| line |
stmt |
bran |
cond |
sub |
pod |
time |
code |
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1
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#$Id$ |
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2
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package Bio::Tools::Run::BlastPlus::Config; |
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3
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1
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1
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5
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use strict; |
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1
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2
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1
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25
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4
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1
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1
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5
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use warnings; |
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1
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2
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1
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21
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5
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1
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1
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4
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no warnings qw(qw); |
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1
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2
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1
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37
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6
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1
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1
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5
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use Bio::Root::Root; |
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1
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2
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1
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15
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7
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1
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1
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3
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use Exporter; |
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1
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2
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1
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35
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8
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1
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1
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4
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use base qw(Bio::Root::Root); |
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1
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2
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1
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429
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9
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10
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our (@ISA, @EXPORT, @EXPORT_OK); |
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11
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push @ISA, 'Exporter'; |
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12
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@EXPORT = qw( |
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13
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@program_commands |
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14
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%command_prefixes |
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15
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%composite_commands |
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16
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@program_params |
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17
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@program_switches |
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18
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%param_translation |
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19
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%command_files |
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20
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$program_name |
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21
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$program_dir |
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22
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$use_dash |
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23
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$join |
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24
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); |
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25
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26
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@EXPORT_OK = qw(); |
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27
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28
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# getting the parms and switches from the usage string: |
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29
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30
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#$ blastp -h | perl -ne '@a = m/\[(.*?)\]/g; for $a (@a) { @b = split(/\s+/,$a); $b[0]=~s/-//; $ptr = (@b==1 ? \@s : \@p ); push @$ptr, $b[0]; } END { print "p arms\n", join("\n",@p), "\n\n", "switches\n", join("\n",@s); }' |
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31
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32
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# '*' indicates a 'pseudo'-program : i.e. each |
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33
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# command has its own executable... |
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34
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35
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our $program_name = '*blast+'; |
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36
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our $use_dash = 'single'; |
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37
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our $join = ' '; |
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38
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39
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our @program_commands = qw( |
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40
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run |
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41
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blastn |
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42
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blastx |
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43
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tblastx |
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44
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tblastn |
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45
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blastp |
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46
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psiblast |
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47
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rpsblast |
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48
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rpstblastn |
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49
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makeblastdb |
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50
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blastdb_aliastool |
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51
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blastdbcmd |
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52
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blastdbcheck |
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53
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convert2blastmask |
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54
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dustmasker |
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55
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segmasker |
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56
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windowmasker |
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57
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); |
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58
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59
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# full command => prefix |
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60
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our %command_prefixes = ( |
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61
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run => 'run', |
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62
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blastn => 'bln', |
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63
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blastx => 'blx', |
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64
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tblastx => 'tbx', |
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65
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tblastn => 'tbn', |
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66
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blastp => 'blp', |
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67
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psiblast => 'psi', |
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68
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rpsblast => 'rps', |
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69
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rpstblastn => 'rpst', |
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70
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makeblastdb => 'mak', |
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71
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blastdb_aliastool => 'dba', |
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72
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blastdbcmd => 'dbc', |
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73
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blastdbcheck => 'dbk', |
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74
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convert2blastmask => 'c2m', |
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75
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dustmasker => 'dms', |
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76
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segmasker => 'sms', |
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77
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windowmasker => 'wms' |
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78
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); |
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79
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80
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# each elt : pfx|wrapper_parm_name |
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81
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82
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our @program_params = qw( |
|
83
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command |
|
84
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tbn|import_search_strategy |
|
85
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tbn|export_search_strategy |
|
86
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tbn|db |
|
87
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tbn|dbsize |
|
88
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tbn|gilist |
|
89
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tbn|negative_gilist |
|
90
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tbn|entrez_query |
|
91
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tbn|subject |
|
92
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tbn|subject_loc |
|
93
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tbn|query |
|
94
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tbn|out |
|
95
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tbn|evalue |
|
96
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tbn|word_size |
|
97
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tbn|gapopen |
|
98
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tbn|gapextend |
|
99
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tbn|xdrop_ungap |
|
100
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tbn|xdrop_gap |
|
101
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tbn|xdrop_gap_final |
|
102
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tbn|searchsp |
|
103
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tbn|db_gencode |
|
104
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tbn|frame_shift_penalty |
|
105
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tbn|max_intron_length |
|
106
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tbn|seg |
|
107
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tbn|soft_masking |
|
108
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tbn|matrix |
|
109
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tbn|threshold |
|
110
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tbn|culling_limit |
|
111
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tbn|best_hit_overhang |
|
112
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tbn|best_hit_score_edge |
|
113
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|
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tbn|window_size |
|
114
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tbn|query_loc |
|
115
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tbn|outfmt |
|
116
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tbn|num_descriptions |
|
117
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tbn|num_alignments |
|
118
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tbn|max_target_seqs |
|
119
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tbn|num_threads |
|
120
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tbn|comp_based_stats |
|
121
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tbn|in_pssm |
|
122
|
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blx|import_search_strategy |
|
123
|
|
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blx|export_search_strategy |
|
124
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blx|db |
|
125
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blx|dbsize |
|
126
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blx|gilist |
|
127
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blx|negative_gilist |
|
128
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|
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blx|entrez_query |
|
129
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blx|db_soft_mask |
|
130
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blx|subject |
|
131
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blx|subject_loc |
|
132
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blx|query |
|
133
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blx|out |
|
134
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blx|evalue |
|
135
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blx|word_size |
|
136
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blx|gapopen |
|
137
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blx|gapextend |
|
138
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blx|xdrop_ungap |
|
139
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|
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blx|xdrop_gap |
|
140
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blx|xdrop_gap_final |
|
141
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blx|searchsp |
|
142
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blx|frame_shift_penalty |
|
143
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blx|max_intron_length |
|
144
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blx|seg |
|
145
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blx|soft_masking |
|
146
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blx|matrix |
|
147
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blx|threshold |
|
148
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|
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blx|culling_limit |
|
149
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blx|best_hit_overhang |
|
150
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blx|best_hit_score_edge |
|
151
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blx|window_size |
|
152
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blx|query_loc |
|
153
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blx|strand |
|
154
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blx|query_gencode |
|
155
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blx|outfmt |
|
156
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blx|num_descriptions |
|
157
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|
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blx|num_alignments |
|
158
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|
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blx|max_target_seqs |
|
159
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blx|num_threads |
|
160
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bln|import_search_strategy |
|
161
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bln|export_search_strategy |
|
162
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bln|task |
|
163
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bln|db |
|
164
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bln|dbsize |
|
165
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bln|gilist |
|
166
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bln|negative_gilist |
|
167
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bln|entrez_query |
|
168
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bln|db_soft_mask |
|
169
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bln|subject |
|
170
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bln|subject_loc |
|
171
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bln|query |
|
172
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|
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bln|out |
|
173
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|
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bln|evalue |
|
174
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|
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bln|word_size |
|
175
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bln|gapopen |
|
176
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bln|gapextend |
|
177
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|
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bln|perc_identity |
|
178
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|
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|
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bln|xdrop_ungap |
|
179
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|
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|
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bln|xdrop_gap |
|
180
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|
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|
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bln|xdrop_gap_final |
|
181
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|
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bln|searchsp |
|
182
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|
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bln|penalty |
|
183
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bln|reward |
|
184
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bln|min_raw_gapped_score |
|
185
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bln|template_type |
|
186
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bln|template_length |
|
187
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bln|dust |
|
188
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|
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bln|filtering_db |
|
189
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bln|window_masker_taxid |
|
190
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bln|window_masker_db |
|
191
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bln|soft_masking |
|
192
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|
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|
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bln|culling_limit |
|
193
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|
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|
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bln|best_hit_overhang |
|
194
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|
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|
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bln|best_hit_score_edge |
|
195
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bln|window_size |
|
196
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bln|use_index |
|
197
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|
bln|index_name |
|
198
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bln|query_loc |
|
199
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bln|strand |
|
200
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bln|outfmt |
|
201
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bln|num_descriptions |
|
202
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|
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|
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bln|num_alignments |
|
203
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|
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|
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bln|max_target_seqs |
|
204
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|
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|
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bln|num_threads |
|
205
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|
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blp|import_search_strategy |
|
206
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|
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|
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|
blp|export_search_strategy |
|
207
|
|
|
|
|
|
|
blp|task |
|
208
|
|
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|
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|
blp|db |
|
209
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blp|dbsize |
|
210
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|
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blp|gilist |
|
211
|
|
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|
blp|negative_gilist |
|
212
|
|
|
|
|
|
|
blp|entrez_query |
|
213
|
|
|
|
|
|
|
blp|db_soft_mask |
|
214
|
|
|
|
|
|
|
blp|subject |
|
215
|
|
|
|
|
|
|
blp|subject_loc |
|
216
|
|
|
|
|
|
|
blp|query |
|
217
|
|
|
|
|
|
|
blp|out |
|
218
|
|
|
|
|
|
|
blp|evalue |
|
219
|
|
|
|
|
|
|
blp|word_size |
|
220
|
|
|
|
|
|
|
blp|gapopen |
|
221
|
|
|
|
|
|
|
blp|gapextend |
|
222
|
|
|
|
|
|
|
blp|xdrop_ungap |
|
223
|
|
|
|
|
|
|
blp|xdrop_gap |
|
224
|
|
|
|
|
|
|
blp|xdrop_gap_final |
|
225
|
|
|
|
|
|
|
blp|searchsp |
|
226
|
|
|
|
|
|
|
blp|seg |
|
227
|
|
|
|
|
|
|
blp|soft_masking |
|
228
|
|
|
|
|
|
|
blp|matrix |
|
229
|
|
|
|
|
|
|
blp|threshold |
|
230
|
|
|
|
|
|
|
blp|culling_limit |
|
231
|
|
|
|
|
|
|
blp|best_hit_overhang |
|
232
|
|
|
|
|
|
|
blp|best_hit_score_edge |
|
233
|
|
|
|
|
|
|
blp|window_size |
|
234
|
|
|
|
|
|
|
blp|query_loc |
|
235
|
|
|
|
|
|
|
blp|outfmt |
|
236
|
|
|
|
|
|
|
blp|num_descriptions |
|
237
|
|
|
|
|
|
|
blp|num_alignments |
|
238
|
|
|
|
|
|
|
blp|max_target_seqs |
|
239
|
|
|
|
|
|
|
blp|num_threads |
|
240
|
|
|
|
|
|
|
blp|comp_based_stats |
|
241
|
|
|
|
|
|
|
psi|import_search_strategy |
|
242
|
|
|
|
|
|
|
psi|export_search_strategy |
|
243
|
|
|
|
|
|
|
psi|db |
|
244
|
|
|
|
|
|
|
psi|dbsize |
|
245
|
|
|
|
|
|
|
psi|gilist |
|
246
|
|
|
|
|
|
|
psi|negative_gilist |
|
247
|
|
|
|
|
|
|
psi|entrez_query |
|
248
|
|
|
|
|
|
|
psi|subject |
|
249
|
|
|
|
|
|
|
psi|subject_loc |
|
250
|
|
|
|
|
|
|
psi|query |
|
251
|
|
|
|
|
|
|
psi|out |
|
252
|
|
|
|
|
|
|
psi|evalue |
|
253
|
|
|
|
|
|
|
psi|word_size |
|
254
|
|
|
|
|
|
|
psi|gapopen |
|
255
|
|
|
|
|
|
|
psi|gapextend |
|
256
|
|
|
|
|
|
|
psi|xdrop_ungap |
|
257
|
|
|
|
|
|
|
psi|xdrop_gap |
|
258
|
|
|
|
|
|
|
psi|xdrop_gap_final |
|
259
|
|
|
|
|
|
|
psi|searchsp |
|
260
|
|
|
|
|
|
|
psi|seg |
|
261
|
|
|
|
|
|
|
psi|soft_masking |
|
262
|
|
|
|
|
|
|
psi|matrix |
|
263
|
|
|
|
|
|
|
psi|threshold |
|
264
|
|
|
|
|
|
|
psi|culling_limit |
|
265
|
|
|
|
|
|
|
psi|best_hit_overhang |
|
266
|
|
|
|
|
|
|
psi|best_hit_score_edge |
|
267
|
|
|
|
|
|
|
psi|window_size |
|
268
|
|
|
|
|
|
|
psi|query_loc |
|
269
|
|
|
|
|
|
|
psi|outfmt |
|
270
|
|
|
|
|
|
|
psi|num_descriptions |
|
271
|
|
|
|
|
|
|
psi|num_alignments |
|
272
|
|
|
|
|
|
|
psi|max_target_seqs |
|
273
|
|
|
|
|
|
|
psi|num_threads |
|
274
|
|
|
|
|
|
|
psi|comp_based_stats |
|
275
|
|
|
|
|
|
|
psi|gap_trigger |
|
276
|
|
|
|
|
|
|
psi|num_iterations |
|
277
|
|
|
|
|
|
|
psi|out_pssm |
|
278
|
|
|
|
|
|
|
psi|out_ascii_pssm |
|
279
|
|
|
|
|
|
|
psi|in_msa |
|
280
|
|
|
|
|
|
|
psi|in_pssm |
|
281
|
|
|
|
|
|
|
psi|pseudocount |
|
282
|
|
|
|
|
|
|
psi|inclusion_ethresh |
|
283
|
|
|
|
|
|
|
psi|phi_pattern |
|
284
|
|
|
|
|
|
|
rpst|import_search_strategy |
|
285
|
|
|
|
|
|
|
rpst|export_search_strategy |
|
286
|
|
|
|
|
|
|
rpst|db |
|
287
|
|
|
|
|
|
|
rpst|dbsize |
|
288
|
|
|
|
|
|
|
rpst|gilist |
|
289
|
|
|
|
|
|
|
rpst|negative_gilist |
|
290
|
|
|
|
|
|
|
rpst|entrez_query |
|
291
|
|
|
|
|
|
|
rpst|query |
|
292
|
|
|
|
|
|
|
rpst|out |
|
293
|
|
|
|
|
|
|
rpst|evalue |
|
294
|
|
|
|
|
|
|
rpst|word_size |
|
295
|
|
|
|
|
|
|
rpst|xdrop_ungap |
|
296
|
|
|
|
|
|
|
rpst|xdrop_gap |
|
297
|
|
|
|
|
|
|
rpst|xdrop_gap_final |
|
298
|
|
|
|
|
|
|
rpst|searchsp |
|
299
|
|
|
|
|
|
|
rpst|query_gencode |
|
300
|
|
|
|
|
|
|
rpst|seg |
|
301
|
|
|
|
|
|
|
rpst|soft_masking |
|
302
|
|
|
|
|
|
|
rpst|window_size |
|
303
|
|
|
|
|
|
|
rpst|query_loc |
|
304
|
|
|
|
|
|
|
rpst|strand |
|
305
|
|
|
|
|
|
|
rpst|outfmt |
|
306
|
|
|
|
|
|
|
rpst|num_descriptions |
|
307
|
|
|
|
|
|
|
rpst|num_alignments |
|
308
|
|
|
|
|
|
|
rpst|max_target_seqs |
|
309
|
|
|
|
|
|
|
rpst|num_threads |
|
310
|
|
|
|
|
|
|
mak|in |
|
311
|
|
|
|
|
|
|
mak|dbtype |
|
312
|
|
|
|
|
|
|
mak|title |
|
313
|
|
|
|
|
|
|
mak|mask_data |
|
314
|
|
|
|
|
|
|
mak|out |
|
315
|
|
|
|
|
|
|
mak|max_file_sz |
|
316
|
|
|
|
|
|
|
mak|taxid |
|
317
|
|
|
|
|
|
|
mak|taxid_map |
|
318
|
|
|
|
|
|
|
mak|logfile |
|
319
|
|
|
|
|
|
|
dba|gi_file_in |
|
320
|
|
|
|
|
|
|
dba|gi_file_out |
|
321
|
|
|
|
|
|
|
dba|db |
|
322
|
|
|
|
|
|
|
dba|dbtype |
|
323
|
|
|
|
|
|
|
dba|title |
|
324
|
|
|
|
|
|
|
dba|gilist |
|
325
|
|
|
|
|
|
|
dba|out |
|
326
|
|
|
|
|
|
|
dba|dblist |
|
327
|
|
|
|
|
|
|
dba|num_volumes |
|
328
|
|
|
|
|
|
|
dba|logfile |
|
329
|
|
|
|
|
|
|
tbx|import_search_strategy |
|
330
|
|
|
|
|
|
|
tbx|export_search_strategy |
|
331
|
|
|
|
|
|
|
tbx|db |
|
332
|
|
|
|
|
|
|
tbx|dbsize |
|
333
|
|
|
|
|
|
|
tbx|gilist |
|
334
|
|
|
|
|
|
|
tbx|negative_gilist |
|
335
|
|
|
|
|
|
|
tbx|entrez_query |
|
336
|
|
|
|
|
|
|
tbx|subject |
|
337
|
|
|
|
|
|
|
tbx|subject_loc |
|
338
|
|
|
|
|
|
|
tbx|query |
|
339
|
|
|
|
|
|
|
tbx|out |
|
340
|
|
|
|
|
|
|
tbx|evalue |
|
341
|
|
|
|
|
|
|
tbx|word_size |
|
342
|
|
|
|
|
|
|
tbx|gapopen |
|
343
|
|
|
|
|
|
|
tbx|gapextend |
|
344
|
|
|
|
|
|
|
tbx|xdrop_ungap |
|
345
|
|
|
|
|
|
|
tbx|xdrop_gap |
|
346
|
|
|
|
|
|
|
tbx|xdrop_gap_final |
|
347
|
|
|
|
|
|
|
tbx|searchsp |
|
348
|
|
|
|
|
|
|
tbx|max_intron_length |
|
349
|
|
|
|
|
|
|
tbx|seg |
|
350
|
|
|
|
|
|
|
tbx|soft_masking |
|
351
|
|
|
|
|
|
|
tbx|matrix |
|
352
|
|
|
|
|
|
|
tbx|threshold |
|
353
|
|
|
|
|
|
|
tbx|culling_limit |
|
354
|
|
|
|
|
|
|
tbx|best_hit_overhang |
|
355
|
|
|
|
|
|
|
tbx|best_hit_score_edge |
|
356
|
|
|
|
|
|
|
tbx|window_size |
|
357
|
|
|
|
|
|
|
tbx|query_loc |
|
358
|
|
|
|
|
|
|
tbx|strand |
|
359
|
|
|
|
|
|
|
tbx|query_gencode |
|
360
|
|
|
|
|
|
|
tbx|db_gencode |
|
361
|
|
|
|
|
|
|
tbx|outfmt |
|
362
|
|
|
|
|
|
|
tbx|num_descriptions |
|
363
|
|
|
|
|
|
|
tbx|num_alignments |
|
364
|
|
|
|
|
|
|
tbx|max_target_seqs |
|
365
|
|
|
|
|
|
|
tbx|num_threads |
|
366
|
|
|
|
|
|
|
dbc|db |
|
367
|
|
|
|
|
|
|
dbc|dbtype |
|
368
|
|
|
|
|
|
|
dbc|entry |
|
369
|
|
|
|
|
|
|
dbc|entry_batch |
|
370
|
|
|
|
|
|
|
dbc|pig |
|
371
|
|
|
|
|
|
|
dbc|range |
|
372
|
|
|
|
|
|
|
dbc|strand |
|
373
|
|
|
|
|
|
|
dbc|mask_sequence_with |
|
374
|
|
|
|
|
|
|
dbc|out |
|
375
|
|
|
|
|
|
|
dbc|outfmt |
|
376
|
|
|
|
|
|
|
dbc|line_length |
|
377
|
|
|
|
|
|
|
c2m|in |
|
378
|
|
|
|
|
|
|
c2m|out |
|
379
|
|
|
|
|
|
|
c2m|outfmt |
|
380
|
|
|
|
|
|
|
dms|in |
|
381
|
|
|
|
|
|
|
dms|out |
|
382
|
|
|
|
|
|
|
dms|window |
|
383
|
|
|
|
|
|
|
dms|level |
|
384
|
|
|
|
|
|
|
dms|linker |
|
385
|
|
|
|
|
|
|
dms|outfmt |
|
386
|
|
|
|
|
|
|
sms|in |
|
387
|
|
|
|
|
|
|
sms|out |
|
388
|
|
|
|
|
|
|
sms|infmt |
|
389
|
|
|
|
|
|
|
sms|outfmt |
|
390
|
|
|
|
|
|
|
sms|window |
|
391
|
|
|
|
|
|
|
sms|locut |
|
392
|
|
|
|
|
|
|
sms|hicut |
|
393
|
|
|
|
|
|
|
wms|ustat |
|
394
|
|
|
|
|
|
|
wms|in |
|
395
|
|
|
|
|
|
|
wms|out |
|
396
|
|
|
|
|
|
|
wms|checkdup |
|
397
|
|
|
|
|
|
|
wms|window |
|
398
|
|
|
|
|
|
|
wms|t_extend |
|
399
|
|
|
|
|
|
|
wms|t_thres |
|
400
|
|
|
|
|
|
|
wms|t_high |
|
401
|
|
|
|
|
|
|
wms|t_low |
|
402
|
|
|
|
|
|
|
wms|set_t_high |
|
403
|
|
|
|
|
|
|
wms|set_t_low |
|
404
|
|
|
|
|
|
|
wms|infmt |
|
405
|
|
|
|
|
|
|
wms|outfmt |
|
406
|
|
|
|
|
|
|
wms|sformat |
|
407
|
|
|
|
|
|
|
wms|convert |
|
408
|
|
|
|
|
|
|
wms|fa_list |
|
409
|
|
|
|
|
|
|
wms|mem |
|
410
|
|
|
|
|
|
|
wms|smem |
|
411
|
|
|
|
|
|
|
wms|unit |
|
412
|
|
|
|
|
|
|
wms|genome_size |
|
413
|
|
|
|
|
|
|
wms|dust |
|
414
|
|
|
|
|
|
|
wms|dust_level |
|
415
|
|
|
|
|
|
|
wms|exclude_ids |
|
416
|
|
|
|
|
|
|
wms|ids |
|
417
|
|
|
|
|
|
|
wms|text_match |
|
418
|
|
|
|
|
|
|
wms|use_ba |
|
419
|
|
|
|
|
|
|
); |
|
420
|
|
|
|
|
|
|
|
|
421
|
|
|
|
|
|
|
# each elt : pfx|wrapper_switch_name |
|
422
|
|
|
|
|
|
|
our @program_switches = qw( |
|
423
|
|
|
|
|
|
|
tbn|h |
|
424
|
|
|
|
|
|
|
tbn|help |
|
425
|
|
|
|
|
|
|
tbn|ungapped |
|
426
|
|
|
|
|
|
|
tbn|lcase_masking |
|
427
|
|
|
|
|
|
|
tbn|parse_deflines |
|
428
|
|
|
|
|
|
|
tbn|show_gis |
|
429
|
|
|
|
|
|
|
tbn|html |
|
430
|
|
|
|
|
|
|
tbn|remote |
|
431
|
|
|
|
|
|
|
tbn|use_sw_tback |
|
432
|
|
|
|
|
|
|
tbn|version |
|
433
|
|
|
|
|
|
|
blx|h |
|
434
|
|
|
|
|
|
|
blx|help |
|
435
|
|
|
|
|
|
|
blx|ungapped |
|
436
|
|
|
|
|
|
|
blx|lcase_masking |
|
437
|
|
|
|
|
|
|
blx|parse_deflines |
|
438
|
|
|
|
|
|
|
blx|show_gis |
|
439
|
|
|
|
|
|
|
blx|html |
|
440
|
|
|
|
|
|
|
blx|remote |
|
441
|
|
|
|
|
|
|
blx|version |
|
442
|
|
|
|
|
|
|
bln|h |
|
443
|
|
|
|
|
|
|
bln|help |
|
444
|
|
|
|
|
|
|
bln|no_greedy |
|
445
|
|
|
|
|
|
|
bln|ungapped |
|
446
|
|
|
|
|
|
|
bln|lcase_masking |
|
447
|
|
|
|
|
|
|
bln|parse_deflines |
|
448
|
|
|
|
|
|
|
bln|show_gis |
|
449
|
|
|
|
|
|
|
bln|html |
|
450
|
|
|
|
|
|
|
bln|remote |
|
451
|
|
|
|
|
|
|
bln|version |
|
452
|
|
|
|
|
|
|
blp|h |
|
453
|
|
|
|
|
|
|
blp|help |
|
454
|
|
|
|
|
|
|
blp|lcase_masking |
|
455
|
|
|
|
|
|
|
blp|parse_deflines |
|
456
|
|
|
|
|
|
|
blp|show_gis |
|
457
|
|
|
|
|
|
|
blp|html |
|
458
|
|
|
|
|
|
|
blp|ungapped |
|
459
|
|
|
|
|
|
|
blp|remote |
|
460
|
|
|
|
|
|
|
blp|use_sw_tback |
|
461
|
|
|
|
|
|
|
blp|version |
|
462
|
|
|
|
|
|
|
psi|h |
|
463
|
|
|
|
|
|
|
psi|help |
|
464
|
|
|
|
|
|
|
psi|lcase_masking |
|
465
|
|
|
|
|
|
|
psi|parse_deflines |
|
466
|
|
|
|
|
|
|
psi|show_gis |
|
467
|
|
|
|
|
|
|
psi|html |
|
468
|
|
|
|
|
|
|
psi|remote |
|
469
|
|
|
|
|
|
|
psi|use_sw_tback |
|
470
|
|
|
|
|
|
|
psi|version |
|
471
|
|
|
|
|
|
|
rpst|h |
|
472
|
|
|
|
|
|
|
rpst|help |
|
473
|
|
|
|
|
|
|
rpst|ungapped |
|
474
|
|
|
|
|
|
|
rpst|lcase_masking |
|
475
|
|
|
|
|
|
|
rpst|parse_deflines |
|
476
|
|
|
|
|
|
|
rpst|show_gis |
|
477
|
|
|
|
|
|
|
rpst|html |
|
478
|
|
|
|
|
|
|
rpst|remote |
|
479
|
|
|
|
|
|
|
rpst|version |
|
480
|
|
|
|
|
|
|
mak|h |
|
481
|
|
|
|
|
|
|
mak|help |
|
482
|
|
|
|
|
|
|
mak|parse_seqids |
|
483
|
|
|
|
|
|
|
mak|hash_index |
|
484
|
|
|
|
|
|
|
mak|version |
|
485
|
|
|
|
|
|
|
dba|h |
|
486
|
|
|
|
|
|
|
dba|help |
|
487
|
|
|
|
|
|
|
dba|version |
|
488
|
|
|
|
|
|
|
tbx|h |
|
489
|
|
|
|
|
|
|
tbx|help |
|
490
|
|
|
|
|
|
|
tbx|lcase_masking |
|
491
|
|
|
|
|
|
|
tbx|parse_deflines |
|
492
|
|
|
|
|
|
|
tbx|show_gis |
|
493
|
|
|
|
|
|
|
tbx|html |
|
494
|
|
|
|
|
|
|
tbx|remote |
|
495
|
|
|
|
|
|
|
tbx|version |
|
496
|
|
|
|
|
|
|
dbc|h |
|
497
|
|
|
|
|
|
|
dbc|help |
|
498
|
|
|
|
|
|
|
dbc|info |
|
499
|
|
|
|
|
|
|
dbc|target_only |
|
500
|
|
|
|
|
|
|
dbc|get_dups |
|
501
|
|
|
|
|
|
|
dbc|ctrl_a |
|
502
|
|
|
|
|
|
|
dbc|version |
|
503
|
|
|
|
|
|
|
c2m|h |
|
504
|
|
|
|
|
|
|
c2m|help |
|
505
|
|
|
|
|
|
|
c2m|parse_seqids |
|
506
|
|
|
|
|
|
|
c2m|version |
|
507
|
|
|
|
|
|
|
dms|h |
|
508
|
|
|
|
|
|
|
dms|help |
|
509
|
|
|
|
|
|
|
dms|xmlhelp |
|
510
|
|
|
|
|
|
|
dms|parse_seqids |
|
511
|
|
|
|
|
|
|
dms|version-full |
|
512
|
|
|
|
|
|
|
sms|h |
|
513
|
|
|
|
|
|
|
sms|help |
|
514
|
|
|
|
|
|
|
sms|xmlhelp |
|
515
|
|
|
|
|
|
|
sms|parse_seqids |
|
516
|
|
|
|
|
|
|
sms|version-full |
|
517
|
|
|
|
|
|
|
wms|h |
|
518
|
|
|
|
|
|
|
wms|help |
|
519
|
|
|
|
|
|
|
wms|xmlhelp |
|
520
|
|
|
|
|
|
|
wms|parse_seqids |
|
521
|
|
|
|
|
|
|
wms|version-full |
|
522
|
|
|
|
|
|
|
wms|mk_counts |
|
523
|
|
|
|
|
|
|
); |
|
524
|
|
|
|
|
|
|
|
|
525
|
|
|
|
|
|
|
#each pair : pfx|wrapper_opt_name => command_line_name (without dashes) |
|
526
|
|
|
|
|
|
|
# for blast+, the options are all long and mnemonic, so a param translation |
|
527
|
|
|
|
|
|
|
# isn't required. In CommandExts, a parameter name should be passed through |
|
528
|
|
|
|
|
|
|
# as-is, if a translation is not found---. |
|
529
|
|
|
|
|
|
|
our %param_translation = ( |
|
530
|
|
|
|
|
|
|
); |
|
531
|
|
|
|
|
|
|
|
|
532
|
|
|
|
|
|
|
our %composite_commands = ( |
|
533
|
|
|
|
|
|
|
); |
|
534
|
|
|
|
|
|
|
|
|
535
|
|
|
|
|
|
|
our %command_files = ( |
|
536
|
|
|
|
|
|
|
); |
|
537
|
|
|
|
|
|
|
|
|
538
|
|
|
|
|
|
|
1; |