Revision history for Perl extension Bio::Homology::InterologWalk.
0.6b Wed May 8 10:29:40 2013
Experimental Support for MITAB 2.7 format. IntACT now exports to MITAB 2.7 rather than 2.5.
-setup_ensembl_adaptor() - get_forward_orthologies() - get_backward_orthologies() - get_direct_interactions() : now using $registry->alias_exists() directive to check if user selected species exists in db (change introduced by Ensembl 65+ - moving towards compatibility)
-get_interactions() - get_direct_interactions() - _build_query_options() - _get_interactor_name() - _get_interactor_uniprot_id(): experimental support for MITAB 2.7 format (replacing MITAB 2.5 for IntACT ppi representation)
-_process_homologies(): deals with "projections" (Ensembl 65+ - moving towards compatibility)
0.58 Wed Feb 1 12:28:53 2012
-get_forward_orthologies(): fixed bug provoking exception when using 'all' DBs
-get_backward_orthologies(): fixed bug provoking exception when using 'all' DBs
0.57 Tue Nov 1 14:41:07 2011
-improved documentation
-setup_ensembl_adaptor(): added support for set_reconnect_when_lost() - introduced in API v64
0.55 Thu Sep 8 15:06:45 2011
interface changes:
- get_direct_interactions(): introduced flag to allow for retrieval of chimeric (taxonA != taxonB)
PPIs if desired
- do_attributes(): removed label_type flag. Now only "external name" can be used to populate
name attribute file
- do_attributes(): introduced 'label_chimeric' to comply with changes in get_direct_interactions().
Introduced dynamic retrieval of gene_adaptor to find chimeric species and label gene names by
species name
bugfixes:
- _get_interactor_name(): fixed (gene name) problem due to intact change
- _get_ens_id_from_props(): included 'flybase' case due to intact change in properties field
- _get_ens_id_from_props(): introduced ensembl ID count: if only 1, accepted, if more, ambiguous case.
0.52 Wed Aug 17 12:09:02 2011
- removed hard-coded species hash
- updated interface and documentation
- added warnings for unsupported usage of non-metazoan Ensemblgenomes species
- get_backward_orthologies(): introduced basic support for NCBI taxonomy climb for cases of unrecognised taxon
scientific name/taxon id
0.511 Sat Aug 6 10:56:09 2011
- updated species hash in main module
0.510 Thu Jul 21 18:06:34 2011
- removed no_output flags throughout
- documentation update
- changed get_forward_orthologies() interface to explicity allow appending data to partial file after
remote connection failure
0.505 Fri Jul 1 16:10:52 2011
- naming corrections
- documentation update
0.501 Sat May 7 14:02:02 2011
- compute_confidence_score(): boolean variables restored
- corrected version bug
0.5 Fri May 6 12:46:25 2011
- First Beta Release
- _get_ens_id(): added cygid option to deal with embedded yeast ids
- merged get_ensembl_id_from_ensembl() and get_ensembl_id_from_uniprot()
- merged all duplicates between the pacakges: Bio::Homology::InterologWalk and
Bio::Homology::InterologWalk::Direct
- get_direct_interactions(): rewritten and moved to Bio::Homology::InterologWalk
- removed Bio:Homology::InterologWalk::Direct package. All unmerged subroutines moved to
Bio::Homology::InterologWalk
- get_interactions(): rewritted to gather 'properties' field from MITAB data
- get_backward_orthologies(): rewritten to use 'properties' field from MITAB data
- _clean_ids(): removed
0.12 Wed Jan 12 12:07:01 2011
- Modified Makefile.PL to avoid failing tests when prerequisite
software on testers' machines is missing
0.11 Thu Dec 16 11:45:26 2010
- InterologWalk.pm: introduced look-up table for Genomes Taxa
- changed db names throughout for better readability
- setup_ensembl_adaptor(): fixed pan_homology bug
- setup_ensembl_adaptor(): removed 'default' db
- get_forward_orthologies(): updated docs
- get_forward_orthologies(): introduced genome name check when taxon id fails
- get_backward_orthologies(): updated docs
- get_backward_orthologies(): introduced genome name check when taxon id fails
- process_homologies(): introduced protein adaptor check
0.09 Tue Oct 19 18:45:26 2010
- fixed undefined canonical peptide member bug in _process_homologies()
- fixed registry timeout bug in compute_multiple_taxa_mean()
0.08 Thu Oct 07 12:12:26 2010
- removed commented lines in doScores.pl
- fixed empty candidate bug in get_backward_orthologies()
0.07 Tue Oct 05 14:50:26 2010
- rewrote _process_homologies() to get rid of "possible_ortholog"
paralogy class
- fixed extension bug in getDirectInteractions.pl
0.06 Sat Sep 18 19:50:26 2010
- introduced new method for computing conservation score for the
putative PPI: compute_conservation_score(). Status is experimental.
- rewritten doScores.pl to show usage of compute_conservation_score().
- rewritten Makefile.PL with new prerequisite checking scheme.
- rewritten interface to _build_query_options().
0.05 Thu Sep 09 18:50:26 2010
- do_attributes() now writes two attribute files: name attribute
and novel id attribute.
- Interface redesigned for do_networks() and do_attributes()
to simplify introduction of new node attribute file
- sample usage file doNets.pl rewritten to show usage of new interface
for the two methods
0.04 Fri Sep 03 01:09:26 2010
- removed version bug
- removed local library requirement in test script
0.03 Thu Sep 02 15:42:09 2010
- Relaxed Perl Version Requirement to 5.8.6
- fixed input namefile bug in getDirectInteractions.pl
- Removed DBI requirement (implicitly required by DBD::CSV)
- included MAC note in README
- changed arguments in compute_multiple_taxa_mean() in doScores.pl
- included "usage" conditions in doScores.pl and doNets.pl. No "default" filename anymore:
ensembl version in filename is dynamic, it would have broken soon.
0.02 Tue Aug 31 09:51:26 2010
- POD reformatted
0.01 Sun Aug 29 19:09:26 2010
- original version; created by h2xs 1.23 with options
-XA -n Bio::Homology::InterologWalk