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BioRuby 2.0.5 RELEASE NOTES ↑

Some fixes have been made in BioRuby 2.0.5 after the release of 2.0.4.

Fixes ↑

  • Bio::UniProtKB#ft: Additional bug fixes for parsing FT lines since UniProt release 2019_11. (github.com/bioruby/bioruby/issues/147 )

  • Bio::UniProtKB#oh: Fixed parse error when parsing 1A_AMVLE (P03589).

  • Bio::Blast::Remote::GenomeNet: Fixed errors caused by the change of GenomeNet BLAST webpage’s internal URL (which is unofficial internal URL and may subject to be changed without notices).

  • Bio::PTS1: Fixed errors due to the PTS1 website URL change from http to https.

Changes for developers ↑

Changes of CI (Continuous Integration) ↑

  • Started using GitHub Actions for CI.

  • Stopped using Travis-CI for CI.

  • Fixed AppVeyor CI errors.

Changes of Gemfile and related files ↑

  • Gemfile: Added “matrix” and “rexml” gems that are excluded from the default gems in recent Ruby versions.

  • gemfiles/*: Removed because of the CI changes.

Others ↑

  • .gitignore is added.

BioRuby 2.0.4 RELEASE NOTES ↑

Some fixes have been made in BioRuby 2.0.4 after the release of 2.0.3.

Fixes ↑

  • Bio::UniProtKB#ft: Supports text format change of FT lines since UniProt release 2019_11. (github.com/bioruby/bioruby/issues/147 )

  • Bio::UniProtKB#protein_name and #synonyms methods may raise error after calling Bio::UniProtKB#de method.

BioRuby 2.0.3 RELEASE NOTES ↑

Some bug fixes have been made in BioRuby 2.0.3 after the release of 2.0.2.

Bug fixes ↑

Incompatible changes ↑

Bio::Sequence::* incompatible changes since Ruby 3.0.0 ↑

Since Ruby 3.0.0, the following methods in Bio::Sequence::NA, Bio::Sequence::AA, and Bio::Sequence::Generic return or yield String instance, instead of the Bio::Sequence::* instance.

  • dump

  • scrub

For details about Ruby 3.0.0 incompatible changes, see News for Ruby 3.0.0.

BioRuby 2.0.2 RELEASE NOTES ↑

Some bugs fixes have been made in BioRuby 2.0.2 after the release of 2.0.1.

Bug fixes ↑

Known issues ↑

A known issue about Ruby 3.0 is added to KNOWN_ISSUES.rdoc. The issue will be fixed in the near future.

BioRuby 2.0.1 RELEASE NOTES ↑

Some bug fixes and improvements have been made to the BioRuby 2.0.1 after the version 2.0.0 is released.

Bug fixes ↑

  • Bio::GFF::GFF2::Record.parse did not return correct object.

Improvement of sample scripts ↑

The following scripts in the sample/ directiry are newly added.

  • color_scheme_aa.rb: Example of Bio::ColorScheme for an amino acid sequence.

  • fastq2html.rb: Visualization of FASTQ sequences, colored by quality scores.

  • rev_comp.rb: Shows reverse-complement sequences of the given sequences.

The floowing scripts are modified to fix bug and/or to improve features.

  • na2aa.rb: Completely rewritten to fix bug. Shows translated sequences.

  • color_scheme_na.rb: Added support for various sequence formats.

CWL (Common Workflow Language) workflow files are added ↑

CWL (Common Workflow Language) workflow files are added for some sample scripts. The usage of each sample script will be clarified with the CWL workflow files.

Two type of files are prepared for CWL workflow engine. *.cwl is a workflow definition file for each sample script. *.testdata.yaml describes sample input data for each CWL workflow.

In this version, cwl files for the 3 sample scripts are added.

  • fastq2html.rb: fastq2html.cwl with fastq2html.testdata.yaml

  • na2aa.rb: na2aa.cwl with na2aa.testdata.yaml

  • rev_comp.rb: rev_comp.cwl with rev_comp.testdata.yaml

BioRuby 2.0.0 RELEASE NOTES ↑

A lot of changes have been made to the BioRuby 2.0.0 after the version 1.5.x is released. This document describes important and/or incompatible changes since the BioRuby 1.5.0 release.

For known problems, see KNOWN_ISSUES.rdoc.

Features moved to separete gems ↑

Some features are moved to separate gems because of reducing complexity and/or to avoid external library dependency of BioRuby core.

BioRuby Shell is moved to “bio-shell” ↑

BioRuby Shell is split to “bio-shell” gem.

Executable files are moved to “bio-executables” ↑

To avoid unexpected loading of executable files by some Rails software, all executable commands are moved to “bio-executables” gem (except the “bioruby” command that is included in the above “bio-shell” gem).

Fast BLAST XML result parser by using Expat XML Parser is moved to “bio-blast-xmlparser” ↑

Fast BLAST XML result parser by using Expat XML Parser is split to “bio-blast-xmlparser” gem, because of external C library dependency. Please install “bio-blast-xmlparser” gem if possible. If it is installed, BioRuby automatically use it.

Bio::PhyloXML is moved to “bioruby-phyloxml” ↑

Bio::PhyloXML is split to “bioruby-phyloxml” gem.

NOTE: Please uninstall “bio-phyloxml” gem, that have been created as a preliminary trial of splitting a module in 2012 and have not been maintained after that.

Bio::SQL is moved to “bio-biosql” ↑

Bio::SQL is split to “bio-biosql” gem.

New features and improvements ↑

HTTPS is used to access NCBI web services ↑

As you may know, NCBI announced that all HTTP resources will be switched to HTTPS on September 30, 2016. To follow the transition, all URLs for accessing NCBI E-utilities in BioRuby are changed to use HTTPS.

In BioRuby, the following classes/modules are affected.

  • Bio::NCBI::REST and descending classes

  • Bio::PubMed

In some rare cases (especially when building Ruby and/or OpenSSL by yourself from source code), Ruby does not include SSL/TLS support, or Ruby fails to detect SSL root certificates. In such cases, you may need to reinstall or upgrade Ruby, OpenSSL (or alternatives), and/or SSL root certificates with appropriate configuration options. Alternatively, installing binary packages is generally a good idea.

KEGG::GENES#diseases and related methods are added ↑

The following methods are added to KEGG::GENES, contributed by @kojix2.

  • networks_as_strings

  • diseases_as_strings

  • diseases_as_hash

  • diseases

  • drug_targets_as_strings

Pre-calculated ambiguity codon tables in Bio::CodonTable ↑

Pre-calculated ambiguity codon tables are added, contributed by Tomoaki NISHIYAMA.

Bug fixes ↑

  • Fixed a parser bug in Bio::Fasta::Report, FASTA output (-m 10) parser, contributed by William Van Etten and Mark Wilkinson via GitHub.

  • HTTPS is used to access GenomeNet BLAST web service, contributed by @ramadis via GitHub.

  • Bio::AAindex documentation fix, suggested by @kojix2 via GitHub.

  • Suppress warning messages in Ruby 2.4 and later.

Incompatible changes ↑

Bio::Taxonomy is removed and merged to Bio::PhyloXML::Taxonomy ↑

Bio::Taxonomy in lib/bio/db/phyloxml/phyloxml_elements.rb was written for PhyloXML in 2009. It was intended to become general taxonomy data class in BioRuby in these days. However, no efforts have been made to improve the Bio::Taxonomy class, and it still remains to be a PhyloXML specific class. Because Bio::PhyloXML is split as a different Gem (Biogem) package, we now decide to remove Bio::Taxonomy and merge it to Bio::PhyloXML::Taxonomy.

In the codes using Bio::Taxonomy directly, changing Bio::Taxonomy to Bio::PhyloXML::Taxonomy or adding the following monkey patch may be needed.

module Bio
   unless defined? Taxonomy
      Taxonomy = Bio::PhyloXML::Taxonomy
   end
end

In the future, Bio::Taxonomy might be added as general taxonomy data class. The new Bio::Taxonomy might be incompatible with the current Bio::Taxonmy.

Some features are moved to separete gems ↑

Some features are split to separete gems and removed from this “bio” gem. See the above “Features moved to separete gems” topics for details.

Known issues ↑

The following issues are added or updated. See KNOWN_ISSUES.rdoc for other already known issues.

Other important news ↑

Ruby 1.8 is no longer supported ↑

Ruby 1.8.x is no longer supported. Though unsupported, some components may still run on Ruby 1.8.7. Please use Ruby 1.8.7 at your own risk with this version of BioRuby.

Installation without RubyGems is no longer supported ↑

Installation by using setup.rb without RubyGems is no longer supported, and setup.rb is no longer included in BioRuby distribution.