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script/lccnorm view on Meta::CPAN
If no file is specified, or if the file name C<-> is specified, standard input
will be processed.
Normalization of call number ranges is a special challenge, because ranges are
not normally specified using the exact endpoint. Consider the range C<B708-B713>; while
C<B708> does indicate the beginning point -- a no call number that comes before B 708 can
fall within the range -- the end point is only a guide, not a strict limit, since the intent
is that call numbers such as C<B 713 .H94> and C<B 713 .W55 L86> B<do> fall within the
range. Unfortunately, ranges are often specified ambiguously; for example, the call number
C<B 713.14 G92> might or might not be considered to fall within this range.
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lib/BigIP/iControl.pm view on Meta::CPAN
=head3 create_subscription_list (%args)
my $subscription = $ic->create_subscription_list (
name => 'my_subscription_name',
url => 'http://company.com/my/eventnotification/endpoint,
username => 'username',
password => 'password',
ttl => -1,
min_events_per_timeslice => 10,
max_timeslice => 10
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t/05remote.t view on Meta::CPAN
Bio::DB::Big->init();
subtest 'Testing opening remote BigWig file' => sub {
my $httpd = $get_server->();
my $url_root = $httpd->endpoint;
my $bw_file = "${url_root}/test.bw";
note $bw_file;
{
my $big = Bio::DB::Big->open($bw_file);
is($big->type(), 0, 'Type of file should be 0 i.e. a bigwig file');
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lib/Bio/DB/Das/Chado/Segment/Feature.pm view on Meta::CPAN
} else {
$self->{start} = $start if !defined($self->{start}) || $start > $self->{start};
$self->{stop} = $stop if !defined($self->{stop}) || $stop < $self->{stop};
}
# fix up endpoints of targets too (for homologies only)
# my $h = $feat->group;
# next unless $h && $h->isa('Bio::DB::GFF::Homol'); # always false (for now)
# next unless $g && $g->isa('Bio::DB::GFF::Homol');
# ($start,$stop) = ($h->{start},$h->{stop});
# if ($h->strand >= 0) {
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lib/Bio/DB/GFF/Feature.pm view on Meta::CPAN
$self->{stop} = $low
if (!defined($self->{stop})) || $low < $self->{stop};
}
}
# fix up endpoints of targets too (for homologies only)
my $h = $feat->group;
next unless $h && $h->isa('Bio::DB::GFF::Homol');
next unless $g && $g->isa('Bio::DB::GFF::Homol');
($start,$stop) = ($h->{start},$h->{stop});
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eg/subsequence.cgi view on Meta::CPAN
sub print_form {
print p("This web page permits you to extract a short subsequence of DNA from a large GenBank entry. This is especially useful in an era of huge \"contigs\" of genomic DNA, where you only want to extract a few hundred base pairs for subsequent ana...
print p,"This program also illustrates the power of ",a({-href => 'http://www.BioPerl.org/'}, "BioPerl"), ", a powerful set of tools for molecular biology analysis. The ", a({-href => 'subsequence.pl.txt'}, "source code"), " for this program is le...
print p,"You must specify the GenBank accession number along with a start position. You may specify either the length of the subsequence you wish to extract or, equivalently, the endpoint.\n";
print "The sequence may be reverse-complemented if you wish, e.g., the reverse complement of <font color=green>ATCGC</font> is <font color=yellow>GCGAT</font>.\n";
print p,"To test this web page, try accession NT_004002, start 50000, length 400.\n";
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lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
The positional form is as follows:
$db->get_features_by_location($seqid [[,$start,]$end])
The $seqid is the name of the sequence on which the feature resides,
and start and end are optional endpoints for the match. If the
endpoints are missing then any feature on the indicated seqid is
returned.
Examples:
get_features_by_location('chr1'); # all features on chromosome 1
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Das/Feature.pm view on Meta::CPAN
} else {
$self->{start} = $start if !defined($self->{start}) || $start > $self->{start};
$self->{stop} = $stop if !defined($self->{stop}) || $stop < $self->{stop};
}
# fix up endpoints of targets too
my $st = $feat->{target};
next unless $t && $st;
($start,$stop) = (@{$st}[1,2]);
if ($start < $stop) {
$t->[1] = $start if !defined($t->[1]) || $start < $t->[1]; # start
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lib/Bio/EBI/RNAseqAPI.pm view on Meta::CPAN
This module provides a Perl-based interface to the L<EMBL-EBI|http://www.ebi.ac.uk> L<RNA-seq analysis API|http://www.ebi.ac.uk/fg/rnaseq/api/>.
The RNA-seq Analysis API enables access to analysis results for thousands of
publicly available gene expression datasets. This module provides functions to
access each endpoint provided by the API.
For more information about the API, see its L<documentation|http://www.ebi.ac.uk/fg/rnaseq/api/doc>.
=head1 SYNOPSIS
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lib/Bio/MAGETAB/SDRF.pm view on Meta::CPAN
push @list_of_rows, @{ $subrow_list };
}
}
else {
# Recursion endpoint.
push @list_of_rows, [ $node ];
}
return \@list_of_rows;
}
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* Fixed the padded alignments returned for hard-clipped alignments.
Version 1.10
* Added a new Bio::DB::Bam method for caching remote files' indices in the
temp directory. This is used by default by high-level API.
* Fixed bug in soft and hard clipping code; query endpoints should be
correct now.
* Fixed bug in get_all_tags() which was choking on "Z" style tags and giving
scrambled results.
* $feature->query now reports the DNA query in canonical (ref)
coordinates; only $feature->target reverse complements the query
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scripts/bam2wig.pl view on Meta::CPAN
'd|mid!' => \$use_mid, # record mid point
'a|span!' => \$use_span, # record span
'cspan!' => \$use_cspan, # record center span
'e|extend!' => \$use_extend, # extend read
'smartcov!' => \$use_smartpe, # smart paired coverage
'ends!' => \$use_ends, # record paired-end endpoints
'coverage!' => \$use_coverage, # calculate coverage
'position=s' => \$position, # legacy option
'l|splice|split!' => \$splice, # split splices
'p|pe!' => \$paired, # paired-end alignments
'P|fastpe!' => \$fastpaired, # fast paired-end alignments
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Bio/DB/GFF/Feature.pm view on Meta::CPAN
$self->{stop} = $low
if (!defined($self->{stop})) || $low < $self->{stop};
}
}
# fix up endpoints of targets too (for homologies only)
my $h = $feat->group;
next unless $h && $h->isa('Bio::DB::GFF::Homol');
next unless $g && $g->isa('Bio::DB::GFF::Homol');
($start,$stop) = ($h->{start},$h->{stop});
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lib/Bluesky.pm view on Meta::CPAN
( @captions ? ( captions => \@captions ) : () ), ( defined $alt ? ( alt => $alt ) : () ),
( defined $aspectRatio ? ( aspectRatio => $aspectRatio ) : () )
};
if (0) {
# You may upload videos as plain blobs but this endpoint allows you to check on processing status
# Testing because HTTP::Tiny does not support multipart
# I need to get auth token for new service via 'com.atproto.server.getServiceAuth'
my $boundary = join '', map { [ 0 .. 9, 'a' .. '4' ]->[ rand 36 ] } 1 .. 5 + rand(10);
my $job = $at->post(
'https://video.bsky.app/xrpc/app.bsky.video.uploadVideo?did=' . $at->did . '&name=upload.mp4',
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lib/BmltClient/ApiClient.pm view on Meta::CPAN
}
$self->{http_timeout} = $seconds;
}
# make the HTTP request
# @param string $resourcePath path to method endpoint
# @param string $method method to call
# @param array $queryParams parameters to be place in query URL
# @param array $postData parameters to be placed in POST body
# @param array $headerParams parameters to be place in request header
# @return mixed
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lib/Mojolicious/Plugin/BoardStreams.pm view on Meta::CPAN
},
});
});
$app->hook(around_action => async sub ($next, $c, $action, $last) {
if ($last and $c->stash->{'boardstreams.endpoint'}) {
$c->render_later;
try {
my $ret = $next->();
await $ret if $ret->$_can('then');
return await $c->bs->init_client_p;
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src/boost/geometry/strategies/agnostic/point_in_poly_oriented_winding.hpp view on Meta::CPAN
calculation_type const p = get<D>(point);
calculation_type const s1 = get<D>(seg1);
calculation_type const s2 = get<D>(seg2);
// Check if one of segment endpoints is at same level of point
bool eq1 = math::equals(s1, p);
bool eq2 = math::equals(s2, p);
if (eq1 && eq2)
{
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include/boost/regex/v4/basic_regex_creator.hpp view on Meta::CPAN
//
first = char_set.ranges_begin();
last = char_set.ranges_end();
while(first != last)
{
// first grab the endpoints of the range:
digraph<charT> c1 = *first;
c1.first = this->m_traits.translate(c1.first, this->m_icase);
c1.second = this->m_traits.translate(c1.second, this->m_icase);
++first;
digraph<charT> c2 = *first;
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lib/Bot/ChatBots/Messenger/Sender.pod view on Meta::CPAN
=head2 B<< url >>
my $fb_messenger_url = $obj->url;
The Facebook Messenger API endpoint. Defaults to
L<https://graph.facebook.com/v2.6/me/messages>.
=head1 METHODS
This class consumes the following roles (inheriting all its methods):
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eg/README.md view on Meta::CPAN
the command line with the first program:
$ ./longpoll $TOKEN
The second program needs a place to be installed and run, as well as
exposing an HTTPS type of endpoint, so you need to do an extra mile
to see it at work.
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examples/pendulum.pl view on Meta::CPAN
for (1..$precision){
$world->Step( $timestep, $vIters, $pIters );
$world->ClearForces();
}
my $endpoint = $bobs[$#bobs]{body}->GetPosition();
my $current_path_pos
= [ w2s( $endpoint->x ), w2s( s2w($height) - $endpoint->y ) ];
# trace path on bg
$bg->draw_line( $prev_path_pos, $current_path_pos, $pathColor )
if $prev_path_pos;
$prev_path_pos = $current_path_pos;
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lib/Brackup/Target/Riak.pm view on Meta::CPAN
I<(Mandatory.)> Must be "B<Riak>".
=item B<riak_host_url>
URL specifying your riak cluster endpoint. Default: http://127.0.0.1:8098/.
=item B<riak_r>
riak read quorum - how many replicas need to agree when retrieving an object.
Default: 2.