view release on metacpan or search on metacpan
lib/Bio/DOOP/Sequence.pm view on Meta::CPAN
sub get_ver {
my $self = shift;
return($self->{VERSION});
}
=head2 get_annot_id
Returns the sequence annotation primary id. This is the internal ID from the MySQL database.
Return type: string
my $annotation_id = $seq->get_annot_id;
=cut
sub get_annot_id {
my $self = shift;
return($self->{ANNOT});
}
=head2 get_orig_id
view release on metacpan or search on metacpan
lib/Bio/Tools/EUtilities/EUtilDataI.pm view on Meta::CPAN
shift->warn("Object may not need an iterator. Please check the documentation.");
}
sub _add_data {
shift->throw_not_implemented;
}
sub to_string {
shift->throw_not_implemented;
}
sub _text_wrap {
shift;
view release on metacpan or search on metacpan
nextchar|||
ninstr|||
no_bareword_allowed|||
no_fh_allowed|||
no_op|||
not_a_number|||
nothreadhook||5.008000|
nuke_stacks|||
num_overflow|||n
offer_nice_chunk|||
oopsAV|||
# if !defined(__PATCHLEVEL_H_INCLUDED__) && !(defined(PATCHLEVEL) && defined(SUBVERSION))
# define PERL_PATCHLEVEL_H_IMPLICIT
# include <patchlevel.h>
# endif
# if !(defined(PERL_VERSION) || (defined(SUBVERSION) && defined(PATCHLEVEL)))
# include <could_not_find_Perl_patchlevel.h>
# endif
# ifndef PERL_REVISION
# define PERL_REVISION (5)
/* Replace: 1 */
# define PERL_VERSION PATCHLEVEL
view release on metacpan or search on metacpan
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
=cut
sub fetch_all_by_outward_search {
my $self = shift;
my ($ref_feature, $respect_strand, $opposite_strand, $downstream, $upstream, $start_search_range,
$limit,$not_overlapping,$five_prime,$three_prime, $max_range) =
rearrange([qw(FEATURE SAME_STRAND OPPOSITE_STRAND DOWNSTREAM UPSTREAM RANGE LIMIT NOT_OVERLAPPING FIVE_PRIME THREE_PRIME MAX_RANGE)], @_);
my $factor = 1;
$limit ||= 1;
$start_search_range ||= 1000;
my $current_search_range = $start_search_range;
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
-SAME_STRAND => $respect_strand,
-OPPOSITE_STRAND => $opposite_strand,
-DOWNSTREAM => $downstream,
-UPSTREAM => $upstream,
-LIMIT => $limit,
-NOT_OVERLAPPING => $not_overlapping,
-FIVE_PRIME => $five_prime,
-THREE_PRIME => $three_prime,
)
};
$factor++;
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
Caller : general
=cut
sub fetch_all_nearest_by_Feature{
my $self = shift;
my ($ref_feature, $respect_strand, $opposite_strand, $downstream, $upstream, $search_range,$limit,$not_overlapping,$five_prime,$three_prime) =
rearrange([qw(FEATURE SAME_STRAND OPPOSITE_STRAND DOWNSTREAM UPSTREAM RANGE LIMIT NOT_OVERLAPPING FIVE_PRIME THREE_PRIME)], @_);
if ( !defined($search_range)) {
$search_range ||= 1000;
}
$limit ||= 1;
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
@candidates = grep { ($_->strand == 1) ? $_->seq_region_end > $ref_feature->end : $_->seq_region_start > $ref_feature->end } @candidates;
}
}
# Then sort and prioritise the candidates
my $finalists; # = [[feature, distance, centre-weighted distance, length, dbID],..]
$finalists = $self->select_nearest($ref_feature,\@candidates,$limit,$not_overlapping,$five_prime,$three_prime);
$finalists = [ map { [ splice @$_,0,2 ]} @$finalists ]; # Remove the ugly bits from the sight of users.
return $finalists;
}
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
Arg [2] : Listref of Features to be considered for nearness.
Arg [3] : Integer, limited number of Features to return. Equally near features are all returned in spite of this limit
Arg [4] : Boolean, Overlapping prohibition. Overlapped Features are forgotten
Arg [5] : Boolean, use the 5' ends of the nearby features for distance calculation
Arg [6] : Boolean, use the 3' ends of the nearby features for distance calculation
Example : $feature_list = $feature_adaptor->select_nearest($ref_feature,\@candidates,$limit,$not_overlapping)
Description: Take a list of possible features, and determine which is nearest. Nearness is a
tricky concept. Beware of using the distance between Features, as it may not be the number you think
it should be.
Returntype : listref of Features ordered by proximity
Caller : BaseFeatureAdaptor->fetch_all_nearest_by_Feature
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
sub select_nearest {
my $self = shift;
my $ref_feature = shift;
my $candidates = shift;
my $limit = shift;
my $not_overlapping = shift;
my $five_prime = shift;
my $three_prime = shift;
# Convert circular coordinates to linear ones for distance calculation
my $ref_start = ($ref_feature->start < $ref_feature->end) ? $ref_feature->start : $ref_feature->start - $ref_feature->length; # Not ->end, in case circular
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
? $neighbour->seq_region_start : $neighbour->seq_region_start - $neighbour->length; # Not ->end, in case it is circular
my $neigh_midpoint = $self->_compute_midpoint($neighbour);
my $neigh_end = $neighbour->seq_region_end;
# discard overlaps early if not required.
next if ( $not_overlapping
&& (
( $neigh_start >= $ref_start && $neigh_end <= $ref_end )
|| ( $neigh_end <= $ref_end && $neigh_end >= $ref_start )
)
);
lib/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm view on Meta::CPAN
next unless ($shortest_distance || $adjusted_distance);
}
else {
($shortest_distance,$adjusted_distance) = $self->_compute_nearest_end(@args);
}
push @$position_matrix,[ $neighbour, $shortest_distance, $adjusted_distance, $neighbour->length, $neighbour->display_id] unless ($not_overlapping && $shortest_distance == 0);
}
# Order by distance, then centre-to-centre distance, then smallest feature first, then an arbitrary ID.
# $position_matrix looks like this:
# [ [ $feature, closest measure of distance, size, dbID ] ]
view release on metacpan or search on metacpan
lib/Bio/FeatureIO.pm view on Meta::CPAN
=cut
sub next_feature {
my ($self, $seq) = @_;
$self->throw_not_implemented;
}
=head2 write_feature
Title : write_feature
lib/Bio/FeatureIO.pm view on Meta::CPAN
=cut
sub write_feature {
my ($self, $seq) = @_;
$self->throw_not_implemented();
}
=head2 _load_format_module
Title : _load_format_module
view release on metacpan or search on metacpan
t/boilerplate.t view on Meta::CPAN
use 5.006;
use strict;
use warnings;
use Test::More tests => 13;
sub not_in_file_ok
{
my ($filename, %regex) = @_;
open(my $fh, '<', $filename) || die "couldn't open $filename for reading: $!";
my $ref = do {local $/; <$fh>};
t/boilerplate.t view on Meta::CPAN
}
sub module_boilerplate_ok
{
my ($module) = @_;
not_in_file_ok($module =>
'the great new $MODULENAME' => qr/ - The great new /,
'boilerplate description' => qr/Quick summary of what the module/,
'stub function definition' => qr/function[12]/,
);
return;
t/boilerplate.t view on Meta::CPAN
TODO:
{
local $TODO = "Need to replace the boilerplate text";
not_in_file_ok(README =>
"The README is used..." => qr/The README is used/,
"'version information here'" => qr/to provide version information/,
);
not_in_file_ok(Changes =>
"placeholder date/time" => qr(Date/time)
);
module_boilerplate_ok('lib/Bio/GeneDesign.pm');
module_boilerplate_ok('lib/Bio/GeneDesign/Basic.pm');
view release on metacpan or search on metacpan
bin/gonz_compcol.pl view on Meta::CPAN
= dict_slurp( $a_f, { key_idx => $opt{a}, val_idx => $opt{va}, uniq => 0, concat_keys => $opt{concat} } );
my $b_data
= dict_slurp( $b_f, { key_idx => $opt{b}, val_idx => $opt{vb}, uniq => 0, concat_keys => $opt{concat} } );
my @both = grep { exists( $b_data->{$_} ) } keys %$a_data;
my @not_in_a = grep { !exists( $a_data->{$_} ) } keys %$b_data;
my @not_in_b = grep { !exists( $b_data->{$_} ) } keys %$a_data;
say "A: $a_f";
say "B: $b_f";
say "";
bin/gonz_compcol.pl view on Meta::CPAN
say "first 3:";
say " " . join( "\n ", @both[ 0 .. 2 ] );
}
say "";
say "UNIQUE TO A: " . scalar @not_in_b;
if ( scalar @not_in_b > 0 ) {
say "first 3:";
say " " . join( "\n ", @not_in_b[ 0 .. 2 ] );
}
say "";
say "UNIQUE TO B: " . scalar @not_in_a;
if ( scalar @not_in_a > 0 ) {
say "first 3:";
say " " . join( "\n ", @not_in_a[ 0 .. 2 ] );
}
say "";
my %both = map { $_ => 1 } @both;
view release on metacpan or search on metacpan
lib/Bio/Graphics/ConfiguratorI.pm view on Meta::CPAN
=cut
sub get_sections {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 get_tags
Title : get_tags
lib/Bio/Graphics/ConfiguratorI.pm view on Meta::CPAN
=cut
sub get_tags {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 get
Title : get
lib/Bio/Graphics/ConfiguratorI.pm view on Meta::CPAN
=cut
sub get {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 set
Title : set
lib/Bio/Graphics/ConfiguratorI.pm view on Meta::CPAN
=cut
sub set {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 get_and_eval
lib/Bio/Graphics/ConfiguratorI.pm view on Meta::CPAN
=cut
sub get_and_eval {
my ($self) = @_;
$self->throw_not_implemented();
}
1;
view release on metacpan or search on metacpan
lib/Bio/Grep/Backend/Agrep.pm view on Meta::CPAN
open my $MAPFILE, '>', "$filename.map";
my $in = Bio::SeqIO->new( -file => $filename, -format => $args{format} );
my $id = 1;
while ( my $seq = $in->next_seq() ) {
print ${MAPFILE} $seq->id . "\n"
or $self->_cannot_print("$filename.dat");
print ${DATFILE} $id . q{:} . $seq->seq . "\n"
or $self->_cannot_print("$filename.map");
$id++;
}
close $DATFILE;
close $MAPFILE;
$self->_create_index_and_alphabet_file($filename);
view release on metacpan or search on metacpan
scripts/cl_syntax_error.pl view on Meta::CPAN
job->log->info("Running $idx_item->[0] -> $result_prefix");
jspew( $result_prefix . ".env.json", \%ENV );
jspew( $result_prefix . ".item.json", $idx_item );
sleep 1;
function_that_does_not_exist();
},
post_task => sub {
my $c = job->config;
open my $fh, '>', File::Spec->catfile( $c->{result_dir}, 'finished' )
view release on metacpan or search on metacpan
lib/Bio/KBase/InvocationService/ValidCommands.pm view on Meta::CPAN
{ cmd => 'text_search', link => '' },
{ cmd => 'traits_to_alleles', link => '' },
]},
{ name => 'anno_scripts', title => 'Annotation service scripts', items => [
{ cmd => 'a_and_b', link => '' },
{ cmd => 'a_not_b', link => '' },
{ cmd => 'annotate_genome', link => '' },
{ cmd => 'assign_functions_to_CDSs', link => '' },
{ cmd => 'call_CDSs', link => '' },
{ cmd => 'call_RNAs', link => '' },
{ cmd => 'call_pyrrolysoproteins', link => '' },
view release on metacpan or search on metacpan
MAGE/XML/Handler/ObjectHandlerI.pm view on Meta::CPAN
our $VERSION = '0.99';
sub new {
my $pack = shift;
my $self = bless {}, $pack;
$self->throw_not_implemented("new not defined for ".ref(caller()));
}
sub handle {
my $self = shift;
$self->throw_not_implemented("handle not defined for ".ref(caller()));
}
1;
__END__
view release on metacpan or search on metacpan
MAGE/Base.pm view on Meta::CPAN
my ($self, $msg) = @_;
die(caller().': '.$msg);
}
=item throw_not_implemented
Title : throw_not_implemented
Usage :
Function:
Example :
Returns :
Args :
=cut
sub throw_not_implemented {
my ($self) = @_;
die("Abstract method ".caller()." implementing class did not provide method");
}
view release on metacpan or search on metacpan
t/testlib/CommonTests.pm view on Meta::CPAN
my $predicate = "has_$key";
ok( ! $obj->$predicate, qq{and optional "$key" attribute predicate method agrees} );
}
# Required attributes with an unrecognised impostor; should fail.
my %with_unrecognised = ( 'this_is_not_a_recognised_attribute' => 1, %{ $required } );
dies_ok( sub { $obj = instantiate( $class, \%with_unrecognised ) },
"instantiation with an unrecognised arg fails" );
# Construct a full instance as our return value.
my $all = { %{ $optional }, %{ $required } };
view release on metacpan or search on metacpan
lib/Bio/MLST/Check.pm view on Meta::CPAN
}
sub input_fasta_files_exist
{
my($self) = @_;
my $file_not_found = 0;
for my $fastafile (@{$self->_input_fasta_files})
{
unless( -e $fastafile )
{
print qq[Input fasta file not found: $fastafile\n];
$file_not_found++;
}
}
return $file_not_found ? 0:1;
}
no Moose;
__PACKAGE__->meta->make_immutable;
1;
view release on metacpan or search on metacpan
t/boilerplate.t view on Meta::CPAN
use 5.006;
use strict;
use warnings;
use Test::More tests => 3;
sub not_in_file_ok {
my ($filename, %regex) = @_;
open( my $fh, '<', $filename )
or die "couldn't open $filename for reading: $!";
my %violated;
t/boilerplate.t view on Meta::CPAN
}
}
sub module_boilerplate_ok {
my ($module) = @_;
not_in_file_ok($module =>
'the great new $MODULENAME' => qr/ - The great new /,
'boilerplate description' => qr/Quick summary of what the module/,
'stub function definition' => qr/function[12]/,
);
}
TODO: {
local $TODO = "Need to replace the boilerplate text";
not_in_file_ok(README =>
"The README is used..." => qr/The README is used/,
"'version information here'" => qr/to provide version information/,
);
not_in_file_ok(Changes =>
"placeholder date/time" => qr(Date/time)
);
module_boilerplate_ok('lib/Bio/MaxQuant/Evidence/Statistics.pm');
view release on metacpan or search on metacpan
lib/Bio/Metabolic/Substrate.pm view on Meta::CPAN
use Carp;
use overload
"\"\"" => \&substrate_to_string,
"==" => \&equals,
"!=" => \¬_equals,
"cmp" => \&compare_names;
our $VERSION = '0.06';
=head1 METHODS
lib/Bio/Metabolic/Substrate.pm view on Meta::CPAN
}
return 1;
}
=head2 Method not_equals
Compares two substrates. If one of the substrates has attributes the set of
attributes is compared. If both objects are without attributes, the names are
compared. Returns 0 upon equality, 1 otherwise.
=cut
sub not_equals {
return 1 - equals(@_);
}
=head2 Method is_empty
view release on metacpan or search on metacpan
t/charactersblock_methods-02.t view on Meta::CPAN
},
{
'id' => '3',
'char_label' => 'P6.p_requirement_for_late_induction',
'states' => {
'1' => 'not_required',
'2' => 'required',
'3' => '(not_applicable)'
}
}
];
# 2 Dependence_on_gonadal_induction_before_VPCs_divide / no_gonad_requirement dependent_on_gonad,
view release on metacpan or search on metacpan
t/boilerplate.t view on Meta::CPAN
use strict;
use warnings;
use Test::More tests => 3;
sub not_in_file_ok {
my ($filename, %regex) = @_;
open( my $fh, '<', $filename )
or die "couldn't open $filename for reading: $!";
my %violated;
t/boilerplate.t view on Meta::CPAN
}
}
sub module_boilerplate_ok {
my ($module) = @_;
not_in_file_ok($module =>
'the great new $MODULENAME' => qr/ - The great new /,
'boilerplate description' => qr/Quick summary of what the module/,
'stub function definition' => qr/function[12]/,
);
}
TODO: {
local $TODO = "Need to replace the boilerplate text";
not_in_file_ok(README =>
"The README is used..." => qr/The README is used/,
"'version information here'" => qr/to provide version information/,
);
not_in_file_ok(Changes =>
"placeholder date/time" => qr(Date/time)
);
module_boilerplate_ok('lib/Bio/Oxbench/Util.pm');
view release on metacpan or search on metacpan
beagle_wrap.c view on Meta::CPAN
# if !defined(__PATCHLEVEL_H_INCLUDED__) && !(defined(PATCHLEVEL) && defined(SUBVERSION))
# define PERL_PATCHLEVEL_H_IMPLICIT
# include <patchlevel.h>
# endif
# if !(defined(PERL_VERSION) || (defined(SUBVERSION) && defined(PATCHLEVEL)))
# include <could_not_find_Perl_patchlevel.h>
# endif
# ifndef PERL_REVISION
# define PERL_REVISION (5)
# define PERL_VERSION PATCHLEVEL
# define PERL_SUBVERSION SUBVERSION
view release on metacpan or search on metacpan
lib/Bio/Phylo/Forest.pm view on Meta::CPAN
if ( $tree->is_default ) {
if ( not $seen_default ) {
$seen_default++;
}
else {
$tree->set_not_default;
}
}
}
if ($seen_default) {
if ( my $tree = $self->get_default_tree ) {
$tree->set_not_default;
}
}
$self->SUPER::insert(@_);
}
else {
view release on metacpan or search on metacpan
lib/Bio/PhyloXS/Forest/Tree.xs view on Meta::CPAN
Tree* set_as_default(Tree* self) {
self->is_default = 1;
return self;
}
Tree* set_not_default(Tree* self) {
self->is_default = 0;
return self;
}
int is_default(Tree* self) {
lib/Bio/PhyloXS/Forest/Tree.xs view on Meta::CPAN
Tree *
set_as_default (self)
Tree * self
Tree *
set_not_default (self)
Tree * self
int
is_default (self)
Tree * self
view release on metacpan or search on metacpan
lib/Bio/PrimerDesigner.pm view on Meta::CPAN
=cut
my $self = shift;
# technically, this should be 'os_is_not_windows'
unless ( defined $self->{'os_is_unix'} ) {
#$self->{'os_is_unix'} = ( $^O =~ /(n[iu]x|darwin)/ ) ? 1 : 0;
$self->{'os_is_unix'} = ( $^O !~ /^MSWin/i ) ? 1 : 0;
}
view release on metacpan or search on metacpan
xt/boilerplate.t view on Meta::CPAN
use warnings;
use Test::More;
plan tests => 3;
sub not_in_file_ok {
my ($filename, %regex) = @_;
open( my $fh, '<', $filename )
or die "couldn't open $filename for reading: $!";
my %violated;
xt/boilerplate.t view on Meta::CPAN
}
}
sub module_boilerplate_ok {
my ($module) = @_;
not_in_file_ok($module =>
'the great new $MODULENAME' => qr/ - The great new /,
'boilerplate description' => qr/Quick summary of what the module/,
'stub function definition' => qr/function[12]/,
);
}
TODO: {
local $TODO = "Need to replace the boilerplate text";
not_in_file_ok(README =>
"The README is used..." => qr/The README is used/,
"'version information here'" => qr/to provide version information/,
);
not_in_file_ok(Changes =>
"placeholder date/time" => qr(Date/time)
);
module_boilerplate_ok('lib/Bio/RNA/BarMap.pm');
view release on metacpan or search on metacpan
xt/boilerplate.t view on Meta::CPAN
use warnings;
use Test::More;
plan tests => 3;
sub not_in_file_ok {
my ($filename, %regex) = @_;
open( my $fh, '<', $filename )
or die "couldn't open $filename for reading: $!";
my %violated;
xt/boilerplate.t view on Meta::CPAN
}
}
sub module_boilerplate_ok {
my ($module) = @_;
not_in_file_ok($module =>
'the great new $MODULENAME' => qr/ - The great new /,
'boilerplate description' => qr/Quick summary of what the module/,
'stub function definition' => qr/function[12]/,
);
}
TODO: {
local $TODO = "Need to replace the boilerplate text";
not_in_file_ok(README =>
"The README is used..." => qr/The README is used/,
"'version information here'" => qr/to provide version information/,
);
not_in_file_ok(Changes =>
"placeholder date/time" => qr(Date/time)
);
module_boilerplate_ok('lib/Bio/RNA/Barriers.pm');
view release on metacpan or search on metacpan
xt/boilerplate.t view on Meta::CPAN
use warnings;
use Test::More;
plan tests => 3;
sub not_in_file_ok {
my ($filename, %regex) = @_;
open( my $fh, '<', $filename )
or die "couldn't open $filename for reading: $!";
my %violated;
xt/boilerplate.t view on Meta::CPAN
}
}
sub module_boilerplate_ok {
my ($module) = @_;
not_in_file_ok($module =>
'the great new $MODULENAME' => qr/ - The great new /,
'boilerplate description' => qr/Quick summary of what the module/,
'stub function definition' => qr/function[12]/,
);
}
TODO: {
local $TODO = "Need to replace the boilerplate text";
not_in_file_ok(README =>
"The README is used..." => qr/The README is used/,
"'version information here'" => qr/to provide version information/,
);
not_in_file_ok(Changes =>
"placeholder date/time" => qr(Date/time)
);
module_boilerplate_ok('lib/Bio/RNA/Treekin.pm');
view release on metacpan or search on metacpan
lib/Bio/RetrieveAssemblies/WGS.pm view on Meta::CPAN
my ($self) = @_;
if ( $self->annotation ) {
# Only get files with annotation
return "http://www.ncbi.nlm.nih.gov/Traces/wgs/?page=1&term=" . $self->query
. "&order=prefix&dir=a&state=live&project=WGS&update_date=any&create_date=any&have_annot_contigs=on&have_annot_scaffolds=on&retmode=text&size=all";
}
else {
# Get everything bar TSA
return "http://www.ncbi.nlm.nih.gov/Traces/wgs/?&size=100&term=" . $self->query
. "&project=WGS&order=prefix&dir=asc&version=last&state=live&update_date=any&create_date=any&retmode=text&size=all";
view release on metacpan or search on metacpan
lib/Bio/Roary/PostAnalysis.pm view on Meta::CPAN
system("create_pan_genome_plots.R") unless ( $self->dont_create_rplots == 1 );
$self->logger->info("Create EMBL files");
$self->_create_embl_files;
my $clusters_not_exceeded = 1;
if ( $self->output_multifasta_files ) {
$self->logger->info("Creating files with the nucleotide sequences for every cluster");
$clusters_not_exceeded = $self->_groups_multifastas_nuc_obj->create_files();
}
$self->_delete_intermediate_files;
if ( $clusters_not_exceeded == 0 && $self->output_multifasta_files ) {
$self->logger->error("Exiting early because number of clusters is too high");
exit();
}
}
view release on metacpan or search on metacpan
t/boilerplate.t view on Meta::CPAN
use 5.006;
use strict;
use warnings;
use Test::More tests => 3;
sub not_in_file_ok {
my ($filename, %regex) = @_;
open( my $fh, '<', $filename )
or die "couldn't open $filename for reading: $!";
my %violated;
t/boilerplate.t view on Meta::CPAN
}
}
sub module_boilerplate_ok {
my ($module) = @_;
not_in_file_ok($module =>
'the great new $MODULENAME' => qr/ - The great new /,
'boilerplate description' => qr/Quick summary of what the module/,
'stub function definition' => qr/function[12]/,
);
}
TODO: {
local $TODO = "Need to replace the boilerplate text";
not_in_file_ok(README =>
"The README is used..." => qr/The README is used/,
"'version information here'" => qr/to provide version information/,
);
not_in_file_ok(Changes =>
"placeholder date/time" => qr(Date/time)
);
module_boilerplate_ok('lib/Bio/SSRTool.pm');
view release on metacpan or search on metacpan
t/SearchIO/blastxml.t view on Meta::CPAN
is($iter->number, $iter_count);
is($iter->num_hits, shift @$di);
is($iter->num_hits_new, shift @$di);
is($iter->num_hits_old, shift @$di);
is(scalar($iter->newhits_below_threshold), shift @$di);
is(scalar($iter->newhits_not_below_threshold), shift @$di);
is(scalar($iter->newhits_unclassified), shift @$di);
is(scalar($iter->oldhits_below_threshold), shift @$di);
is(scalar($iter->oldhits_newly_below_threshold), shift @$di);
is(scalar($iter->oldhits_not_below_threshold), shift @$di);
my $hit_count = 0;
if ($iter_count == 1) {
while( my $hit = $result->next_hit ) {
my $d = shift @valid_hit_data;
is($hit->name, shift @$d);
t/SearchIO/blastxml.t view on Meta::CPAN
is($iter->number, $iter_count);
is($iter->num_hits, shift @$di);
is($iter->num_hits_new, shift @$di);
is($iter->num_hits_old, shift @$di);
is(scalar($iter->newhits_below_threshold), shift @$di);
is(scalar($iter->newhits_not_below_threshold), shift @$di);
is(scalar($iter->newhits_unclassified), shift @$di);
is(scalar($iter->oldhits_below_threshold), shift @$di);
is(scalar($iter->oldhits_newly_below_threshold), shift @$di);
is(scalar($iter->oldhits_not_below_threshold), shift @$di);
my $hit_count = 0;
if ($iter_count == 1) {
while( my $hit = $result->next_hit ) {
my $d = shift @valid_hit_data;
is($hit->name, shift @$d);