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bioperl-0.04.3
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Changes for version 0.04.3 - 1999-02-04

  • Bio::Root::Object.pm and Global.pm now detect when script is run as a CGI and suppress output that is only appropriate when running interactively.
  • Bio::Root::Err::_set_context() adds name of script ($0).
  • Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm regarding the use of the static objects via the qw(:obj) tag.
  • Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to CORE::reverse, avoiding Perl warnings.
  • Bug fixes in Bio::Tools::Blast modules (version 0.074) and example scripts (see Bio::Tools::Blast::CHANGES).
  • examples/seq/seqtools.pl no longer always warns about using -prot or -nucl command-line arguments; only when using the -debug argument.
  • Methods added to Bio::Root::Utilities: create_filehandle(), get_newline_char(), and taste_file() to generalize filehandle creation and autodetect newline characters in files/streams (see bug report #19).
  • Bio::Root::IOManager::read() now handles timeouts and uses Utilities::create_filehandle().
  • Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead of hardwiring in "\n".
  • Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW

Documentation

Notes
Bioperl
Coordinated OOP-Perl Modules for Biology

Modules

Bio::Parse
The Bioperl ReadSeq interface
Bio::Root::Err
Exception class for Perl 5 objects
Bio::Root::IOManager
Input and output manager for Perl5 objects.
Bio::Root::Object
A core Perl 5 object.
Bio::Root::Utilities
General-purpose utility module
Bio::Root::Vector
Interface for managing linked lists of Perl5 objects.
Bio::Root::Xref
A generic cross-reference object.
Bio::Seq
bioperl sequence object
Bio::SimpleAlign
Multiple alignments held as a set of sequences
Bio::Tools::AlignFactory
Base object for alignment factories
Bio::Tools::Blast
Bioperl BLAST sequence analysis object
Bio::Tools::Blast::HSP
Bioperl BLAST High-Scoring Segment Pair object
Bio::Tools::Blast::HTML
Bioperl Utility module for HTML formatting Blast reports
Bio::Tools::Blast::Run::LocalBlast
Bioperl module for running Blast analyses locally.
Bio::Tools::Blast::Run::Webblast
Bioperl module for running Blast analyses remotely.
Bio::Tools::Blast::Sbjct
Bioperl BLAST "Hit" object
Bio::Tools::Fasta
Bioperl Fasta utility object
Bio::Tools::RestrictionEnzyme
Bioperl object for a restriction endonuclease object.
Bio::Tools::SeqAnal
Bioperl sequence analysis base class.
Bio::Tools::SeqPattern
Bioperl object for a sequence pattern or motif
Bio::Tools::WWW
Bioperl manager for web resources related to biology.
Bio::Tools::pSW
DESCRIPTION of Object
Bio::UnivAln
Bioperl alignment object

Provides

Bio::Root::Global
in Bio/Root/Global.pm
bp_sw
in Compile/SW/bp_sw.pm

Examples

Other files