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bump alpha to test ODBA-related bug fix

svn path=/bioperl-live/branches/branch-1-6/; revision=16191
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1 parent 2834e5b commit 744beb7b4bf472974049a31745ddb1efedc4546f cjfields committed
Showing with 20 additions and 6 deletions.
  1. +14 −0 Bio/DB/Flat/BDB/fasta.pm
  2. +1 −1 Bio/Root/Build.pm
  3. +1 −1 Bio/Root/Version.pm
  4. +1 −1 t/LocalDB/Index.t
  5. +3 −3 t/LocalDB/Registry.t
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14 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;
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2 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);
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2 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 $VERSION;
sub import {
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2 t/LocalDB/Index.t
@@ -95,7 +95,7 @@ is ($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" );
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6 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');

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