Bioinfo

 view release on metacpan or  search on metacpan

Build.PL  view on Meta::CPAN

  "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,

META.json  view on Meta::CPAN

            "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",

META.yml  view on Meta::CPAN

    - 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);