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revision 1.15, Wed Feb 16 22:42:49 2011 UTC revision 1.16, Sat Feb 19 17:51:25 2011 UTC
# Line 348  Line 348 
348  #     min_q_cov     =>  $frac_cov       #  minimum fraction coverage of query sequence (D = 0.50)  #     min_q_cov     =>  $frac_cov       #  minimum fraction coverage of query sequence (D = 0.50)
349  #     min_s_cov     =>  $frac_cov       #  minimum fraction coverage of subject sequence (D = 0.01)  #     min_s_cov     =>  $frac_cov       #  minimum fraction coverage of subject sequence (D = 0.01)
350  #     n_result      =>  $max_results    #  maxiumn restuls returned (D = 1000)  #     n_result      =>  $max_results    #  maxiumn restuls returned (D = 1000)
351    #     n_cpu         =>  $n_thread       #  number of blastpgp threads (D = 2)
352  #     n_thread      =>  $n_thread       #  number of blastpgp threads (D = 2)  #     n_thread      =>  $n_thread       #  number of blastpgp threads (D = 2)
353  #     query         =>  $q_file_name    #  query sequence file (D = most complete)  #     query         =>  $q_file_name    #  query sequence file (D = most complete)
354  #     query         => \@q_seq_entry    #  query sequence (D = most complete)  #     query         => \@q_seq_entry    #  query sequence (D = most complete)
# Line 366  Line 367 
367    
368      $opts->{ e_value }  ||= $opts->{ max_e_val } || $opts->{ max_e_value } || 0.01;      $opts->{ e_value }  ||= $opts->{ max_e_val } || $opts->{ max_e_value } || 0.01;
369      $opts->{ n_result } ||= $opts->{ nresult }   || 1000;      $opts->{ n_result } ||= $opts->{ nresult }   || 1000;
370      $opts->{ n_thread } ||= $opts->{ nthread }   || 2;      $opts->{ n_thread } ||= $opts->{ nthread }   || $opts->{ n_cpu } || $opts->{ ncpu } || 2;
371      my $max_q_uncov_c = $opts->{ max_q_uncov_c  } || $opts->{ max_q_uncov }  || 20;      my $max_q_uncov_c = $opts->{ max_q_uncov_c  } || $opts->{ max_q_uncov }  || 20;
372      my $max_q_uncov_n = $opts->{ max_q_uncov_n  } || $opts->{ max_q_uncov }  || 20;      my $max_q_uncov_n = $opts->{ max_q_uncov_n  } || $opts->{ max_q_uncov }  || 20;
373      my $min_q_cov     = $opts->{ min_q_cov }      || $opts->{ min_frac_cov } || 0.50;      my $min_q_cov     = $opts->{ min_q_cov }      || $opts->{ min_frac_cov } || 0.50;
# Line 530  Line 531 
531      elsif ( defined $query && -f $query )      elsif ( defined $query && -f $query )
532      {      {
533          $qfile = $query;          $qfile = $query;
534            ( $query ) = gjoseqlib::read_fasta( $qfile );
535      }      }
536      elsif ( $profile )    #  Build it from profile      elsif ( $profile )    #  Build it from profile
537      {      {
# Line 543  Line 545 
545          die "blastpgp requires database.";          die "blastpgp requires database.";
546      }      }
547    
     ($query) = gjoseqlib::read_fasta($qfile);  
548      $opts->{ query_used } = $query;      $opts->{ query_used } = $query;
549    
550      my $e_val = $opts->{ e_value }  || $opts->{ max_e_val } || $opts->{ max_e_value }            ||    0.01;      my $e_val = $opts->{ e_value }  || $opts->{ max_e_val } || $opts->{ max_e_value }            ||    0.01;
# Line 695  Line 696 
696      elsif ( defined $query && -f $query )      elsif ( defined $query && -f $query )
697      {      {
698          $qfile = $query;          $qfile = $query;
699            ( $query ) = gjoseqlib::read_fasta( $qfile );
700      }      }
701      elsif ( $profile )    #  Build it from profile      elsif ( $profile )    #  Build it from profile
702      {      {
# Line 708  Line 710 
710          die "blastpgpn requires database.";          die "blastpgpn requires database.";
711      }      }
712    
     ($query) = gjoseqlib::read_fasta($qfile);  
713      $opts->{ query_used } = $query;      $opts->{ query_used } = $query;
714    
715      my $e_val = $opts->{ e_value }  || $opts->{ max_e_val } || $opts->{ max_e_value }            ||    0.01;      my $e_val = $opts->{ e_value }  || $opts->{ max_e_val } || $opts->{ max_e_value }            ||    0.01;

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