Massive check of file open lines. Changed bareword filehandles
to lexical with three-argument opens calls, added die/throw
and reason of failure $! where missing, and made error messages
more uniform and consistent with Florent Angly messages for Root
(like quoting of filenames). Also deleted a few unused open
filehandles and some unnecessary parenthesis. Tests pass.
SeqFeatureDB Postgres: Changed the use of system("cp") command
to the more portable File::Copy. Tested and works fine.
Bio/Ontology/InterProTerm: Fixed an uninitialized warning in
"to_string" method, and cleaned indentation and tabs from test file
SearchResultEventBuilder: Simplified calculation of 'HSP-query_length'
and 'HSP-hit_length' in "end_hsp" subroutine. Also fixed an
undefined value warning for $hit_bits in "_add_hit"
SeqIO/Tinyseq.pm: Fixed an uninitialized value warning from
"_get_writer" by changing '$Bio::SeqIO::tinyseq::VERSION' to
'$Bio::Root::Version::VERSION'. Also cleaned tabs, indentation
and trailing whitespace from both module and test file.
Unflattener: Fix for Bug #3458. Incorporated Bastien Chevreux
suggestions to improve error reports from "problem" subroutine
by adding feature location and locus_tag. Also merged all
tests from 'Unflattener2.t' into 'Unflattener.t' to have
all tests in a single file.
SeqIO/Genbank: Complete elimination of the use of '$_',
except inside map/grep blocks. Also extensive cleanup of tabs,
parenthesis, indentation, etc. Test suite pass.
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