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"dist_version" => "0.1.15",
"license" => "perl",
"module_name" => "Bioinfo",
"recursive_test_files" => 1,
"requires" => {
"Data::Dumper" => 0,
"Exporter" => 0,
"FindBin" => 0,
"IO::All" => 0,
"List::Util" => 0,
"Modern::Perl" => 0,
"Moo" => 0,
"MooX::Cmd" => 0,
"MooX::Options" => 0,
"Moose" => 0,
"Parallel::ForkManager" => 0,
"XML::Twig" => 0,
"lib" => 0,
"namespace::autoclean" => 0,
"namespace::clean" => 0,
"strict" => 0,
"Module::Build" : "0.28"
}
},
"runtime" : {
"requires" : {
"Data::Dumper" : "0",
"Exporter" : "0",
"FindBin" : "0",
"IO::All" : "0",
"List::Util" : "0",
"Modern::Perl" : "0",
"Moo" : "0",
"MooX::Cmd" : "0",
"MooX::Options" : "0",
"Moose" : "0",
"Parallel::ForkManager" : "0",
"XML::Twig" : "0",
"lib" : "0",
"namespace::autoclean" : "0",
"namespace::clean" : "0",
"strict" : "0",
- inc
- share
- t
- xt
requires:
Data::Dumper: '0'
Exporter: '0'
FindBin: '0'
IO::All: '0'
List::Util: '0'
Modern::Perl: '0'
Moo: '0'
MooX::Cmd: '0'
MooX::Options: '0'
Moose: '0'
Parallel::ForkManager: '0'
XML::Twig: '0'
lib: '0'
namespace::autoclean: '0'
namespace::clean: '0'
strict: '0'
bin/biotools view on Meta::CPAN
#!/usr/bin/env perl
use Modern::Perl;
use FindBin;
use lib "$FindBin::Bin/../lib";
use Bioinfo::App;
our $VERSION = '0.1.15'; # VERSION
# ABSTRACT: a bioinformatics toolkit that I used often
# PODNAME: biotools
Bioinfo::App->new_with_cmd;
lib/Bioinfo.pm view on Meta::CPAN
package Bioinfo;
use Moo;
use Modern::Perl;
use namespace::clean;
our $VERSION = '0.1.15'; # VERSION:
# ABSTRACT: my perl module and CLIs for Biology
1;
__END__
lib/Bioinfo/App.pm view on Meta::CPAN
package Bioinfo::App;
use Modern::Perl;
use Moo;
use MooX::Cmd;
use MooX::Options;
our $VERSION = '0.1.15'; # VERSION:
# ABSTRACT: my perl module and CLIs for Biology
sub execute {
lib/Bioinfo/App/Cmd/Blast.pm view on Meta::CPAN
package Bioinfo::App::Cmd::Blast;
use Modern::Perl;
use Moo;
use MooX::Cmd;
use MooX::Options prefer_commandline => 1;
our $VERSION = '0.1.15'; # VERSION:
# ABSTRACT: various operator related to Blast+
sub execute {
lib/Bioinfo/App/Cmd/Blast/Cmd/ParseXML.pm view on Meta::CPAN
package Bioinfo::App::Cmd::Blast::Cmd::ParseXML;
use Modern::Perl;
use Moo;
use MooX::Cmd;
use MooX::Options prefer_commandline => 1;
use IO::All;
use XML::Twig;
our $VERSION = '0.1.15'; # VERSION:
# ABSTRACT: parse XML file of blast+(with outfmt=5) into tabular format
lib/Bioinfo/App/Cmd/Blast/Cmd/SplitSubmit.pm view on Meta::CPAN
package Bioinfo::App::Cmd::Blast::Cmd::SplitSubmit;
use Modern::Perl;
use Moo;
use MooX::Cmd;
use MooX::Options prefer_commandline => 1;
use IO::All;
use Bioinfo::PBS::Queue;
our $VERSION = '0.1.15'; # VERSION:
# ABSTRACT: submit blast after splitting a fasta file into multiple files;
lib/Bioinfo/App/Cmd/Blast/Cmd/SplitSubmitB.pm view on Meta::CPAN
package Bioinfo::App::Cmd::Blast::Cmd::SplitSubmitB;
use Modern::Perl;
use Moo;
use MooX::Cmd;
use MooX::Options prefer_commandline => 1;
use IO::All;
use Bioinfo::PBS::Queue;
our $VERSION = '0.1.15'; # VERSION:
# ABSTRACT: submit blast after splitting a fasta file into multiple files;
lib/Bioinfo/App/Cmd/Fasta.pm view on Meta::CPAN
package Bioinfo::App::Cmd::Fasta;
use Modern::Perl;
use Moo;
use MooX::Cmd;
use MooX::Options prefer_commandline => 1;
our $VERSION = '0.1.15'; # VERSION:
# ABSTRACT: my perl module and CLIs for Biology
sub execute {
lib/Bioinfo/App/Cmd/Fasta/Cmd/GetByID.pm view on Meta::CPAN
package Bioinfo::App::Cmd::Fasta::Cmd::GetByID;
use Modern::Perl;
use Moo;
use Bioinfo::Fasta;
use MooX::Cmd;
use MooX::Options prefer_commandline => 1;
use IO::All;
use Data::Dumper;
our $VERSION = '0.1.15'; # VERSION:
# ABSTRACT: my perl module and CLIs for Biology
lib/Bioinfo/App/Cmd/Fasta/Cmd/Split.pm view on Meta::CPAN
package Bioinfo::App::Cmd::Fasta::Cmd::Split;
use Modern::Perl;
use Moo;
use MooX::Cmd;
use MooX::Options prefer_commandline => 1;
use IO::All;
our $VERSION = '0.1.15'; # VERSION:
# ABSTRACT: my perl module and CLIs for Biology
option input => (
lib/Bioinfo/App/Cmd/Fasta/Cmd/SplitBlast.pm view on Meta::CPAN
package Bioinfo::App::Cmd::Fasta::Cmd::SplitBlast;
use Modern::Perl;
use Moo;
use MooX::Cmd;
use MooX::Options prefer_commandline => 1;
use IO::All;
use Bioinfo::PBS::Queue;
our $VERSION = '0.1.15'; # VERSION:
# ABSTRACT: my perl module and CLIs for Biology
lib/Bioinfo/PBS.pm view on Meta::CPAN
package Bioinfo::PBS;
use Moose;
use Modern::Perl;
use IO::All;
use namespace::autoclean;
our $VERSION = '0.1.15'; # VERSION:
# ABSTRACT: my perl module and CLIs for Biology
has cpu => (
is => 'rw',
isa => 'Int',
lib/Bioinfo/PBS/Queue.pm view on Meta::CPAN
package Bioinfo::PBS::Queue;
use Moose;
use Modern::Perl;
use Parallel::ForkManager;
use IO::All;
use List::Util 'uniq';
use namespace::autoclean;
our $VERSION = '0.1.15'; # VERSION:
# ABSTRACT: used to submit a batch of task to Torque cluster
has tasks => (
t/01-podsyntax.t view on Meta::CPAN
use Modern::Perl;
use Test::More;
use Test::Pod;
use Test::Pod::Coverage 1.00;
all_pod_files_ok;
# all_pod_coverage_ok();
t/02-bioinfo_pbs.t view on Meta::CPAN
use Modern::Perl;
use Test::More;
use IO::All;
my $module;
BEGIN {
$module = 'Bioinfo::PBS';
use_ok($module);
}
my @attrs = qw(cpu name cmd path job_id);
my @methods = qw(get_sh qsub wait job_stat);
t/03-bioinfo_pbs_queue.t view on Meta::CPAN
#!/usr/bin/env perl
use Modern::Perl;
use Test::More;
use IO::All;
my $module;
BEGIN {
$module = 'Bioinfo::PBS::Queue';
use_ok($module);
}
my @attrs = qw(tasks name run_queue finished_queue stage);
my @methods = qw(execute);