codon tables and valid sequences symbols (CodonTable, IUPAC)
   o Phylogenetic program parsing (PAML, Molphy, Phylip)
 - Map genetic and physical map representations
 - Graphics render a sequence with its features in the standard
   'tracks'gram.
 - 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 superceeded by
 new developement 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 1.0.2
 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.