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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;


option input => (
  is  => 'ro',
  required  => 1,
  format  => 's',
  short => 'i',
  doc => 'a file of fasta format'
);


option num => (
  is  => 'ro',
  format  => 'i',
  short => 'n',
  default => sub { '6' },
  doc => 'number of files that the fasta file will be split'
);


option db => (
  is  => 'rw',
  format => 's',
  short => 'd',
  default => sub { 'nr_plant' },
  doc => 'the database that blast will use',
);


option type => (
  is  => 'rw',
  format => 's',
  short => 't',
  default => sub { 'pbs' },
  doc => "where the blast will be runned, enum['local','pbs']. default:'pbs'"
);


option blast => (
  is => 'rw',
  format => 's',
  short => 'b',
  default => sub { 'blastp' },
  doc => 'which blast program will be used',
);


option cpu => (
  is => 'ro',
  format => 'i',
  short => 'c',
  default => sub { '4' },