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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
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/
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
- doc/ - Documentation utilities
- 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(these are quite out-of-date)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
o Documentation
For documentation on BioPerl see the HOWTO documents and tutorials
online at http://bioperl.org.
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.
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