diff --git a/Bio/DB/Flat/BDB/fasta.pm b/Bio/DB/Flat/BDB/fasta.pm index 07e1ec1477..06a2d07042 100644 --- a/Bio/DB/Flat/BDB/fasta.pm +++ b/Bio/DB/Flat/BDB/fasta.pm @@ -81,5 +81,19 @@ sub seq_to_ids { \%ids; } +sub parse_one_record { + my $self = shift; + my $fh = shift; + + # fasta parses by changing $/ to '\n>', need to adjust accordingly + my $adj = ( $^O =~ /mswin/i ) ? -2 : -1; + my $parser = + $self->{cached_parsers}{fileno($fh)} + ||= Bio::SeqIO->new(-fh=>$fh,-format=>$self->default_file_format); + my $seq = $parser->next_seq or return; + $self->{flat_alphabet} ||= $seq->alphabet; + my $ids = $self->seq_to_ids($seq); + return ($ids, $adj); +} 1; diff --git a/Bio/Root/Build.pm b/Bio/Root/Build.pm index f0968eee38..72fbd4eebc 100644 --- a/Bio/Root/Build.pm +++ b/Bio/Root/Build.pm @@ -85,7 +85,7 @@ BEGIN { use strict; use warnings; -our $VERSION = '1.006000_005'; +our $VERSION = '1.006000_006'; our @extra_types = qw(options excludes_os feature_requires test); # test must always be last in the list! our $checking_types = "requires|conflicts|".join("|", @extra_types); diff --git a/Bio/Root/Version.pm b/Bio/Root/Version.pm index a0392f9343..d9f31db2f3 100644 --- a/Bio/Root/Version.pm +++ b/Bio/Root/Version.pm @@ -98,7 +98,7 @@ methods. Internal methods are usually preceded with a _ package Bio::Root::Version; use strict; -our $VERSION = '1.006000_005'; +our $VERSION = '1.006000_006'; $VERSION = eval $VERSION; sub import { diff --git a/t/LocalDB/Index.t b/t/LocalDB/Index.t index 7567760d58..5f0aefcb47 100644 --- a/t/LocalDB/Index.t +++ b/t/LocalDB/Index.t @@ -95,7 +95,7 @@ is ($seq->display_id(), 'ROA1_HUMAN'); # test id_parser $ind = Bio::Index::Swissprot->new(-filename => 'Wibbl4', - -write_flag => 1); + -write_flag => 1); $ind->id_parser(\&get_id); $ind->make_index(test_input_file('roa1.swiss')); ok ( -e "Wibbl4" || -e "Wibbl4.pag" ); diff --git a/t/LocalDB/Registry.t b/t/LocalDB/Registry.t index f9303c9bcd..b11b5aca1f 100755 --- a/t/LocalDB/Registry.t +++ b/t/LocalDB/Registry.t @@ -31,7 +31,7 @@ SKIP: { is $entries, 7; SKIP: { - test_skip(-tests => 2, -requires_modules => [qw(DB_File BerkeleyDB)]); + test_skip(-tests => 2, -requires_modules => [qw(DB_File)]); my $bdb = Bio::DB::Flat->new(-directory => $tmpdir, -dbname => 'testbdb', @@ -45,7 +45,7 @@ SKIP: { SKIP: { test_skip(-tests => 9, - -requires_modules => [qw(LWP::UserAgent HTTP::Request::Common BerkeleyDB)], + -requires_modules => [qw(LWP::UserAgent HTTP::Request::Common)], -requires_networking => 1); my $registry = Bio::DB::Registry->new(); @@ -61,7 +61,7 @@ SKIP: { is $sequence, "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA"; SKIP: { - test_skip(-tests => 4, -requires_modules => [qw(DB_File BerkeleyDB)]); + test_skip(-tests => 4, -requires_modules => [qw(DB_File)]); ok grep /testbdb/,@available_services; $db = $registry->get_database('testbdb');