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revision 1.12, Mon Dec 27 00:17:33 2010 UTC revision 1.13, Wed Dec 29 21:50:32 2010 UTC
# Line 330  Line 330 
330  #  #
331  #     Report records:  #     Report records:
332  #  #
333  #         [ $sid, $slen, $status, $frac_id, $frac_pos,  #         [ $sid, $score, $e_value, $slen, $status,
334    #                 $frac_id, $frac_pos,
335  #                 $q_uncov_n_term, $q_uncov_c_term,  #                 $q_uncov_n_term, $q_uncov_c_term,
336  #                 $s_uncov_n_term, $s_uncov_c_term ]  #                 $s_uncov_n_term, $s_uncov_c_term ]
337  #  #
# Line 353  Line 354 
354  #     stderr        =>  $file           #  blastpgp stderr (D = /dev/stderr)  #     stderr        =>  $file           #  blastpgp stderr (D = /dev/stderr)
355  #  #
356  #  If supplied, query must be identical to a profile sequence, but no gaps.  #  If supplied, query must be identical to a profile sequence, but no gaps.
357    #  If not supplied, $opts{ query } will be set to the most compete sequence.
358  #  #
359  #-------------------------------------------------------------------------------  #-------------------------------------------------------------------------------
360    
# Line 390  Line 392 
392              #     0    1    2    3     4     5    6     7     8   9   10   11   12  13   14              #     0    1    2    3     4     5    6     7     8   9   10   11   12  13   14
393    
394              my $hsp0 = $hsps->[0];              my $hsp0 = $hsps->[0];
395              my ( $scr, $nmat, $nid, $npos, $q1, $q2, $qseq, $s1, $s2, $sseq ) = ( @$hsp0 )[ 0, 4, 5, 6, 9, 10, 11, 12, 13, 14 ];              my ( $scr, $exp, $nmat, $nid, $npos, $q1, $q2, $qseq, $s1, $s2, $sseq ) = ( @$hsp0 )[ 0, 1, 4, 5, 6, 9, 10, 11, 12, 13, 14 ];
396    
397              my $status;              my $status;
398              if    ( $q1-1     > $max_q_uncov_n )     { $status = 'missing start' }              if    ( $q1-1     > $max_q_uncov_n )     { $status = 'missing start' }
# Line 407  Line 409 
409                  $status = 'included';                  $status = 'included';
410              }              }
411    
412              $report{ $sid } = [ $sid, $slen, $status, $nid/$nmat, $npos/$nmat, $q1-1, $qlen-$q2, $s1-1, $slen-$s2 ];              my $frac_id  = sprintf("%.3f", $nid/$nmat);
413                my $frac_pos = sprintf("%.3f", $npos/$nmat);
414    
415                $report{ $sid } = [ $sid, $scr, $exp, $slen, $status, $frac_id, $frac_pos, $q1-1, $qlen-$q2, $s1-1, $slen-$s2 ];
416          }          }
417      }      }
418    
# Line 460  Line 465 
465  #     query       =>  $q_file_name   # most complete  #     query       =>  $q_file_name   # most complete
466  #     query       => \@q_seq_entry   # most complete  #     query       => \@q_seq_entry   # most complete
467  #  #
468    #  If not supplied, $opts{ query } will be set to the most compete sequence.
469  #-------------------------------------------------------------------------------  #-------------------------------------------------------------------------------
470    
471  sub blastpgp  sub blastpgp
# Line 537  Line 543 
543          die "blastpgp requires database.";          die "blastpgp requires database.";
544      }      }
545    
546        $opts->{ query } ||= $query;
547    
548      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;
549      my $n_cpu = $opts->{ n_thread } || $opts->{ nthread } || $opts->{ n_cpu } || $opts->{ ncpu } ||    2;      my $n_cpu = $opts->{ n_thread } || $opts->{ nthread } || $opts->{ n_cpu } || $opts->{ ncpu } ||    2;
550      my $nkeep = $opts->{ n_result } || $opts->{ nresult }                                        || 1000;      my $nkeep = $opts->{ n_result } || $opts->{ nresult }                                        || 1000;
# Line 602  Line 610 
610  #     stderr     =>  $file          # place to send blast stderr (D = /dev/null)  #     stderr     =>  $file          # place to send blast stderr (D = /dev/null)
611  #     tmp        =>  $temp_dir      # location for temp files  #     tmp        =>  $temp_dir      # location for temp files
612  #  #
613    #  If not supplied, $opts{ query } will be set to the most compete sequence.
614    #
615  #  depricated alternatives:  #  depricated alternatives:
616  #  #
617  #     prot_file  =>  $trans_file    # put translation db here  #     prot_file  =>  $trans_file    # put translation db here
# Line 698  Line 708 
708          die "blastpgpn requires database.";          die "blastpgpn requires database.";
709      }      }
710    
711        $opts->{ query } ||= $query;
712    
713      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;
714      my $n_cpu = $opts->{ n_thread } || $opts->{ nthread } || $opts->{ n_cpu } || $opts->{ ncpu } ||    2;      my $n_cpu = $opts->{ n_thread } || $opts->{ nthread } || $opts->{ n_cpu } || $opts->{ ncpu } ||    2;
715      my $nkeep = $opts->{ n_result } || $opts->{ nresult }                                        || 1000;      my $nkeep = $opts->{ n_result } || $opts->{ nresult }                                        || 1000;

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