cjfields

$VAR1 = bless( {
                 '_secondary_ids' => [],
                 '_dblinks' => {
                                 '_default' => [
                                                 bless( {
                                                          'database' => 'MetaCyc',
                                                          'primary_id' => 'PWY-681',
                                                          '_root_verbose' => 0
                                                        }, 'Bio::Annotation::DBLink' ),
                                                 bless( {

cjfields

cjfields@pyrimidine:~/tests/perl6$ cat lives_ok.pl 
use v6;

use Test;
lives_ok { warn('Foo') };
done_testing;
cjfields@pyrimidine:~/tests/perl6$ perl6 lives_ok.pl 
not ok 1 - 
1..1
# Looks like you failed 1 tests of 1

cjfields

#!/usr/bin/perl 

use strict;

use warnings;

use Bio::DB::EUtilities;
use Bio::SeqIO;
use Bio::Seq::SeqBuilder;

cjfields

[GENERAL]
description =  BLASTZ alignments for Oryza sativa 

# The synteny database
join        = dbi:mysql:database=rice_synteny;host=localhost;user=nobody

# This option maps the relationship between the species data sources, names and descriptions
# The value for "name" (the first column) is the symbolic name that gbrowse_syn users to identify each species.
# This value is also used in two other places in the gbrowse_syn configuration: 
# the species name in the "examples" directive and the species name in the .aln file 

cjfields

Group10	12642577	553507	0
Group11	14521977	687845	0
Group1	29934090	1123268	0
Group12	11309010	438679	0
Group13	10266737	389981	0
Group14	9976661	436939	0
Group15	10159687	569461	0
Group16	7072872	237769	0
Group2	16072177	1518762	0
Group3	13621520	658251	0

cjfields

cjfields@pyrimidine:~/src/bamtools/build$ cmake ..
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info

cjfields

1..34
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::SeqFeature::Annotated;

--------------------- WARNING ---------------------
MSG: [1/5] tried to fetch http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD, but server threw 404.  retrying...
---------------------------------------------------

--------------------- WARNING ---------------------

cjfields

# grab a feature
if ($sf->has_tag('foo')) {
    my @old = $sf->remove_tag('foo');
    # modify or add new
    $sf->add_tag_value('foo', $new);
}

cjfields

cjfields@pyrimidine:~/tests/seq$ cat locations_bm.pl 
#!/usr/bin/perl -w

use Modern::Perl;
use Bio::SeqIO;
use Benchmark qw(cmpthese);

my $file = shift;

cmpthese(10, {

cjfields

....

Do you want to run tests requiring a valid email address? y/n [n] y
Enter email address:  cjfields@bioperl.org
Could not get valid metadata. Error is: Invalid metadata structure. Errors:
'Perl_5' for 'license' does not have a URL scheme (resources -> license)
[Validation: 1.2], Expected a map structure from string or file.
(optional_features -> Bio::FeatureIO::gff -> requires) [Validation: 1.2],
Expected a map structure from string or file. (optional_features ->
Bio::WebAgent -> requires) [Validation: 1.2], Expected a map structure from