Add the COLLATE NOCASE constraint to the name.name,
attribute.attribute_value, and typelist.tag; and remove the user of the
LOWER() function; to allow the use of indexes instead of full-table
scans. Add the COLLATE NOCASE opterator to affected queries for
backwards compatibility with Bio::DB::SeqFeature::Store databases
created without the COLLATE NOCASE constraints.
SeqIO/embl.pm: At 'next_seq' subroutine, added a little more
flexibility to the ID field in the ID line, to allow custom IDs
Used quoted strings in Bio::Species to avoid a 'Invalid [] range in regex' error, Species.t and genbank.t pass
Merge pull request #66 from nathanweeks/sqlite_collate_nocase

Use COLLATE NOCASE instead of LOWER() for Bio::DB::SeqFeature::Store::DBI::SQLite
spellink
allowing lines with species label ($seq) without $rest, as comes with yn00

reported by Volker Brendel
Minor edits
changes all issue tracking in preparation for switch to github issues
Standardized URL to "https://github.com/bioperl/bioperl-live/issues"
instead of "https://github.com/bioperl/bioperl-live/issues/"
(since the first is the dominant form in the other hundreds files)
Minor POD edits
Added 'DB_File' requirement to some tests files that use it,
so they can be skipped if its missing (ContigSpectrum.t,
SeqFeature.t & transfac_pro.t)
Several LocalDB tests were failing for Windows' ActivePerl,
because ActivePerl were producing a ".index.pag" and ".index.dir"
files instead of a single ".index" file (like Strawberry Perl).
Also, ActivePerl were not deleting temporary files if their
tied-hash was not made undef after the untie on DESTROY,
and had to add several explicit DESTROY calls to test files.
Changed argument "requires_modules" to "require_module"
for SeqFeature.t and transfac_pro.t, since its only 1
Added 'Data::Stag' requirement to many tests files
that depend on it, so they can be skipped if its missing
BioFetch.t & SwissProt.t: Fixed some number of skipped tests
and cleaned format and indentation
RemoteBlast.t: Fixed several number of skipped tests,
increased significantly server waiting cycle (sleep + retries)
because server was taking much longer than current setting
to return results, and cleaned format and indentation
RandomFactory.t: Removed unused dependency "Math::Random",
which only appears in this file and not in any module.
A machine without the module installed still passed all tests.
Taxonomy.t: Added missing 'DB_File' requirement
RemoteBlast_rpsblast.t: Fixed a few number of skipped tests,
and cleaned format and indentation
Build.PL: Demoted 'DB_File' status from "required" to
"recommended", and added in "recommended" missing modules
that are requested by some test files (Bio::Phylo, XML::DOM
and XML::DOM::XPath). NOTE: The 3 modules added were
confirmed to be correctly installed by ActivePerl.